Starting phenix.real_space_refine on Tue Feb 20 14:27:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/02_2024/6wps_21864.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/02_2024/6wps_21864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/02_2024/6wps_21864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/02_2024/6wps_21864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/02_2024/6wps_21864.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/02_2024/6wps_21864.pdb" } resolution = 3.1 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= 0.004 sd= 0.066 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 117 5.16 5 C 17909 2.51 5 N 4593 2.21 5 O 5497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "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 GLU 868": "OE1" <-> "OE2" Residue "A TYR 873": "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 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 868": "OE1" <-> "OE2" Residue "B TYR 873": "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 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 868": "OE1" <-> "OE2" Residue "E TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28116 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7386 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7395 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7395 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.82, per 1000 atoms: 0.53 Number of scatterers: 28116 At special positions: 0 Unit cell: (148.05, 144.9, 179.55, 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 117 16.00 O 5497 8.00 N 4593 7.00 C 17909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.09 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.23 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.23 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.10 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.23 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA S 3 " - " MAN S 5 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " BETA1-6 " NAG N 1 " - " FUC N 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 6 " " NAG X 1 " - " FUC X 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG A1319 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1314 " - " ASN E1074 " " NAG E1319 " - " ASN E 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 343 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E1098 " " NAG W 1 " - " ASN E1134 " " NAG X 1 " - " ASN E 343 " Time building additional restraints: 11.63 Conformation dependent library (CDL) restraints added in 5.1 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 21.8% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.935A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.541A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.993A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.770A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 6.935A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.540A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.993A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.770A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 759 removed outlier: 6.935A pdb=" N SER E 758 " --> pdb=" O GLN E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN E 774 " --> pdb=" O ILE E 770 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.542A pdb=" N GLY E 885 " --> pdb=" O THR E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.993A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 982 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.769A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.091A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.661A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.423A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.294A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.651A pdb=" N ALA A 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.412A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.091A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.660A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.294A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.078A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.078A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.413A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF4, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.661A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN E 122 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.293A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AG4, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.899A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR E 660 " --> pdb=" O SER E 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.899A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AG9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 116 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.413A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 11 1242 hydrogen bonds defined for protein. 3312 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: 13.91 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7795 1.33 - 1.48: 8760 1.48 - 1.62: 11999 1.62 - 1.76: 9 1.76 - 1.90: 150 Bond restraints: 28713 Sorted by residual: bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE ARG E 454 " pdb=" CZ ARG E 454 " ideal model delta sigma weight residual 1.326 1.378 -0.052 1.10e-02 8.26e+03 2.28e+01 bond pdb=" CB ILE B 468 " pdb=" CG1 ILE B 468 " ideal model delta sigma weight residual 1.530 1.622 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.622 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 28708 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.30: 643 105.30 - 112.48: 14657 112.48 - 119.67: 9026 119.67 - 126.86: 14582 126.86 - 134.04: 170 Bond angle restraints: 39078 Sorted by residual: angle pdb=" C ILE G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 119.78 127.24 -7.46 1.03e+00 9.43e-01 5.25e+01 angle pdb=" C ILE D 59 " pdb=" N PRO D 60 " pdb=" CA PRO D 60 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 angle pdb=" C ASP E 808 " pdb=" N PRO E 809 " pdb=" CA PRO E 809 " ideal model delta sigma weight residual 119.56 126.88 -7.32 1.02e+00 9.61e-01 5.16e+01 angle pdb=" C ASP A 808 " pdb=" N PRO A 809 " pdb=" CA PRO A 809 " ideal model delta sigma weight residual 119.56 126.86 -7.30 1.02e+00 9.61e-01 5.12e+01 ... (remaining 39073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 17339 21.48 - 42.95: 398 42.95 - 64.43: 89 64.43 - 85.90: 45 85.90 - 107.38: 18 Dihedral angle restraints: 17889 sinusoidal: 7665 harmonic: 10224 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.38 67.38 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS E1082 " pdb=" SG CYS E1082 " pdb=" SG CYS E1126 " pdb=" CB CYS E1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.37 67.37 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.37 67.37 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 17886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3292 0.085 - 0.169: 1048 0.169 - 0.254: 289 0.254 - 0.339: 68 0.339 - 0.423: 12 Chirality restraints: 4709 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.01e+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 -2.49 0.09 2.00e-02 2.50e+03 1.97e+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 -2.49 0.09 2.00e-02 2.50e+03 1.93e+01 ... (remaining 4706 not shown) Planarity restraints: 4951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 331 " 0.046 2.00e-02 2.50e+03 4.62e-02 2.66e+01 pdb=" CG ASN E 331 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN E 331 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 331 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.046 2.00e-02 2.50e+03 4.59e-02 2.64e+01 pdb=" CG ASN B 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.046 2.00e-02 2.50e+03 4.58e-02 2.62e+01 pdb=" CG ASN A 331 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.055 2.00e-02 2.50e+03 ... (remaining 4948 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 9505 2.87 - 3.38: 24884 3.38 - 3.89: 48554 3.89 - 4.39: 55527 4.39 - 4.90: 91903 Nonbonded interactions: 230373 Sorted by model distance: nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.364 2.520 nonbonded pdb=" NZ LYS A 557 " pdb=" OD2 ASP A 574 " model vdw 2.364 2.520 nonbonded pdb=" NZ LYS E 557 " pdb=" OD2 ASP E 574 " model vdw 2.365 2.520 nonbonded pdb=" NH1 ARG B 346 " pdb=" OD1 ASP D 93 " model vdw 2.430 2.520 nonbonded pdb=" NH1 ARG E 346 " pdb=" OD1 ASP G 93 " model vdw 2.430 2.520 ... (remaining 230368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 499 or (resid 500 and (name N o \ r name CA or name C or name O or name CB )) or resid 501 through 772 or (resid 7 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 1140 or resid 1301 through 1319)) selection = (chain 'E' and (resid 27 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 499 or (resid 500 and (name N o \ r name CA or name C or name O or name CB )) or resid 501 through 772 or (resid 7 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 1140 or resid 1301 through 1319)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.020 Extract box with map and model: 14.380 Check model and map are aligned: 0.450 Set scattering table: 0.230 Process input model: 77.650 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.340 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 : 0.013 0.092 28713 Z= 0.854 Angle : 1.339 8.638 39078 Z= 0.901 Chirality : 0.092 0.423 4709 Planarity : 0.005 0.028 4903 Dihedral : 11.022 107.375 11187 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.10 % Allowed : 0.82 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 3438 helix: -0.00 (0.18), residues: 666 sheet: 0.96 (0.17), residues: 858 loop : 0.51 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.007 TRP C 47 HIS 0.006 0.001 HIS E1048 PHE 0.020 0.004 PHE B 497 TYR 0.037 0.005 TYR B 495 ARG 0.003 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 745 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.6989 (p90) cc_final: 0.6757 (p90) REVERT: A 764 ASN cc_start: 0.8251 (m-40) cc_final: 0.7901 (m-40) REVERT: A 1105 THR cc_start: 0.7429 (t) cc_final: 0.6505 (m) REVERT: D 50 TYR cc_start: 0.8084 (p90) cc_final: 0.7883 (p90) REVERT: D 55 ARG cc_start: 0.6313 (ttm110) cc_final: 0.5867 (ttm110) REVERT: E 95 THR cc_start: 0.7552 (p) cc_final: 0.7304 (p) REVERT: E 764 ASN cc_start: 0.8225 (m-40) cc_final: 0.7903 (m-40) REVERT: G 36 TRP cc_start: 0.7775 (m100) cc_final: 0.7324 (m100) outliers start: 3 outliers final: 3 residues processed: 748 average time/residue: 0.4215 time to fit residues: 485.5446 Evaluate side-chains 401 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 398 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain E residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 275 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 318 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 787 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 935 GLN A1054 GLN H 3 GLN H 59 ASN B 196 ASN B 703 ASN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1054 GLN C 3 GLN C 39 GLN C 59 ASN E 66 HIS E 218 GLN E 519 HIS ** E 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 919 ASN E 935 GLN E1054 GLN E1101 HIS F 3 GLN F 59 ASN F 116 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 28713 Z= 0.239 Angle : 0.621 8.804 39078 Z= 0.331 Chirality : 0.046 0.207 4709 Planarity : 0.004 0.045 4903 Dihedral : 6.816 73.469 5313 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.23 % Allowed : 7.64 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3438 helix: 1.19 (0.21), residues: 645 sheet: 0.55 (0.15), residues: 960 loop : 0.14 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1102 HIS 0.011 0.001 HIS G 92 PHE 0.031 0.002 PHE D 72 TYR 0.024 0.002 TYR G 50 ARG 0.005 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 430 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.3665 (OUTLIER) cc_final: 0.2953 (t80) REVERT: A 902 MET cc_start: 0.7410 (mmt) cc_final: 0.7189 (mmt) REVERT: H 116 ASN cc_start: 0.7327 (m-40) cc_final: 0.6993 (m-40) REVERT: L 55 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.6594 (mtm-85) REVERT: B 421 TYR cc_start: 0.3924 (OUTLIER) cc_final: 0.3060 (t80) REVERT: D 50 TYR cc_start: 0.8149 (p90) cc_final: 0.7870 (p90) REVERT: D 73 THR cc_start: 0.7174 (p) cc_final: 0.6922 (p) REVERT: E 95 THR cc_start: 0.7484 (p) cc_final: 0.7214 (p) REVERT: E 421 TYR cc_start: 0.4106 (m-80) cc_final: 0.3403 (t80) REVERT: E 1002 GLN cc_start: 0.7278 (tt0) cc_final: 0.6984 (tt0) REVERT: G 55 ARG cc_start: 0.6541 (ttp-110) cc_final: 0.6135 (mtm-85) outliers start: 65 outliers final: 38 residues processed: 473 average time/residue: 0.3941 time to fit residues: 298.1706 Evaluate side-chains 380 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 340 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain F residue 115 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.5980 chunk 98 optimal weight: 8.9990 chunk 265 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 319 optimal weight: 0.5980 chunk 344 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 658 ASN A 703 ASN A 914 ASN A 955 ASN H 3 GLN B 207 HIS B 658 ASN B 764 ASN B 787 GLN B 914 ASN B 935 GLN B1054 GLN C 3 GLN E 207 HIS E 914 ASN E1054 GLN F 3 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28713 Z= 0.262 Angle : 0.576 10.311 39078 Z= 0.303 Chirality : 0.045 0.184 4709 Planarity : 0.004 0.062 4903 Dihedral : 6.282 66.159 5313 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.67 % Allowed : 8.98 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3438 helix: 1.42 (0.21), residues: 648 sheet: 0.39 (0.16), residues: 960 loop : 0.07 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1102 HIS 0.007 0.001 HIS D 92 PHE 0.037 0.002 PHE D 72 TYR 0.019 0.002 TYR B1067 ARG 0.007 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 366 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.3733 (OUTLIER) cc_final: 0.2930 (t80) REVERT: A 874 THR cc_start: 0.8568 (p) cc_final: 0.8019 (t) REVERT: A 994 ASP cc_start: 0.6634 (m-30) cc_final: 0.6306 (m-30) REVERT: A 1029 MET cc_start: 0.8527 (tpp) cc_final: 0.7946 (tpp) REVERT: H 116 ASN cc_start: 0.7418 (m-40) cc_final: 0.7086 (m-40) REVERT: L 55 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6758 (mtm-85) REVERT: L 90 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: B 421 TYR cc_start: 0.3814 (OUTLIER) cc_final: 0.2866 (t80) REVERT: B 761 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8206 (t) REVERT: B 984 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7874 (mt) REVERT: D 50 TYR cc_start: 0.8139 (p90) cc_final: 0.7851 (p90) REVERT: E 95 THR cc_start: 0.7377 (p) cc_final: 0.7060 (p) REVERT: E 421 TYR cc_start: 0.4098 (m-80) cc_final: 0.3359 (t80) REVERT: E 804 GLN cc_start: 0.7549 (mt0) cc_final: 0.7200 (mt0) REVERT: E 904 TYR cc_start: 0.7338 (m-10) cc_final: 0.6992 (m-10) REVERT: G 55 ARG cc_start: 0.6685 (ttp-110) cc_final: 0.6194 (mtm-85) outliers start: 78 outliers final: 49 residues processed: 424 average time/residue: 0.4013 time to fit residues: 275.2747 Evaluate side-chains 375 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 321 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 998 THR Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 115 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 320 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 303 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN H 39 GLN L 39 GLN B 519 HIS C 3 GLN D 90 GLN F 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28713 Z= 0.235 Angle : 0.553 8.482 39078 Z= 0.290 Chirality : 0.045 0.287 4709 Planarity : 0.004 0.066 4903 Dihedral : 5.860 56.415 5313 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.77 % Allowed : 9.76 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3438 helix: 1.39 (0.21), residues: 651 sheet: 0.25 (0.16), residues: 966 loop : 0.02 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 105 HIS 0.006 0.001 HIS G 92 PHE 0.024 0.002 PHE E 497 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 340 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8241 (pp) REVERT: A 421 TYR cc_start: 0.3851 (OUTLIER) cc_final: 0.2976 (t80) REVERT: A 759 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: A 1029 MET cc_start: 0.8539 (tpp) cc_final: 0.7965 (tpp) REVERT: H 98 ARG cc_start: 0.8287 (tmm-80) cc_final: 0.7800 (ttp-170) REVERT: H 116 ASN cc_start: 0.7508 (m-40) cc_final: 0.7202 (m-40) REVERT: B 410 ILE cc_start: 0.8427 (mm) cc_final: 0.8132 (mt) REVERT: B 421 TYR cc_start: 0.3909 (m-80) cc_final: 0.2904 (t80) REVERT: B 914 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7850 (p0) REVERT: B 984 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7809 (mt) REVERT: D 50 TYR cc_start: 0.8115 (p90) cc_final: 0.7871 (p90) REVERT: E 66 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.6978 (m-70) REVERT: E 95 THR cc_start: 0.7335 (p) cc_final: 0.7018 (p) REVERT: E 421 TYR cc_start: 0.4105 (m-80) cc_final: 0.3246 (t80) REVERT: F 98 ARG cc_start: 0.8154 (tmm-80) cc_final: 0.7510 (ttp-170) REVERT: F 102 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7859 (mtp85) outliers start: 81 outliers final: 50 residues processed: 403 average time/residue: 0.4089 time to fit residues: 268.3650 Evaluate side-chains 364 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 308 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 975 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 4 optimal weight: 0.0060 chunk 252 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 289 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN C 3 GLN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28713 Z= 0.240 Angle : 0.548 7.701 39078 Z= 0.283 Chirality : 0.045 0.380 4709 Planarity : 0.004 0.066 4903 Dihedral : 5.569 48.485 5313 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.84 % Allowed : 11.10 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3438 helix: 1.60 (0.21), residues: 630 sheet: 0.16 (0.16), residues: 966 loop : -0.09 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.007 0.001 HIS D 92 PHE 0.020 0.002 PHE L 72 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 337 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6658 (m-10) cc_final: 0.6410 (m-80) REVERT: A 390 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8330 (pp) REVERT: A 421 TYR cc_start: 0.4086 (OUTLIER) cc_final: 0.3814 (m-80) REVERT: A 1029 MET cc_start: 0.8583 (tpp) cc_final: 0.8083 (tpp) REVERT: H 116 ASN cc_start: 0.7469 (m-40) cc_final: 0.7241 (m-40) REVERT: L 72 PHE cc_start: 0.7127 (m-10) cc_final: 0.6648 (m-10) REVERT: B 421 TYR cc_start: 0.3989 (m-80) cc_final: 0.2877 (t80) REVERT: B 759 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6821 (t80) REVERT: B 977 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8199 (mp) REVERT: B 984 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7865 (mt) REVERT: D 50 TYR cc_start: 0.8100 (p90) cc_final: 0.7828 (p90) REVERT: E 66 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6944 (m-70) REVERT: E 95 THR cc_start: 0.7386 (p) cc_final: 0.7066 (p) REVERT: E 421 TYR cc_start: 0.4393 (m-80) cc_final: 0.3257 (t80) REVERT: F 98 ARG cc_start: 0.8228 (tmm-80) cc_final: 0.7885 (ttp-170) REVERT: F 102 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7738 (ttp-110) outliers start: 83 outliers final: 57 residues processed: 400 average time/residue: 0.3852 time to fit residues: 249.2051 Evaluate side-chains 372 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 309 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 0.3980 chunk 305 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 339 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 3 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28713 Z= 0.193 Angle : 0.518 8.317 39078 Z= 0.269 Chirality : 0.044 0.324 4709 Planarity : 0.004 0.063 4903 Dihedral : 5.240 46.459 5313 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.60 % Allowed : 12.30 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3438 helix: 1.62 (0.21), residues: 642 sheet: 0.10 (0.15), residues: 972 loop : -0.07 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 PHE 0.028 0.001 PHE L 72 TYR 0.019 0.001 TYR C 95 ARG 0.007 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 324 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6719 (m-10) cc_final: 0.6411 (m-80) REVERT: A 421 TYR cc_start: 0.4120 (OUTLIER) cc_final: 0.3861 (m-80) REVERT: A 1029 MET cc_start: 0.8573 (tpp) cc_final: 0.8043 (tpp) REVERT: H 116 ASN cc_start: 0.7533 (m-40) cc_final: 0.7226 (m-40) REVERT: B 421 TYR cc_start: 0.4059 (m-80) cc_final: 0.2889 (t80) REVERT: B 643 PHE cc_start: 0.7698 (t80) cc_final: 0.7497 (t80) REVERT: B 759 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6547 (t80) REVERT: B 977 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 984 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7919 (mt) REVERT: B 985 ASP cc_start: 0.6829 (p0) cc_final: 0.6505 (p0) REVERT: D 50 TYR cc_start: 0.7993 (p90) cc_final: 0.7358 (p90) REVERT: E 66 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6863 (m-70) REVERT: E 95 THR cc_start: 0.7357 (p) cc_final: 0.7056 (p) REVERT: E 410 ILE cc_start: 0.8330 (mm) cc_final: 0.8082 (mm) REVERT: E 421 TYR cc_start: 0.4498 (m-80) cc_final: 0.3282 (t80) REVERT: E 758 SER cc_start: 0.8173 (m) cc_final: 0.7952 (t) REVERT: E 1002 GLN cc_start: 0.7500 (tt0) cc_final: 0.7151 (tt0) REVERT: F 98 ARG cc_start: 0.8200 (tmm-80) cc_final: 0.7938 (tmm-80) REVERT: F 102 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7631 (ttp-110) outliers start: 76 outliers final: 50 residues processed: 382 average time/residue: 0.3912 time to fit residues: 245.7512 Evaluate side-chains 358 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 303 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 248 optimal weight: 0.0870 chunk 192 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 338 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28713 Z= 0.217 Angle : 0.524 7.623 39078 Z= 0.272 Chirality : 0.045 0.386 4709 Planarity : 0.004 0.048 4903 Dihedral : 5.066 46.507 5313 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.54 % Allowed : 13.02 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3438 helix: 1.55 (0.21), residues: 639 sheet: 0.03 (0.15), residues: 993 loop : -0.05 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.005 0.001 HIS D 92 PHE 0.014 0.001 PHE E 168 TYR 0.020 0.001 TYR H 95 ARG 0.008 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 312 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6773 (m-10) cc_final: 0.6431 (m-80) REVERT: A 340 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: A 1029 MET cc_start: 0.8604 (tpp) cc_final: 0.8054 (tpp) REVERT: H 116 ASN cc_start: 0.7613 (m-40) cc_final: 0.7322 (m-40) REVERT: B 410 ILE cc_start: 0.8261 (mm) cc_final: 0.7960 (mt) REVERT: B 421 TYR cc_start: 0.4316 (m-80) cc_final: 0.4086 (m-80) REVERT: B 646 ARG cc_start: 0.7130 (mtm-85) cc_final: 0.6920 (mtm180) REVERT: B 759 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6665 (t80) REVERT: B 977 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 984 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 1032 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7537 (m) REVERT: C 80 TYR cc_start: 0.6693 (m-80) cc_final: 0.6471 (m-80) REVERT: C 84 ARG cc_start: 0.6381 (mmm-85) cc_final: 0.6126 (mtm180) REVERT: D 50 TYR cc_start: 0.7814 (p90) cc_final: 0.6974 (p90) REVERT: E 66 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7034 (m-70) REVERT: E 95 THR cc_start: 0.7518 (p) cc_final: 0.7198 (p) REVERT: E 421 TYR cc_start: 0.4683 (m-80) cc_final: 0.3244 (t80) REVERT: E 1002 GLN cc_start: 0.7507 (tt0) cc_final: 0.7174 (tt0) REVERT: F 102 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7656 (ttp-110) outliers start: 74 outliers final: 57 residues processed: 374 average time/residue: 0.3681 time to fit residues: 225.7402 Evaluate side-chains 358 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 295 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 215 optimal weight: 0.7980 chunk 230 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 116 ASN C 39 GLN C 116 ASN D 39 GLN E 196 ASN E1005 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 28713 Z= 0.371 Angle : 0.617 8.138 39078 Z= 0.318 Chirality : 0.047 0.369 4709 Planarity : 0.004 0.045 4903 Dihedral : 5.533 47.122 5313 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.84 % Allowed : 12.95 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3438 helix: 1.28 (0.21), residues: 639 sheet: -0.07 (0.15), residues: 966 loop : -0.34 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 47 HIS 0.006 0.001 HIS L 92 PHE 0.033 0.002 PHE L 72 TYR 0.021 0.002 TYR E 265 ARG 0.007 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 307 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6869 (m-10) cc_final: 0.6488 (m-80) REVERT: A 340 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 1029 MET cc_start: 0.8715 (tpp) cc_final: 0.8253 (tpp) REVERT: H 25 SER cc_start: 0.7496 (OUTLIER) cc_final: 0.6846 (p) REVERT: H 116 ASN cc_start: 0.7585 (m110) cc_final: 0.7327 (m-40) REVERT: B 759 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7072 (t80) REVERT: B 977 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 984 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8272 (mt) REVERT: C 57 ASN cc_start: 0.7651 (t0) cc_final: 0.7196 (m110) REVERT: C 84 ARG cc_start: 0.6569 (mmm-85) cc_final: 0.6249 (mtm180) REVERT: E 95 THR cc_start: 0.7728 (p) cc_final: 0.7481 (p) REVERT: E 918 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: F 102 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7750 (ttp-110) outliers start: 83 outliers final: 55 residues processed: 379 average time/residue: 0.3689 time to fit residues: 230.3276 Evaluate side-chains 354 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 293 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 975 SER Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 0.7980 chunk 324 optimal weight: 0.3980 chunk 295 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 96 optimal weight: 50.0000 chunk 284 optimal weight: 0.9990 chunk 298 optimal weight: 0.1980 chunk 314 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1101 HIS H 3 GLN E 196 ASN E1005 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28713 Z= 0.191 Angle : 0.527 7.085 39078 Z= 0.275 Chirality : 0.044 0.269 4709 Planarity : 0.004 0.046 4903 Dihedral : 5.063 46.622 5313 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.88 % Allowed : 14.11 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3438 helix: 1.48 (0.21), residues: 639 sheet: -0.05 (0.15), residues: 987 loop : -0.26 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.004 0.001 HIS G 92 PHE 0.015 0.001 PHE B 400 TYR 0.028 0.001 TYR B 495 ARG 0.007 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 316 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.6920 (t80) cc_final: 0.6575 (t80) REVERT: A 269 TYR cc_start: 0.6730 (m-10) cc_final: 0.6271 (m-80) REVERT: A 340 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: A 584 ILE cc_start: 0.8126 (mm) cc_final: 0.7848 (mm) REVERT: A 1029 MET cc_start: 0.8636 (tpp) cc_final: 0.8097 (tpp) REVERT: H 12 LYS cc_start: 0.5903 (mmtp) cc_final: 0.5624 (mmtp) REVERT: H 25 SER cc_start: 0.7315 (OUTLIER) cc_final: 0.6699 (p) REVERT: B 759 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6824 (t80) REVERT: B 977 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8233 (mp) REVERT: B 984 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8286 (mt) REVERT: C 57 ASN cc_start: 0.7520 (t0) cc_final: 0.7165 (m110) REVERT: E 95 THR cc_start: 0.7642 (p) cc_final: 0.7407 (p) REVERT: E 918 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: E 1002 GLN cc_start: 0.7436 (tt0) cc_final: 0.7054 (tt0) REVERT: F 102 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7723 (ttp-110) outliers start: 55 outliers final: 45 residues processed: 365 average time/residue: 0.3613 time to fit residues: 216.9082 Evaluate side-chains 349 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 298 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 975 SER Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.5980 chunk 333 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 231 optimal weight: 6.9990 chunk 349 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN H 3 GLN H 119 GLN C 116 ASN E 196 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28713 Z= 0.262 Angle : 0.554 7.942 39078 Z= 0.287 Chirality : 0.045 0.407 4709 Planarity : 0.004 0.047 4903 Dihedral : 5.097 46.484 5313 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.78 % Allowed : 14.63 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3438 helix: 1.43 (0.21), residues: 639 sheet: -0.12 (0.15), residues: 969 loop : -0.32 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.015 0.001 HIS E 655 PHE 0.023 0.002 PHE E 643 TYR 0.027 0.002 TYR B 495 ARG 0.006 0.000 ARG L 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 296 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6810 (m-10) cc_final: 0.6345 (m-80) REVERT: A 340 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: A 1029 MET cc_start: 0.8638 (tpp) cc_final: 0.8083 (tpp) REVERT: H 12 LYS cc_start: 0.5981 (mmtp) cc_final: 0.5717 (mmtp) REVERT: B 759 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 977 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 984 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8316 (mt) REVERT: C 57 ASN cc_start: 0.7533 (t0) cc_final: 0.7217 (m110) REVERT: C 80 TYR cc_start: 0.6577 (m-80) cc_final: 0.6374 (m-80) REVERT: E 95 THR cc_start: 0.7692 (p) cc_final: 0.7450 (p) REVERT: E 918 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: E 1002 GLN cc_start: 0.7478 (tt0) cc_final: 0.7124 (tt0) REVERT: F 102 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7698 (ttp-110) REVERT: G 34 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7787 (mp) outliers start: 52 outliers final: 46 residues processed: 341 average time/residue: 0.3857 time to fit residues: 214.2745 Evaluate side-chains 344 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 292 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 975 SER Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 1.9990 chunk 296 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 0.0020 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN H 3 GLN E 196 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.169364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.138164 restraints weight = 41470.410| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.81 r_work: 0.3739 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 28713 Z= 0.275 Angle : 0.682 59.191 39078 Z= 0.379 Chirality : 0.045 0.523 4709 Planarity : 0.004 0.046 4903 Dihedral : 5.099 46.478 5313 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.02 % Allowed : 14.46 % Favored : 83.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3438 helix: 1.41 (0.21), residues: 651 sheet: -0.12 (0.15), residues: 969 loop : -0.34 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.020 0.001 HIS E 655 PHE 0.026 0.001 PHE E 643 TYR 0.025 0.001 TYR B 495 ARG 0.006 0.000 ARG L 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6622.96 seconds wall clock time: 120 minutes 47.96 seconds (7247.96 seconds total)