Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 14:43:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/04_2023/6wps_21864.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/04_2023/6wps_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_21864/04_2023/6wps_21864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/04_2023/6wps_21864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/04_2023/6wps_21864.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wps_21864/04_2023/6wps_21864.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 15.16, per 1000 atoms: 0.54 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: 11.84 Conformation dependent library (CDL) restraints added in 4.2 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: 2.60 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: 14.44 Time building geometry restraints manager: 12.51 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 - 17.58: 15684 17.58 - 35.15: 490 35.15 - 52.73: 101 52.73 - 70.31: 48 70.31 - 87.88: 21 Dihedral angle restraints: 16344 sinusoidal: 6120 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 16341 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.450 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 76.290 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.700 ------------------------------------------------------------------------------- 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 : 10.403 87.884 9642 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 % 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 *********************** 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 : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 748 average time/residue: 0.4266 time to fit residues: 492.2957 Evaluate side-chains 400 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 397 time to evaluate : 3.116 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2398 time to fit residues: 5.6667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A 919 ASN A 935 GLN A1054 GLN H 3 GLN H 59 ASN B 196 ASN B 703 ASN B 914 ASN B 935 GLN B1054 GLN C 3 GLN C 39 GLN C 59 ASN E 66 HIS E 218 GLN E 519 HIS ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 914 ASN 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 28713 Z= 0.227 Angle : 0.618 8.382 39078 Z= 0.330 Chirality : 0.045 0.194 4709 Planarity : 0.004 0.049 4903 Dihedral : 4.643 22.743 3762 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 2.23 % 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: 0.61 (0.14), residues: 3438 helix: 1.19 (0.21), residues: 645 sheet: 0.55 (0.15), residues: 960 loop : 0.15 (0.14), residues: 1833 *********************** 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 494 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 429 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 34 residues processed: 470 average time/residue: 0.3956 time to fit residues: 298.7905 Evaluate side-chains 383 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 349 time to evaluate : 3.171 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2462 time to fit residues: 20.1005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 265 optimal weight: 0.0270 chunk 217 optimal weight: 5.9990 chunk 87 optimal weight: 0.0570 chunk 319 optimal weight: 2.9990 chunk 344 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- 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 955 ASN H 3 GLN B 207 HIS B 658 ASN B 935 GLN C 3 GLN E 207 HIS F 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 28713 Z= 0.295 Angle : 0.593 9.986 39078 Z= 0.312 Chirality : 0.046 0.210 4709 Planarity : 0.004 0.064 4903 Dihedral : 4.441 22.102 3762 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3438 helix: 1.39 (0.21), residues: 648 sheet: 0.36 (0.16), residues: 963 loop : 0.03 (0.14), residues: 1827 *********************** 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 422 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 372 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 30 residues processed: 410 average time/residue: 0.3815 time to fit residues: 253.7100 Evaluate side-chains 350 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 320 time to evaluate : 3.100 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2494 time to fit residues: 18.4495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 35 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 320 optimal weight: 0.9980 chunk 339 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 303 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 B 519 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN C 3 GLN C 116 ASN D 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 28713 Z= 0.225 Angle : 0.543 8.236 39078 Z= 0.285 Chirality : 0.044 0.366 4709 Planarity : 0.004 0.067 4903 Dihedral : 4.371 20.563 3762 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.37 % 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: 0.39 (0.14), residues: 3438 helix: 1.53 (0.21), residues: 633 sheet: 0.23 (0.16), residues: 951 loop : -0.10 (0.14), residues: 1854 *********************** 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 383 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 343 time to evaluate : 3.175 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 371 average time/residue: 0.3982 time to fit residues: 237.2141 Evaluate side-chains 328 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 308 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2422 time to fit residues: 13.3927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 252 optimal weight: 2.9990 chunk 139 optimal weight: 0.0970 chunk 289 optimal weight: 0.6980 chunk 234 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS B 764 ASN B1054 GLN C 3 GLN E1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 28713 Z= 0.176 Angle : 0.510 7.690 39078 Z= 0.266 Chirality : 0.043 0.341 4709 Planarity : 0.004 0.066 4903 Dihedral : 4.179 19.477 3762 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.10 % 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: 0.35 (0.14), residues: 3438 helix: 1.52 (0.21), residues: 660 sheet: 0.16 (0.15), residues: 957 loop : -0.13 (0.14), residues: 1821 *********************** 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 376 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 344 time to evaluate : 3.170 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 367 average time/residue: 0.4126 time to fit residues: 244.2980 Evaluate side-chains 317 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 302 time to evaluate : 3.281 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2644 time to fit residues: 11.5835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 39 GLN C 116 ASN E1054 GLN F 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.107 28713 Z= 0.498 Angle : 0.687 10.325 39078 Z= 0.353 Chirality : 0.050 0.331 4709 Planarity : 0.005 0.066 4903 Dihedral : 4.768 24.795 3762 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.27 % 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: -0.08 (0.14), residues: 3438 helix: 1.03 (0.21), residues: 648 sheet: -0.10 (0.15), residues: 948 loop : -0.33 (0.14), residues: 1842 *********************** 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 347 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 310 time to evaluate : 3.447 Fit side-chains outliers start: 37 outliers final: 20 residues processed: 337 average time/residue: 0.4021 time to fit residues: 220.1295 Evaluate side-chains 305 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 285 time to evaluate : 3.377 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2765 time to fit residues: 15.1502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 285 optimal weight: 0.0070 chunk 189 optimal weight: 0.0980 chunk 338 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 156 optimal weight: 0.0870 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.071 28713 Z= 0.162 Angle : 0.522 9.953 39078 Z= 0.273 Chirality : 0.044 0.379 4709 Planarity : 0.004 0.055 4903 Dihedral : 4.339 21.624 3762 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.72 % 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: 0.15 (0.14), residues: 3438 helix: 1.38 (0.21), residues: 651 sheet: -0.05 (0.15), residues: 990 loop : -0.21 (0.14), residues: 1797 *********************** 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 341 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 333 average time/residue: 0.4029 time to fit residues: 217.6236 Evaluate side-chains 299 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 288 time to evaluate : 3.142 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2511 time to fit residues: 9.4835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B1005 GLN D 90 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: 0.7568 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 28713 Z= 0.399 Angle : 0.634 9.273 39078 Z= 0.325 Chirality : 0.048 0.489 4709 Planarity : 0.004 0.050 4903 Dihedral : 4.621 22.049 3762 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3438 helix: 1.09 (0.21), residues: 651 sheet: -0.21 (0.15), residues: 966 loop : -0.39 (0.14), residues: 1821 *********************** 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 320 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 303 time to evaluate : 2.915 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 314 average time/residue: 0.3951 time to fit residues: 200.4581 Evaluate side-chains 296 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 287 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2638 time to fit residues: 8.6735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 0.9980 chunk 324 optimal weight: 0.7980 chunk 295 optimal weight: 0.6980 chunk 315 optimal weight: 0.5980 chunk 189 optimal weight: 0.5980 chunk 137 optimal weight: 0.0570 chunk 247 optimal weight: 0.9990 chunk 96 optimal weight: 0.0570 chunk 284 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 chunk 314 optimal weight: 0.7980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN H 3 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 65 GLN D 39 GLN E 196 ASN ** E1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN F 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 28713 Z= 0.173 Angle : 0.524 8.836 39078 Z= 0.272 Chirality : 0.044 0.423 4709 Planarity : 0.004 0.049 4903 Dihedral : 4.316 29.101 3762 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.34 % 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: 0.06 (0.14), residues: 3438 helix: 1.39 (0.21), residues: 651 sheet: -0.13 (0.15), residues: 975 loop : -0.28 (0.14), residues: 1812 *********************** 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 324 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 314 time to evaluate : 3.138 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 323 average time/residue: 0.3995 time to fit residues: 209.4925 Evaluate side-chains 292 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 289 time to evaluate : 3.132 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2562 time to fit residues: 5.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 349 optimal weight: 10.0000 chunk 321 optimal weight: 0.7980 chunk 278 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1119 ASN H 3 GLN B1005 GLN C 39 GLN C 119 GLN D 39 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 655 HIS E1002 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 28713 Z= 0.352 Angle : 0.603 9.079 39078 Z= 0.311 Chirality : 0.047 0.421 4709 Planarity : 0.004 0.047 4903 Dihedral : 4.543 31.125 3762 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3438 helix: 1.23 (0.21), residues: 651 sheet: -0.17 (0.15), residues: 969 loop : -0.46 (0.14), residues: 1818 ********************** 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 296 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 288 time to evaluate : 3.272 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 295 average time/residue: 0.4124 time to fit residues: 197.2377 Evaluate side-chains 286 residues out of total 3057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 280 time to evaluate : 3.384 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2457 time to fit residues: 7.1635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 256 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 286 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN H 3 GLN B1005 GLN D 90 GLN E1002 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.168374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.142296 restraints weight = 41373.693| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.93 r_work: 0.3630 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 28713 Z= 0.202 Angle : 0.532 9.421 39078 Z= 0.278 Chirality : 0.044 0.350 4709 Planarity : 0.004 0.048 4903 Dihedral : 4.321 29.517 3762 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.17 % 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: -0.01 (0.14), residues: 3438 helix: 1.38 (0.21), residues: 651 sheet: -0.18 (0.15), residues: 975 loop : -0.34 (0.14), residues: 1812 =============================================================================== Job complete usr+sys time: 5818.36 seconds wall clock time: 107 minutes 18.22 seconds (6438.22 seconds total)