Starting phenix.real_space_refine on Fri Feb 23 15:20:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5s_30994/02_2024/7e5s_30994.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5s_30994/02_2024/7e5s_30994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5s_30994/02_2024/7e5s_30994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5s_30994/02_2024/7e5s_30994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5s_30994/02_2024/7e5s_30994.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5s_30994/02_2024/7e5s_30994.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 165 5.16 5 C 24696 2.51 5 N 6463 2.21 5 O 7592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 77": "OD1" <-> "OD2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "O ARG 23": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ARG 19": "NH1" <-> "NH2" Residue "R PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 100": "NH1" <-> "NH2" Residue "S TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 20": "NH1" <-> "NH2" Residue "U TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 68": "NH1" <-> "NH2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 68": "NH1" <-> "NH2" Residue "V ASP 91": "OD1" <-> "OD2" Residue "V TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38916 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8366 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8334 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8354 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "I" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "R" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 899 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "T" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "U" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} 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: "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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 Time building chain proxies: 19.76, per 1000 atoms: 0.51 Number of scatterers: 38916 At special positions: 0 Unit cell: (213.2, 221.52, 215.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 165 16.00 O 7592 8.00 N 6463 7.00 C 24696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=1.25 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.50 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.91 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.35 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.82 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.37 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=1.48 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 15 " - pdb=" SG CYS C 136 " distance=2.04 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=1.42 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.07 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=1.47 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 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 91 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 97 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG M 1 " - " NAG M 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B1134 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " Time building additional restraints: 14.43 Conformation dependent library (CDL) restraints added in 6.6 seconds 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9304 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 86 sheets defined 16.9% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.600A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.576A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.957A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.253A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.656A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.844A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.558A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.617A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.905A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.843A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.219A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.518A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.751A 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 945 through 968 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.549A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.620A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.008A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.559A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.794A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.546A pdb=" N LEU C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.220A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.530A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.765A 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 945 through 968 removed outlier: 3.672A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.510A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.545A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.098A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'N' and resid 80 through 84 removed outlier: 4.333A pdb=" N GLU N 84 " --> pdb=" O THR N 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 Processing helix chain 'Q' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU Q 84 " --> pdb=" O THR Q 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 removed outlier: 4.333A pdb=" N GLU S 84 " --> pdb=" O THR S 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 33 Processing helix chain 'V' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.845A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.845A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.504A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.725A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.617A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.990A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.535A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.754A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.662A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.332A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.682A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.019A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.166A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.594A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.327A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.617A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 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 654 through 655 removed outlier: 5.815A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.468A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.509A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.719A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.719A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.516A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 115 through 120 removed outlier: 3.592A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 152 through 155 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.556A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.959A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (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: 5.917A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.458A 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 727 removed outlier: 6.529A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.369A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 21 through 22 removed outlier: 3.593A pdb=" N PHE D 70 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.154A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.977A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.517A pdb=" N ILE E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.434A pdb=" N TYR E 109 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.559A pdb=" N PHE H 70 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 52 through 53 removed outlier: 5.155A pdb=" N SER H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS H 38 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR I 113 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.551A pdb=" N THR J 113 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.615A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.278A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP L 73 " --> pdb=" O THR L 78 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.253A pdb=" N ILE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER L 59 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.466A pdb=" N TYR L 109 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.689A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR N 91 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL N 100 " --> pdb=" O THR N 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 20 through 23 Processing sheet with id=AH3, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.886A pdb=" N CYS O 22 " --> pdb=" O PHE O 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER O 70 " --> pdb=" O ASP O 73 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 39 through 41 removed outlier: 4.022A pdb=" N VAL O 88 " --> pdb=" O GLN O 41 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA P 80 " --> pdb=" O CYS P 23 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AH8, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.689A pdb=" N ASP Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR Q 91 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL Q 100 " --> pdb=" O THR Q 91 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id=AI2, first strand: chain 'R' and resid 3 through 4 removed outlier: 3.502A pdb=" N LEU R 18 " --> pdb=" O MET R 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR R 78 " --> pdb=" O ASP R 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP R 73 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 11 through 12 Processing sheet with id=AI4, first strand: chain 'R' and resid 45 through 50 removed outlier: 7.418A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N MET R 34 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR R 109 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP S 86 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR S 91 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL S 100 " --> pdb=" O THR S 91 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 20 through 23 Processing sheet with id=AI8, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.622A pdb=" N PHE T 71 " --> pdb=" O CYS T 23 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU T 105 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'U' and resid 3 through 4 removed outlier: 3.838A pdb=" N GLN U 3 " --> pdb=" O SER U 26 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER U 26 " --> pdb=" O GLN U 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'U' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA U 80 " --> pdb=" O CYS U 23 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'U' and resid 46 through 49 Processing sheet with id=AJ4, first strand: chain 'V' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA V 80 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'V' and resid 46 through 49 removed outlier: 3.838A pdb=" N VAL V 38 " --> pdb=" O TYR V 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR V 96 " --> pdb=" O VAL V 38 " (cutoff:3.500A) 1439 hydrogen bonds defined for protein. 3822 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: 19.20 Time building geometry restraints manager: 15.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8215 1.33 - 1.45: 9826 1.45 - 1.58: 21555 1.58 - 1.70: 1 1.70 - 1.82: 216 Bond restraints: 39813 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " ideal model delta sigma weight residual 1.532 1.638 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.460 1.499 -0.039 8.60e-03 1.35e+04 2.05e+01 bond pdb=" N GLN K 79 " pdb=" CA GLN K 79 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" N GLN T 79 " pdb=" CA GLN T 79 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.87e+01 bond pdb=" N ILE B 664 " pdb=" CA ILE B 664 " ideal model delta sigma weight residual 1.457 1.495 -0.038 9.00e-03 1.23e+04 1.77e+01 ... (remaining 39808 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.99: 1007 105.99 - 113.10: 20517 113.10 - 120.21: 17214 120.21 - 127.32: 15207 127.32 - 134.43: 255 Bond angle restraints: 54200 Sorted by residual: angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 111.28 123.58 -12.30 1.09e+00 8.42e-01 1.27e+02 angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 119.05 128.03 -8.98 1.11e+00 8.12e-01 6.54e+01 angle pdb=" N CYS A 131 " pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " ideal model delta sigma weight residual 111.69 125.33 -13.64 1.74e+00 3.30e-01 6.15e+01 angle pdb=" C ASP P 110 " pdb=" CA ASP P 110 " pdb=" CB ASP P 110 " ideal model delta sigma weight residual 110.17 125.32 -15.15 1.97e+00 2.58e-01 5.91e+01 angle pdb=" CA GLY B 184 " pdb=" C GLY B 184 " pdb=" O GLY B 184 " ideal model delta sigma weight residual 122.22 117.33 4.89 6.50e-01 2.37e+00 5.66e+01 ... (remaining 54195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 22450 17.87 - 35.75: 1172 35.75 - 53.62: 216 53.62 - 71.50: 26 71.50 - 89.37: 20 Dihedral angle restraints: 23884 sinusoidal: 9334 harmonic: 14550 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 -177.63 -89.37 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 3.69 89.31 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" C ASP P 110 " pdb=" N ASP P 110 " pdb=" CA ASP P 110 " pdb=" CB ASP P 110 " ideal model delta harmonic sigma weight residual -122.60 -145.36 22.76 0 2.50e+00 1.60e-01 8.28e+01 ... (remaining 23881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 5866 0.194 - 0.387: 302 0.387 - 0.581: 4 0.581 - 0.774: 1 0.774 - 0.968: 1 Chirality restraints: 6174 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.01e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.63e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.01e+01 ... (remaining 6171 not shown) Planarity restraints: 6985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 2 " 0.353 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG e 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG e 2 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG e 2 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG e 2 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.353 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG Z 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " 0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG c 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.172 2.00e-02 2.50e+03 ... (remaining 6982 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 12 2.19 - 2.87: 14306 2.87 - 3.55: 53649 3.55 - 4.22: 94192 4.22 - 4.90: 157668 Nonbonded interactions: 319827 Sorted by model distance: nonbonded pdb=" NE2 HIS L 35 " pdb=" CD1 TRP L 47 " model vdw 1.513 3.340 nonbonded pdb=" OG1 THR B1100 " pdb=" C1 NAG Y 1 " model vdw 1.589 3.470 nonbonded pdb=" OD1 ASN B 331 " pdb=" O THR B 523 " model vdw 1.881 3.040 nonbonded pdb=" OH TYR C 473 " pdb=" CB TYR C 489 " model vdw 1.966 3.440 nonbonded pdb=" C LEU B 452 " pdb=" CE2 TYR B 495 " model vdw 1.971 3.570 ... (remaining 319822 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 14 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB )) or resid 247 through 404 or (resid 405 through 406 a \ nd (name N or name CA or name C or name O or name CB )) or resid 407 or (resid 4 \ 08 through 409 and (name N or name CA or name C or name O or name CB )) or resid \ 410 through 426 or (resid 427 through 428 and (name N or name CA or name C or n \ ame O or name CB )) or resid 429 through 508 or (resid 509 and (name N or name C \ A or name C or name O or name CB )) or resid 510 through 515 or (resid 516 and ( \ name N or name CA or name C or name O or name CB )) or resid 517 through 1013 or \ (resid 1014 through 1016 and (name N or name CA or name C or name O or name CB \ )) or resid 1017 through 1147)) selection = (chain 'B' and (resid 14 through 494 or (resid 495 and (name N or name CA or nam \ e C or name O or name CB )) or resid 496 through 508 or (resid 509 and (name N o \ r name CA or name C or name O or name CB )) or resid 510 through 1147)) selection = (chain 'C' and (resid 14 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB )) or resid 247 through 407 or (resid 408 through 409 a \ nd (name N or name CA or name C or name O or name CB )) or resid 410 through 494 \ or (resid 495 and (name N or name CA or name C or name O or name CB )) or resid \ 496 through 1013 or (resid 1014 through 1016 and (name N or name CA or name C o \ r name O or name CB )) or resid 1017 through 1105 or (resid 1106 and (name N or \ name CA or name C or name O or name CB )) or resid 1107 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'T' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'U' selection = (chain 'V' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 120)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 15.660 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 100.570 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4519 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 : 0.012 0.106 39813 Z= 0.768 Angle : 1.407 15.146 54200 Z= 1.063 Chirality : 0.101 0.968 6174 Planarity : 0.010 0.304 6973 Dihedral : 10.849 80.795 14415 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.48 % Favored : 95.22 % Rotamer: Outliers : 1.35 % Allowed : 5.77 % Favored : 92.87 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.12), residues: 4976 helix: 4.22 (0.18), residues: 745 sheet: 0.45 (0.14), residues: 1280 loop : -0.54 (0.11), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 47 HIS 0.008 0.001 HIS V 36 PHE 0.023 0.002 PHE D 82 TYR 0.030 0.002 TYR J 94 ARG 0.008 0.001 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 400 time to evaluate : 4.661 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: B 434 ILE cc_start: 0.4448 (OUTLIER) cc_final: 0.4188 (mt) REVERT: D 46 LEU cc_start: 0.4213 (mt) cc_final: 0.2682 (mm) REVERT: P 71 MET cc_start: 0.0054 (mtm) cc_final: -0.0499 (mmt) outliers start: 57 outliers final: 5 residues processed: 447 average time/residue: 0.5683 time to fit residues: 398.8184 Evaluate side-chains 179 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain R residue 91 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 419 optimal weight: 0.9990 chunk 376 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 389 optimal weight: 40.0000 chunk 150 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 289 optimal weight: 3.9990 chunk 451 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS A 69 HIS A 165 ASN A 211 ASN A 331 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 655 HIS A 675 GLN A 872 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 211 ASN B 282 ASN B 370 ASN B 487 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 675 GLN B 804 GLN B 901 GLN B 935 GLN B 965 GLN B1005 GLN B1011 GLN B1088 HIS C 49 HIS C 52 GLN C 165 ASN C 211 ASN C 370 ASN C 487 ASN C 493 GLN C 675 GLN D 91 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 ASN H 99 GLN I 84 ASN I 105 ASN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 55 ASN L 112 GLN N 6 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN Q 6 GLN R 77 ASN S 6 GLN U 3 GLN U 40 GLN U 114 GLN V 114 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4859 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39813 Z= 0.266 Angle : 0.675 14.142 54200 Z= 0.355 Chirality : 0.046 0.334 6174 Planarity : 0.005 0.090 6973 Dihedral : 5.157 45.238 5921 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 2.14 % Allowed : 9.43 % Favored : 88.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.12), residues: 4976 helix: 2.93 (0.18), residues: 746 sheet: 0.46 (0.13), residues: 1408 loop : -0.54 (0.11), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 112 HIS 0.012 0.002 HIS C1064 PHE 0.035 0.002 PHE V 109 TYR 0.031 0.002 TYR R 94 ARG 0.008 0.001 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 191 time to evaluate : 4.314 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: A 211 ASN cc_start: 0.7959 (m-40) cc_final: 0.7712 (p0) outliers start: 90 outliers final: 34 residues processed: 270 average time/residue: 0.5364 time to fit residues: 236.8025 Evaluate side-chains 193 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 250 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 375 optimal weight: 30.0000 chunk 307 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 452 optimal weight: 20.0000 chunk 488 optimal weight: 8.9990 chunk 402 optimal weight: 20.0000 chunk 448 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 362 optimal weight: 30.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 690 GLN A 901 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1005 GLN B1101 HIS C 66 HIS C 185 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 414 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 655 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN I 105 ASN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN O 57 GLN U 63 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5277 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 39813 Z= 0.430 Angle : 0.769 11.325 54200 Z= 0.404 Chirality : 0.049 0.359 6174 Planarity : 0.006 0.150 6973 Dihedral : 5.758 56.967 5913 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 2.68 % Allowed : 11.14 % Favored : 86.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 4976 helix: 1.59 (0.18), residues: 751 sheet: 0.11 (0.14), residues: 1355 loop : -0.82 (0.11), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 112 HIS 0.011 0.002 HIS C1064 PHE 0.039 0.002 PHE B 797 TYR 0.032 0.002 TYR C 904 ARG 0.021 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 188 time to evaluate : 4.466 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: B 536 ASN cc_start: 0.2678 (OUTLIER) cc_final: 0.1384 (t0) REVERT: B 1064 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.6997 (p90) REVERT: C 34 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8271 (mmt180) REVERT: J 79 LEU cc_start: -0.1943 (OUTLIER) cc_final: -0.3567 (mp) REVERT: V 58 GLU cc_start: 0.5652 (pm20) cc_final: 0.5318 (pm20) outliers start: 113 outliers final: 57 residues processed: 288 average time/residue: 0.5048 time to fit residues: 242.8508 Evaluate side-chains 208 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 147 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 446 optimal weight: 30.0000 chunk 339 optimal weight: 40.0000 chunk 234 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 303 optimal weight: 6.9990 chunk 453 optimal weight: 0.0000 chunk 480 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 430 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 690 GLN A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 185 ASN C 207 HIS C1088 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5245 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39813 Z= 0.243 Angle : 0.590 11.056 54200 Z= 0.308 Chirality : 0.044 0.617 6174 Planarity : 0.004 0.056 6973 Dihedral : 5.302 59.100 5913 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Rotamer: Outliers : 2.00 % Allowed : 12.57 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 4976 helix: 2.11 (0.18), residues: 749 sheet: 0.11 (0.13), residues: 1410 loop : -0.82 (0.11), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 36 HIS 0.006 0.001 HIS C1064 PHE 0.026 0.001 PHE V 65 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 161 time to evaluate : 4.595 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: B 1064 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.6995 (p90) REVERT: C 557 LYS cc_start: 0.2659 (OUTLIER) cc_final: 0.1458 (mmtt) REVERT: C 697 MET cc_start: 0.7327 (ppp) cc_final: 0.7090 (ppp) REVERT: P 71 MET cc_start: 0.1476 (mpp) cc_final: -0.1400 (ttp) REVERT: V 58 GLU cc_start: 0.5562 (pm20) cc_final: 0.5357 (pm20) outliers start: 84 outliers final: 54 residues processed: 236 average time/residue: 0.5096 time to fit residues: 203.3049 Evaluate side-chains 201 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 145 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain V residue 60 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 400 optimal weight: 0.4980 chunk 272 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 357 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 409 optimal weight: 40.0000 chunk 332 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 431 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 317 ASN B 360 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 580 GLN E 35 HIS J 82 GLN N 52 ASN O 41 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5302 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 39813 Z= 0.263 Angle : 0.584 9.907 54200 Z= 0.304 Chirality : 0.043 0.309 6174 Planarity : 0.004 0.088 6973 Dihedral : 5.129 57.495 5913 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.64 % Rotamer: Outliers : 2.47 % Allowed : 13.00 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 4976 helix: 2.17 (0.18), residues: 740 sheet: 0.06 (0.13), residues: 1422 loop : -0.89 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 112 HIS 0.006 0.001 HIS B1064 PHE 0.028 0.001 PHE C 759 TYR 0.023 0.001 TYR V 81 ARG 0.011 0.001 ARG V 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 162 time to evaluate : 4.822 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: B 1064 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7014 (p90) REVERT: C 63 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 329 PHE cc_start: 0.3107 (OUTLIER) cc_final: 0.2589 (m-80) REVERT: C 557 LYS cc_start: 0.2654 (OUTLIER) cc_final: 0.1429 (mmtt) REVERT: J 67 ARG cc_start: 0.4825 (mmp-170) cc_final: 0.4203 (tpm170) REVERT: P 71 MET cc_start: 0.1712 (mpp) cc_final: -0.1780 (ttt) REVERT: P 82 MET cc_start: 0.1522 (tpt) cc_final: 0.1117 (tpt) REVERT: V 58 GLU cc_start: 0.5835 (pm20) cc_final: 0.5604 (pm20) outliers start: 104 outliers final: 68 residues processed: 254 average time/residue: 0.5138 time to fit residues: 219.9995 Evaluate side-chains 212 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 140 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 161 optimal weight: 6.9990 chunk 432 optimal weight: 0.0470 chunk 94 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 480 optimal weight: 5.9990 chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 39 optimal weight: 0.0060 chunk 159 optimal weight: 6.9990 chunk 252 optimal weight: 30.0000 overall best weight: 2.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 914 ASN ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 39813 Z= 0.264 Angle : 0.571 10.033 54200 Z= 0.297 Chirality : 0.043 0.352 6174 Planarity : 0.004 0.073 6973 Dihedral : 5.092 58.923 5910 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 2.30 % Allowed : 13.26 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4976 helix: 2.27 (0.19), residues: 724 sheet: 0.03 (0.13), residues: 1429 loop : -0.92 (0.11), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP U 37 HIS 0.005 0.001 HIS C 207 PHE 0.021 0.001 PHE V 109 TYR 0.030 0.001 TYR Q 33 ARG 0.007 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 142 time to evaluate : 4.004 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: B 166 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6682 (m) REVERT: B 1064 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7008 (p90) REVERT: C 329 PHE cc_start: 0.3217 (OUTLIER) cc_final: 0.2727 (m-80) REVERT: C 557 LYS cc_start: 0.2799 (OUTLIER) cc_final: 0.1671 (mmtt) REVERT: P 71 MET cc_start: 0.1770 (mpp) cc_final: -0.1825 (ttt) REVERT: P 82 MET cc_start: 0.1381 (tpt) cc_final: 0.0869 (tpt) REVERT: U 82 MET cc_start: -0.0844 (mmt) cc_final: -0.1702 (mmp) REVERT: V 58 GLU cc_start: 0.5895 (pm20) cc_final: 0.5627 (pm20) outliers start: 97 outliers final: 65 residues processed: 225 average time/residue: 0.5090 time to fit residues: 193.6966 Evaluate side-chains 201 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 132 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 88 ARG Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 463 optimal weight: 40.0000 chunk 54 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 351 optimal weight: 50.0000 chunk 272 optimal weight: 5.9990 chunk 404 optimal weight: 0.0370 chunk 268 optimal weight: 0.2980 chunk 479 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 chunk 292 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39813 Z= 0.199 Angle : 0.545 11.719 54200 Z= 0.282 Chirality : 0.042 0.317 6174 Planarity : 0.004 0.057 6973 Dihedral : 4.901 58.873 5910 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 2.21 % Allowed : 13.30 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4976 helix: 2.43 (0.19), residues: 719 sheet: 0.04 (0.13), residues: 1413 loop : -0.86 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 112 HIS 0.004 0.001 HIS C 207 PHE 0.021 0.001 PHE V 109 TYR 0.055 0.001 TYR S 33 ARG 0.003 0.000 ARG V 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 142 time to evaluate : 4.335 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: B 166 CYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6543 (m) REVERT: B 1064 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.7000 (p90) REVERT: C 63 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8695 (p) REVERT: C 214 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6980 (mmp-170) REVERT: C 329 PHE cc_start: 0.3297 (OUTLIER) cc_final: 0.2813 (m-80) REVERT: C 557 LYS cc_start: 0.2768 (OUTLIER) cc_final: 0.1556 (mmtt) REVERT: J 67 ARG cc_start: 0.4632 (mmp-170) cc_final: 0.3983 (tpm170) REVERT: J 79 LEU cc_start: -0.1957 (OUTLIER) cc_final: -0.3402 (mp) REVERT: P 71 MET cc_start: 0.1685 (mpp) cc_final: -0.1660 (ttt) REVERT: R 34 MET cc_start: 0.0663 (mmt) cc_final: 0.0357 (mmt) REVERT: R 95 TYR cc_start: 0.1732 (OUTLIER) cc_final: 0.1423 (m-80) REVERT: U 82 MET cc_start: -0.0953 (mmt) cc_final: -0.1656 (mmt) REVERT: V 58 GLU cc_start: 0.5751 (pm20) cc_final: 0.5508 (pm20) outliers start: 93 outliers final: 68 residues processed: 222 average time/residue: 0.5117 time to fit residues: 193.6517 Evaluate side-chains 210 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 134 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 88 ARG Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 296 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 144 optimal weight: 40.0000 chunk 94 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 304 optimal weight: 0.0980 chunk 326 optimal weight: 0.0020 chunk 236 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 376 optimal weight: 50.0000 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 271 GLN ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Q 52 ASN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5268 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39813 Z= 0.151 Angle : 0.531 12.195 54200 Z= 0.274 Chirality : 0.042 0.302 6174 Planarity : 0.004 0.058 6973 Dihedral : 4.709 58.696 5910 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % Rotamer: Outliers : 1.88 % Allowed : 13.99 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 4976 helix: 2.54 (0.19), residues: 729 sheet: 0.05 (0.13), residues: 1439 loop : -0.80 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 36 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE V 65 TYR 0.042 0.001 TYR S 33 ARG 0.004 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 145 time to evaluate : 4.414 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: B 166 CYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6413 (m) REVERT: C 329 PHE cc_start: 0.3271 (OUTLIER) cc_final: 0.2800 (m-80) REVERT: C 557 LYS cc_start: 0.2363 (OUTLIER) cc_final: 0.1488 (mmtt) REVERT: P 71 MET cc_start: 0.1157 (mpp) cc_final: -0.2024 (ttt) REVERT: P 82 MET cc_start: 0.0978 (tpt) cc_final: 0.0438 (tpt) REVERT: R 34 MET cc_start: 0.0643 (mmt) cc_final: 0.0404 (mmt) REVERT: U 82 MET cc_start: -0.1475 (mmt) cc_final: -0.2330 (mmt) REVERT: V 58 GLU cc_start: 0.5906 (pm20) cc_final: 0.5672 (pm20) outliers start: 79 outliers final: 62 residues processed: 214 average time/residue: 0.5122 time to fit residues: 185.7470 Evaluate side-chains 199 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 134 time to evaluate : 4.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 88 ARG Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 435 optimal weight: 50.0000 chunk 458 optimal weight: 0.0570 chunk 418 optimal weight: 7.9990 chunk 446 optimal weight: 20.0000 chunk 268 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 350 optimal weight: 50.0000 chunk 136 optimal weight: 6.9990 chunk 403 optimal weight: 50.0000 chunk 422 optimal weight: 7.9990 chunk 444 optimal weight: 8.9990 overall best weight: 4.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 185 ASN A 872 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 185 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5437 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 39813 Z= 0.404 Angle : 0.669 13.628 54200 Z= 0.347 Chirality : 0.045 0.389 6174 Planarity : 0.004 0.068 6973 Dihedral : 5.398 56.507 5910 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.02 % Favored : 94.84 % Rotamer: Outliers : 2.23 % Allowed : 13.90 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4976 helix: 1.97 (0.19), residues: 728 sheet: -0.32 (0.13), residues: 1466 loop : -0.90 (0.12), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 36 HIS 0.010 0.002 HIS B1064 PHE 0.021 0.002 PHE C 220 TYR 0.030 0.002 TYR R 59 ARG 0.012 0.001 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 150 time to evaluate : 4.187 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: B 166 CYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6596 (m) REVERT: B 536 ASN cc_start: 0.3826 (OUTLIER) cc_final: 0.2470 (t0) REVERT: B 740 MET cc_start: 0.7750 (tpp) cc_final: 0.7497 (mmm) REVERT: B 1064 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.6961 (p90) REVERT: C 557 LYS cc_start: 0.3311 (OUTLIER) cc_final: 0.1803 (mmtt) REVERT: P 71 MET cc_start: 0.1182 (mpp) cc_final: -0.1913 (ttt) REVERT: P 82 MET cc_start: 0.1156 (tpt) cc_final: 0.0429 (tpt) REVERT: R 95 TYR cc_start: 0.1894 (OUTLIER) cc_final: 0.1436 (m-80) REVERT: T 58 VAL cc_start: -0.3624 (OUTLIER) cc_final: -0.3857 (t) REVERT: U 82 MET cc_start: -0.1181 (mmt) cc_final: -0.1869 (mmt) REVERT: V 58 GLU cc_start: 0.6112 (pm20) cc_final: 0.5803 (pm20) outliers start: 94 outliers final: 75 residues processed: 231 average time/residue: 0.4995 time to fit residues: 195.8823 Evaluate side-chains 214 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 133 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 293 optimal weight: 2.9990 chunk 472 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 328 optimal weight: 50.0000 chunk 495 optimal weight: 10.0000 chunk 455 optimal weight: 2.9990 chunk 394 optimal weight: 50.0000 chunk 40 optimal weight: 0.9990 chunk 304 optimal weight: 0.0170 chunk 241 optimal weight: 0.7980 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5350 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39813 Z= 0.185 Angle : 0.562 14.293 54200 Z= 0.288 Chirality : 0.043 0.323 6174 Planarity : 0.004 0.053 6973 Dihedral : 5.074 59.808 5910 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.90 % Rotamer: Outliers : 1.71 % Allowed : 14.61 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4976 helix: 2.33 (0.19), residues: 726 sheet: -0.25 (0.13), residues: 1478 loop : -0.84 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP V 112 HIS 0.004 0.001 HIS C1064 PHE 0.035 0.001 PHE A 464 TYR 0.019 0.001 TYR S 33 ARG 0.004 0.000 ARG C 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 138 time to evaluate : 4.245 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: B 166 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6472 (m) REVERT: B 1064 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6910 (p90) REVERT: C 557 LYS cc_start: 0.2488 (OUTLIER) cc_final: 0.1185 (mmtt) REVERT: J 67 ARG cc_start: 0.4540 (mmp-170) cc_final: 0.3970 (tpm170) REVERT: P 71 MET cc_start: 0.1113 (mpp) cc_final: -0.2311 (ttt) REVERT: P 82 MET cc_start: 0.1173 (tpt) cc_final: 0.0143 (tpt) REVERT: R 95 TYR cc_start: 0.1967 (OUTLIER) cc_final: 0.1484 (m-80) REVERT: T 58 VAL cc_start: -0.3128 (OUTLIER) cc_final: -0.3353 (t) REVERT: U 82 MET cc_start: -0.1282 (mmt) cc_final: -0.2030 (mmt) REVERT: V 58 GLU cc_start: 0.6183 (pm20) cc_final: 0.5928 (pm20) outliers start: 72 outliers final: 56 residues processed: 202 average time/residue: 0.5075 time to fit residues: 173.7007 Evaluate side-chains 192 residues out of total 4338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 131 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain V residue 81 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 313 optimal weight: 0.0370 chunk 420 optimal weight: 40.0000 chunk 120 optimal weight: 7.9990 chunk 363 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 394 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 405 optimal weight: 40.0000 chunk 50 optimal weight: 0.0670 chunk 72 optimal weight: 7.9990 overall best weight: 2.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.087073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.061306 restraints weight = 310116.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.062841 restraints weight = 154241.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.061731 restraints weight = 95135.598| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39813 Z= 0.243 Angle : 0.569 13.331 54200 Z= 0.292 Chirality : 0.043 0.333 6174 Planarity : 0.004 0.051 6973 Dihedral : 5.009 59.005 5909 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.78 % Favored : 95.08 % Rotamer: Outliers : 1.73 % Allowed : 14.64 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 4976 helix: 2.34 (0.19), residues: 732 sheet: -0.31 (0.13), residues: 1490 loop : -0.82 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP V 112 HIS 0.005 0.001 HIS B1064 PHE 0.023 0.001 PHE I 29 TYR 0.017 0.001 TYR E 33 ARG 0.006 0.000 ARG R 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7044.51 seconds wall clock time: 131 minutes 5.02 seconds (7865.02 seconds total)