Starting phenix.real_space_refine on Fri Mar 22 08:05:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2e_23126/03_2024/7l2e_23126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2e_23126/03_2024/7l2e_23126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2e_23126/03_2024/7l2e_23126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2e_23126/03_2024/7l2e_23126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2e_23126/03_2024/7l2e_23126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2e_23126/03_2024/7l2e_23126.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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 138 5.16 5 C 20689 2.51 5 N 5349 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ASP 848": "OD1" <-> "OD2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 848": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 3": "OE1" <-> "OE2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 53": "OD1" <-> "OD2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 3": "OE1" <-> "OE2" Residue "J ASP 26": "OD1" <-> "OD2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K ASP 26": "OD1" <-> "OD2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32641 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "B" Number of atoms: 8743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "C" Number of atoms: 8744 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8916 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 365 " occ=0.50 residue: pdb=" N ATYR B 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 365 " occ=0.50 residue: pdb=" N ATYR C 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 365 " occ=0.50 Time building chain proxies: 28.30, per 1000 atoms: 0.87 Number of scatterers: 32641 At special positions: 0 Unit cell: (194.74, 179.76, 184.04, 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 138 16.00 O 6465 8.00 N 5349 7.00 C 20689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=1.77 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=1.81 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.80 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 603 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 603 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 603 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 122 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 17 " " NAG Q 1 " - " ASN A 165 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 17 " " NAG Y 1 " - " ASN B 165 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN C 122 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 17 " " NAG g 1 " - " ASN C 165 " Time building additional restraints: 12.94 Conformation dependent library (CDL) restraints added in 9.9 seconds 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7530 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 20.7% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.961A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.107A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.433A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 783 removed outlier: 6.085A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.519A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.576A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.230A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 948 through 966 removed outlier: 3.572A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.831A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.077A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.011A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.959A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.135A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.406A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 749 through 783 removed outlier: 6.140A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.593A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 838 removed outlier: 4.185A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.767A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.657A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 948 through 966 removed outlier: 3.590A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.851A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.113A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.989A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.143A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.447A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 749 through 783 removed outlier: 5.964A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.658A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 838 removed outlier: 4.266A pdb=" N GLN C 836 " --> pdb=" O GLY C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.843A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.575A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.195A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 948 through 966 removed outlier: 3.555A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.753A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.050A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.967A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.762A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.559A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.909A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.659A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.776A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.803A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.919A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 5.901A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.229A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.065A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.560A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.910A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.766A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.827A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.578A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.578A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.253A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.560A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.909A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.770A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.792A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.916A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 21 through 24 Processing sheet with id=AH1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH4, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.561A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.561A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 21 through 24 1259 hydrogen bonds defined for protein. 3324 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: 17.17 Time building geometry restraints manager: 14.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5283 1.30 - 1.43: 9405 1.43 - 1.56: 18537 1.56 - 1.69: 2 1.69 - 1.82: 174 Bond restraints: 33401 Sorted by residual: bond pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 1.465 1.404 0.061 1.15e-02 7.56e+03 2.81e+01 bond pdb=" N PRO C 82 " pdb=" CA PRO C 82 " ideal model delta sigma weight residual 1.465 1.404 0.061 1.15e-02 7.56e+03 2.78e+01 bond pdb=" N PRO B 82 " pdb=" CA PRO B 82 " ideal model delta sigma weight residual 1.465 1.404 0.060 1.15e-02 7.56e+03 2.76e+01 bond pdb=" C TYR B 248 " pdb=" O TYR B 248 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.26e-02 6.30e+03 2.46e+01 bond pdb=" C PRO B 82 " pdb=" O PRO B 82 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.12e-02 7.97e+03 2.39e+01 ... (remaining 33396 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.66: 630 104.66 - 112.15: 16331 112.15 - 119.63: 11852 119.63 - 127.12: 16353 127.12 - 134.60: 321 Bond angle restraints: 45487 Sorted by residual: angle pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 117.59 134.58 -16.99 9.90e-01 1.02e+00 2.95e+02 angle pdb=" O ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 121.32 107.49 13.83 8.50e-01 1.38e+00 2.65e+02 angle pdb=" O ASP B 294 " pdb=" C ASP B 294 " pdb=" N PRO B 295 " ideal model delta sigma weight residual 121.32 107.39 13.93 1.15e+00 7.56e-01 1.47e+02 angle pdb=" C ASP A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta sigma weight residual 119.19 132.01 -12.82 1.06e+00 8.90e-01 1.46e+02 angle pdb=" C ASP B 294 " pdb=" N PRO B 295 " pdb=" CA PRO B 295 " ideal model delta sigma weight residual 119.19 131.65 -12.46 1.06e+00 8.90e-01 1.38e+02 ... (remaining 45482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 19276 17.99 - 35.99: 1273 35.99 - 53.98: 209 53.98 - 71.98: 42 71.98 - 89.97: 25 Dihedral angle restraints: 20825 sinusoidal: 9051 harmonic: 11774 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -21.46 -64.54 1 1.00e+01 1.00e-02 5.47e+01 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 -22.19 -63.81 1 1.00e+01 1.00e-02 5.36e+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 -24.42 -61.58 1 1.00e+01 1.00e-02 5.03e+01 ... (remaining 20822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4951 0.128 - 0.256: 289 0.256 - 0.383: 52 0.383 - 0.511: 11 0.511 - 0.639: 13 Chirality restraints: 5316 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 5313 not shown) Planarity restraints: 5851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " -0.318 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C7 NAG B1303 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.318 2.00e-02 2.50e+03 2.74e-01 9.38e+02 pdb=" C7 NAG C1303 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.258 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" C7 NAG b 2 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.364 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.001 2.00e-02 2.50e+03 ... (remaining 5848 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3623 2.75 - 3.29: 30062 3.29 - 3.83: 53304 3.83 - 4.36: 65376 4.36 - 4.90: 113550 Nonbonded interactions: 265915 Sorted by model distance: nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR J 36 " pdb=" OE1 GLN J 89 " model vdw 2.218 2.440 nonbonded pdb=" O GLY A 545 " pdb=" OG SER B 982 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR A 553 " pdb=" OD1 ASP A 586 " model vdw 2.246 2.440 ... (remaining 265910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.33 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.490 Check model and map are aligned: 0.450 Set scattering table: 0.370 Process input model: 106.140 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.560 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:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.007 0.080 33401 Z= 0.449 Angle : 1.110 16.992 45487 Z= 0.740 Chirality : 0.079 0.639 5316 Planarity : 0.015 0.274 5797 Dihedral : 12.297 89.973 13142 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.34 % Allowed : 2.54 % Favored : 97.11 % Cbeta Deviations : 0.66 % 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: 4030 helix: -0.14 (0.18), residues: 717 sheet: 0.16 (0.16), residues: 1092 loop : -0.82 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 64 HIS 0.016 0.002 HIS B 66 PHE 0.031 0.002 PHE A 906 TYR 0.043 0.002 TYR C 495 ARG 0.007 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 354 time to evaluate : 3.703 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6526 (mtt) cc_final: 0.6300 (mtt) REVERT: A 697 MET cc_start: 0.7600 (ttt) cc_final: 0.7262 (ttt) REVERT: A 814 LYS cc_start: 0.8266 (tptt) cc_final: 0.8033 (mmmt) REVERT: A 817 PHE cc_start: 0.7995 (t80) cc_final: 0.7710 (t80) REVERT: A 841 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6816 (mt) REVERT: B 817 PHE cc_start: 0.7729 (t80) cc_final: 0.7405 (t80) REVERT: C 200 TYR cc_start: 0.8336 (m-80) cc_final: 0.7904 (m-80) REVERT: C 854 LYS cc_start: 0.7369 (tptt) cc_final: 0.6899 (mttm) outliers start: 12 outliers final: 3 residues processed: 359 average time/residue: 1.2246 time to fit residues: 536.7618 Evaluate side-chains 219 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 6.9990 chunk 302 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 188 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 957 GLN A 960 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 856 ASN B 960 ASN C 188 ASN C 207 HIS C 211 ASN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 960 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 105 GLN L 31 GLN G 105 GLN J 31 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN I 105 GLN K 31 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 33401 Z= 0.496 Angle : 0.677 8.213 45487 Z= 0.352 Chirality : 0.049 0.169 5316 Planarity : 0.005 0.084 5797 Dihedral : 5.755 53.621 6033 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.34 % Allowed : 7.72 % Favored : 89.94 % 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: -0.57 (0.13), residues: 4030 helix: 0.25 (0.19), residues: 738 sheet: 0.10 (0.16), residues: 1092 loop : -0.81 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 258 HIS 0.013 0.002 HIS C1064 PHE 0.043 0.003 PHE A 906 TYR 0.035 0.003 TYR G 52A ARG 0.008 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 221 time to evaluate : 3.509 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6688 (mtt) cc_final: 0.6480 (mtp) REVERT: A 258 TRP cc_start: 0.6272 (m100) cc_final: 0.5297 (t60) REVERT: A 466 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (ttm-80) REVERT: A 697 MET cc_start: 0.7628 (ttt) cc_final: 0.7302 (ttt) REVERT: A 789 TYR cc_start: 0.7658 (m-80) cc_final: 0.7194 (m-10) REVERT: A 841 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6841 (mt) REVERT: B 96 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: B 258 TRP cc_start: 0.6258 (m100) cc_final: 0.5437 (t60) REVERT: B 814 LYS cc_start: 0.8472 (tppt) cc_final: 0.8008 (mptp) REVERT: B 855 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: C 96 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: C 258 TRP cc_start: 0.6118 (m100) cc_final: 0.5413 (t60) REVERT: C 814 LYS cc_start: 0.8511 (tppt) cc_final: 0.7987 (mptp) REVERT: C 854 LYS cc_start: 0.7683 (tptt) cc_final: 0.7141 (mttp) REVERT: H 58 HIS cc_start: 0.6758 (OUTLIER) cc_final: 0.5708 (m-70) REVERT: I 38 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7118 (ttm170) outliers start: 82 outliers final: 29 residues processed: 277 average time/residue: 1.1622 time to fit residues: 398.6808 Evaluate side-chains 241 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 3.9990 chunk 112 optimal weight: 0.0570 chunk 301 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 362 optimal weight: 7.9990 chunk 392 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 613 GLN C 804 GLN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 82AASN L 38 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN I 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33401 Z= 0.190 Angle : 0.535 8.445 45487 Z= 0.276 Chirality : 0.043 0.209 5316 Planarity : 0.004 0.069 5797 Dihedral : 5.122 52.868 6025 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.63 % Allowed : 10.38 % Favored : 87.99 % 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: -0.36 (0.13), residues: 4030 helix: 0.98 (0.20), residues: 717 sheet: 0.06 (0.16), residues: 1023 loop : -0.76 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 64 HIS 0.009 0.001 HIS B 207 PHE 0.020 0.001 PHE B 906 TYR 0.031 0.001 TYR G 52A ARG 0.005 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 212 time to evaluate : 3.562 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6568 (mtt) cc_final: 0.6362 (mtp) REVERT: A 258 TRP cc_start: 0.6213 (m100) cc_final: 0.5267 (t60) REVERT: A 697 MET cc_start: 0.7587 (ttt) cc_final: 0.7243 (ttt) REVERT: A 789 TYR cc_start: 0.7394 (m-80) cc_final: 0.7031 (m-10) REVERT: A 841 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6964 (mt) REVERT: B 96 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: B 258 TRP cc_start: 0.6137 (m100) cc_final: 0.5452 (t60) REVERT: B 740 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8380 (tpt) REVERT: B 814 LYS cc_start: 0.8463 (tppt) cc_final: 0.7976 (mptp) REVERT: C 258 TRP cc_start: 0.6239 (m100) cc_final: 0.5559 (t60) REVERT: C 814 LYS cc_start: 0.8433 (tppt) cc_final: 0.7906 (mptp) REVERT: C 841 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7436 (pt) REVERT: C 854 LYS cc_start: 0.7650 (tptt) cc_final: 0.7103 (mttp) outliers start: 57 outliers final: 24 residues processed: 251 average time/residue: 1.1888 time to fit residues: 374.4012 Evaluate side-chains 218 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 10.0000 chunk 272 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 345 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 853 GLN A 856 ASN A1005 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 613 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN I 82AASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 33401 Z= 0.402 Angle : 0.610 8.547 45487 Z= 0.313 Chirality : 0.047 0.187 5316 Planarity : 0.005 0.060 5797 Dihedral : 5.186 54.848 6025 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.14 % Allowed : 10.92 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4030 helix: 0.64 (0.19), residues: 753 sheet: -0.05 (0.16), residues: 1050 loop : -0.71 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 35 HIS 0.009 0.002 HIS C1064 PHE 0.032 0.002 PHE C 906 TYR 0.030 0.002 TYR H 52A ARG 0.008 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 212 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: A 150 LYS cc_start: 0.7745 (mppt) cc_final: 0.7317 (mptt) REVERT: A 153 MET cc_start: 0.6683 (mtt) cc_final: 0.6476 (mtp) REVERT: A 697 MET cc_start: 0.7672 (ttt) cc_final: 0.7355 (ttt) REVERT: A 740 MET cc_start: 0.8548 (ttp) cc_final: 0.8335 (ttt) REVERT: A 814 LYS cc_start: 0.8507 (tptm) cc_final: 0.8132 (tppt) REVERT: A 841 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6975 (mt) REVERT: A 843 ASP cc_start: 0.5903 (OUTLIER) cc_final: 0.5479 (p0) REVERT: B 96 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: B 258 TRP cc_start: 0.6169 (m100) cc_final: 0.5527 (t60) REVERT: B 814 LYS cc_start: 0.8429 (tppt) cc_final: 0.7969 (mptp) REVERT: B 855 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: C 69 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6495 (t-170) REVERT: C 96 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: C 258 TRP cc_start: 0.6322 (m100) cc_final: 0.5625 (t60) REVERT: C 532 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7267 (p0) REVERT: C 814 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7959 (mptp) REVERT: C 841 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7324 (pt) REVERT: H 58 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.5539 (m-70) REVERT: I 58 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5871 (m90) outliers start: 75 outliers final: 40 residues processed: 266 average time/residue: 1.1513 time to fit residues: 379.9554 Evaluate side-chains 250 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 329 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 346 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 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 853 GLN A 856 ASN A1083 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 31 GLN K 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33401 Z= 0.209 Angle : 0.526 9.307 45487 Z= 0.269 Chirality : 0.044 0.201 5316 Planarity : 0.004 0.054 5797 Dihedral : 4.893 53.003 6025 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.80 % Allowed : 11.98 % Favored : 86.22 % 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: -0.31 (0.13), residues: 4030 helix: 1.17 (0.20), residues: 714 sheet: -0.06 (0.16), residues: 1065 loop : -0.71 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 35 HIS 0.007 0.001 HIS G 35 PHE 0.023 0.001 PHE A 759 TYR 0.033 0.001 TYR G 52A ARG 0.008 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 204 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: A 153 MET cc_start: 0.6789 (mtt) cc_final: 0.6545 (mtp) REVERT: A 697 MET cc_start: 0.7621 (ttt) cc_final: 0.7302 (ttt) REVERT: A 740 MET cc_start: 0.8485 (ttp) cc_final: 0.8276 (ttt) REVERT: B 96 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: B 258 TRP cc_start: 0.6140 (m100) cc_final: 0.5310 (t60) REVERT: B 814 LYS cc_start: 0.8396 (tppt) cc_final: 0.7964 (mptp) REVERT: B 841 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7384 (pt) REVERT: B 855 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: C 69 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6377 (t-170) REVERT: C 96 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: C 258 TRP cc_start: 0.6189 (m100) cc_final: 0.5652 (t60) REVERT: C 532 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7155 (p0) REVERT: C 814 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7906 (mptp) REVERT: C 841 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7281 (pt) REVERT: H 58 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.5383 (m-70) REVERT: H 94 LYS cc_start: 0.7801 (tttm) cc_final: 0.7601 (pttp) REVERT: G 53 ASP cc_start: 0.8161 (p0) cc_final: 0.7868 (p0) REVERT: G 66 ARG cc_start: 0.7109 (ttp80) cc_final: 0.6901 (ttp-170) outliers start: 63 outliers final: 36 residues processed: 247 average time/residue: 1.1829 time to fit residues: 360.6870 Evaluate side-chains 241 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 0.9990 chunk 347 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 226 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 386 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN B 960 ASN C 207 HIS C 613 GLN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN I 82AASN K 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33401 Z= 0.217 Angle : 0.526 9.516 45487 Z= 0.269 Chirality : 0.044 0.197 5316 Planarity : 0.004 0.051 5797 Dihedral : 4.776 52.993 6023 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 12.35 % Favored : 85.62 % 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: -0.28 (0.13), residues: 4030 helix: 1.21 (0.20), residues: 714 sheet: 0.00 (0.16), residues: 1053 loop : -0.70 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 35 HIS 0.007 0.001 HIS H 35 PHE 0.025 0.001 PHE C 759 TYR 0.036 0.001 TYR I 52A ARG 0.008 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 199 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: A 150 LYS cc_start: 0.7908 (mppt) cc_final: 0.7384 (mptt) REVERT: A 153 MET cc_start: 0.6831 (mtt) cc_final: 0.6582 (mtp) REVERT: A 697 MET cc_start: 0.7625 (ttt) cc_final: 0.7313 (ttt) REVERT: A 740 MET cc_start: 0.8502 (ttp) cc_final: 0.8292 (ttt) REVERT: A 843 ASP cc_start: 0.5864 (OUTLIER) cc_final: 0.5424 (p0) REVERT: B 96 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: B 814 LYS cc_start: 0.8380 (tppt) cc_final: 0.7960 (mptp) REVERT: B 841 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7356 (pt) REVERT: B 855 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7287 (m-10) REVERT: C 96 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6822 (pm20) REVERT: C 258 TRP cc_start: 0.6160 (m100) cc_final: 0.5731 (t60) REVERT: C 532 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7212 (p0) REVERT: C 814 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7951 (mptp) REVERT: C 841 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7305 (pt) REVERT: H 58 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.5365 (m-70) REVERT: G 66 ARG cc_start: 0.7012 (ttp80) cc_final: 0.6797 (ttp-170) REVERT: I 58 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5504 (m90) REVERT: I 82 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.4744 (ptm) outliers start: 71 outliers final: 42 residues processed: 253 average time/residue: 1.1587 time to fit residues: 364.7438 Evaluate side-chains 249 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 195 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 324 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 384 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN A 856 ASN B 960 ASN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN L 31 GLN L 38 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33401 Z= 0.311 Angle : 0.551 9.493 45487 Z= 0.281 Chirality : 0.045 0.191 5316 Planarity : 0.004 0.049 5797 Dihedral : 4.879 53.722 6023 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.12 % Allowed : 12.72 % Favored : 85.16 % 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: -0.36 (0.13), residues: 4030 helix: 1.11 (0.20), residues: 714 sheet: -0.07 (0.16), residues: 1038 loop : -0.73 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 35 HIS 0.007 0.001 HIS G 35 PHE 0.024 0.002 PHE A 759 TYR 0.034 0.002 TYR H 52A ARG 0.006 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 204 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7633 (pt0) REVERT: A 697 MET cc_start: 0.7645 (ttt) cc_final: 0.7337 (ttt) REVERT: A 740 MET cc_start: 0.8523 (ttp) cc_final: 0.8296 (ttt) REVERT: A 843 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5434 (p0) REVERT: B 96 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: B 814 LYS cc_start: 0.8360 (tppt) cc_final: 0.7946 (mptp) REVERT: B 841 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7432 (pt) REVERT: B 854 LYS cc_start: 0.7861 (tptt) cc_final: 0.7244 (mttp) REVERT: B 855 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: C 69 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6358 (t-170) REVERT: C 96 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: C 258 TRP cc_start: 0.6182 (m100) cc_final: 0.5736 (t60) REVERT: C 532 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7308 (p0) REVERT: C 814 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7959 (mptp) REVERT: C 841 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7363 (pt) REVERT: H 58 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.5344 (m-70) REVERT: G 66 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6878 (ttp-170) REVERT: I 58 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.5507 (m90) REVERT: I 82 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4785 (ptm) outliers start: 74 outliers final: 48 residues processed: 258 average time/residue: 1.1500 time to fit residues: 371.4057 Evaluate side-chains 261 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 200 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 262 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 853 GLN A 856 ASN C 207 HIS C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN I 82AASN K 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33401 Z= 0.245 Angle : 0.535 9.837 45487 Z= 0.274 Chirality : 0.044 0.194 5316 Planarity : 0.004 0.049 5797 Dihedral : 4.882 53.389 6023 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.17 % Allowed : 13.01 % Favored : 84.82 % 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: -0.30 (0.13), residues: 4030 helix: 1.18 (0.20), residues: 714 sheet: 0.01 (0.16), residues: 1020 loop : -0.72 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 35 HIS 0.007 0.001 HIS G 35 PHE 0.025 0.002 PHE C 759 TYR 0.043 0.001 TYR H 52A ARG 0.008 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 200 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: A 150 LYS cc_start: 0.7823 (mppt) cc_final: 0.7331 (mptt) REVERT: A 153 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5406 (mtt) REVERT: A 697 MET cc_start: 0.7625 (ttt) cc_final: 0.7314 (ttt) REVERT: A 740 MET cc_start: 0.8511 (ttp) cc_final: 0.8307 (ttt) REVERT: A 814 LYS cc_start: 0.8512 (tppt) cc_final: 0.7969 (mmtp) REVERT: A 843 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5429 (p0) REVERT: B 96 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: B 153 MET cc_start: 0.6615 (mtm) cc_final: 0.6345 (mtp) REVERT: B 220 PHE cc_start: 0.8711 (t80) cc_final: 0.8410 (t80) REVERT: B 814 LYS cc_start: 0.8354 (tppt) cc_final: 0.7940 (mptp) REVERT: B 841 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7434 (pt) REVERT: B 855 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7287 (m-10) REVERT: C 69 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6365 (t-170) REVERT: C 96 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: C 258 TRP cc_start: 0.6218 (m100) cc_final: 0.5742 (t60) REVERT: C 532 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7233 (p0) REVERT: C 814 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7953 (mptp) REVERT: C 841 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7310 (pt) REVERT: C 854 LYS cc_start: 0.7855 (tptt) cc_final: 0.7211 (mttp) REVERT: H 58 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.5338 (m-70) REVERT: I 82 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4774 (ptm) outliers start: 76 outliers final: 51 residues processed: 256 average time/residue: 1.1632 time to fit residues: 370.0836 Evaluate side-chains 261 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 197 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 8.9990 chunk 368 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 323 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 357 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 853 GLN A 856 ASN B 148 ASN B 960 ASN C 607 GLN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN L 31 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 33401 Z= 0.371 Angle : 0.585 9.498 45487 Z= 0.299 Chirality : 0.046 0.190 5316 Planarity : 0.004 0.050 5797 Dihedral : 5.101 55.031 6023 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.17 % Allowed : 13.04 % Favored : 84.79 % 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: -0.42 (0.13), residues: 4030 helix: 0.99 (0.20), residues: 717 sheet: -0.15 (0.16), residues: 1038 loop : -0.72 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 35 HIS 0.007 0.002 HIS G 35 PHE 0.042 0.002 PHE H 67 TYR 0.042 0.002 TYR H 52A ARG 0.007 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 211 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: A 150 LYS cc_start: 0.7995 (mppt) cc_final: 0.7421 (mmpt) REVERT: A 697 MET cc_start: 0.7661 (ttt) cc_final: 0.7342 (ttt) REVERT: A 740 MET cc_start: 0.8539 (ttp) cc_final: 0.8312 (ttt) REVERT: A 843 ASP cc_start: 0.5941 (OUTLIER) cc_final: 0.5528 (p0) REVERT: B 96 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: B 153 MET cc_start: 0.6635 (mtm) cc_final: 0.6335 (mtp) REVERT: B 814 LYS cc_start: 0.8347 (tppt) cc_final: 0.7915 (mptp) REVERT: B 841 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7387 (pt) REVERT: B 854 LYS cc_start: 0.7848 (tptt) cc_final: 0.7236 (mttp) REVERT: B 855 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: C 69 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.6306 (t-170) REVERT: C 96 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: C 153 MET cc_start: 0.6091 (mtm) cc_final: 0.5351 (mtt) REVERT: C 258 TRP cc_start: 0.6223 (m100) cc_final: 0.5750 (t60) REVERT: C 532 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7327 (p0) REVERT: C 841 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7402 (pt) REVERT: H 58 HIS cc_start: 0.6542 (OUTLIER) cc_final: 0.5271 (m-70) REVERT: H 94 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7599 (pttm) REVERT: I 82 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4911 (ptm) outliers start: 76 outliers final: 54 residues processed: 264 average time/residue: 1.1622 time to fit residues: 381.8867 Evaluate side-chains 271 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 205 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 TYR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 0.5980 chunk 378 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 397 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 316 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 194 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 960 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 31 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.328 33401 Z= 0.324 Angle : 0.698 58.987 45487 Z= 0.376 Chirality : 0.047 0.919 5316 Planarity : 0.004 0.048 5797 Dihedral : 5.100 55.013 6023 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.97 % Allowed : 13.38 % Favored : 84.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 4030 helix: 1.00 (0.20), residues: 717 sheet: -0.16 (0.16), residues: 1038 loop : -0.72 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 35 HIS 0.007 0.001 HIS G 35 PHE 0.075 0.002 PHE H 67 TYR 0.028 0.002 TYR H 52A ARG 0.008 0.000 ARG G 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 204 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: A 697 MET cc_start: 0.7656 (ttt) cc_final: 0.7338 (ttt) REVERT: A 740 MET cc_start: 0.8539 (ttp) cc_final: 0.8310 (ttt) REVERT: A 843 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5526 (p0) REVERT: B 96 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7490 (pt0) REVERT: B 153 MET cc_start: 0.6635 (mtm) cc_final: 0.6330 (mtp) REVERT: B 814 LYS cc_start: 0.8345 (tppt) cc_final: 0.7913 (mptp) REVERT: B 841 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7383 (pt) REVERT: B 854 LYS cc_start: 0.7852 (tptt) cc_final: 0.7235 (mttp) REVERT: B 855 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: C 69 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6300 (t-170) REVERT: C 96 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: C 153 MET cc_start: 0.6154 (mtm) cc_final: 0.5385 (mtt) REVERT: C 258 TRP cc_start: 0.6221 (m100) cc_final: 0.5748 (t60) REVERT: C 532 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7323 (p0) REVERT: C 841 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7400 (pt) REVERT: H 58 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.5267 (m-70) REVERT: H 94 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7593 (pttm) REVERT: I 82 MET cc_start: 0.5155 (OUTLIER) cc_final: 0.4902 (ptm) outliers start: 69 outliers final: 56 residues processed: 255 average time/residue: 1.1879 time to fit residues: 376.8339 Evaluate side-chains 271 residues out of total 3486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 203 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 1.9990 chunk 337 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 291 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 317 optimal weight: 0.8980 chunk 132 optimal weight: 0.0970 chunk 325 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 960 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 31 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089034 restraints weight = 80405.766| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.55 r_work: 0.2997 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.328 33401 Z= 0.324 Angle : 0.698 58.985 45487 Z= 0.376 Chirality : 0.047 0.919 5316 Planarity : 0.004 0.048 5797 Dihedral : 5.100 55.013 6023 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.94 % Allowed : 13.44 % Favored : 84.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 4030 helix: 1.00 (0.20), residues: 717 sheet: -0.16 (0.16), residues: 1038 loop : -0.72 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 35 HIS 0.007 0.001 HIS G 35 PHE 0.075 0.002 PHE H 67 TYR 0.028 0.002 TYR H 52A ARG 0.008 0.000 ARG G 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8537.04 seconds wall clock time: 153 minutes 51.70 seconds (9231.70 seconds total)