Starting phenix.real_space_refine on Sat Mar 16 12:35:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxh_42764/03_2024/8uxh_42764_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxh_42764/03_2024/8uxh_42764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxh_42764/03_2024/8uxh_42764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxh_42764/03_2024/8uxh_42764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxh_42764/03_2024/8uxh_42764_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxh_42764/03_2024/8uxh_42764_updated.pdb" } resolution = 3.52 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= 0.008 sd= 0.027 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 876 5.16 5 C 83788 2.51 5 N 22420 2.21 5 O 24540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 711": "OE1" <-> "OE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1055": "NH1" <-> "NH2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1640": "OD1" <-> "OD2" Residue "A GLU 2001": "OE1" <-> "OE2" Residue "A GLU 2079": "OE1" <-> "OE2" Residue "A GLU 2139": "OE1" <-> "OE2" Residue "A ASP 2482": "OD1" <-> "OD2" Residue "A PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2679": "OD1" <-> "OD2" Residue "A ASP 2796": "OD1" <-> "OD2" Residue "A ARG 2886": "NH1" <-> "NH2" Residue "A TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3025": "OD1" <-> "OD2" Residue "A GLU 3650": "OE1" <-> "OE2" Residue "A GLU 3702": "OE1" <-> "OE2" Residue "A TYR 3726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3783": "OE1" <-> "OE2" Residue "A ASP 3832": "OD1" <-> "OD2" Residue "A ASP 3853": "OD1" <-> "OD2" Residue "A GLU 4082": "OE1" <-> "OE2" Residue "A GLU 4146": "OE1" <-> "OE2" Residue "A GLU 4154": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4684": "OE1" <-> "OE2" Residue "A GLU 4838": "OE1" <-> "OE2" Residue "A PHE 4853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4885": "OE1" <-> "OE2" Residue "A GLU 4932": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 711": "OE1" <-> "OE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1055": "NH1" <-> "NH2" Residue "B PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1640": "OD1" <-> "OD2" Residue "B GLU 2001": "OE1" <-> "OE2" Residue "B GLU 2079": "OE1" <-> "OE2" Residue "B GLU 2139": "OE1" <-> "OE2" Residue "B ASP 2482": "OD1" <-> "OD2" Residue "B PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2679": "OD1" <-> "OD2" Residue "B ASP 2796": "OD1" <-> "OD2" Residue "B ARG 2886": "NH1" <-> "NH2" Residue "B TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3025": "OD1" <-> "OD2" Residue "B GLU 3650": "OE1" <-> "OE2" Residue "B GLU 3702": "OE1" <-> "OE2" Residue "B TYR 3726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3783": "OE1" <-> "OE2" Residue "B ASP 3832": "OD1" <-> "OD2" Residue "B ASP 3853": "OD1" <-> "OD2" Residue "B GLU 4082": "OE1" <-> "OE2" Residue "B GLU 4146": "OE1" <-> "OE2" Residue "B GLU 4154": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4684": "OE1" <-> "OE2" Residue "B GLU 4838": "OE1" <-> "OE2" Residue "B PHE 4853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4885": "OE1" <-> "OE2" Residue "B GLU 4932": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C GLU 711": "OE1" <-> "OE2" Residue "C PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 920": "OE1" <-> "OE2" Residue "C PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1055": "NH1" <-> "NH2" Residue "C PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1640": "OD1" <-> "OD2" Residue "C GLU 2001": "OE1" <-> "OE2" Residue "C GLU 2079": "OE1" <-> "OE2" Residue "C GLU 2139": "OE1" <-> "OE2" Residue "C ASP 2482": "OD1" <-> "OD2" Residue "C PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2679": "OD1" <-> "OD2" Residue "C ASP 2796": "OD1" <-> "OD2" Residue "C ARG 2886": "NH1" <-> "NH2" Residue "C TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3025": "OD1" <-> "OD2" Residue "C GLU 3650": "OE1" <-> "OE2" Residue "C GLU 3702": "OE1" <-> "OE2" Residue "C TYR 3726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3783": "OE1" <-> "OE2" Residue "C ASP 3832": "OD1" <-> "OD2" Residue "C ASP 3853": "OD1" <-> "OD2" Residue "C GLU 4082": "OE1" <-> "OE2" Residue "C GLU 4146": "OE1" <-> "OE2" Residue "C GLU 4154": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4684": "OE1" <-> "OE2" Residue "C GLU 4838": "OE1" <-> "OE2" Residue "C PHE 4853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4885": "OE1" <-> "OE2" Residue "C GLU 4932": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D GLU 711": "OE1" <-> "OE2" Residue "D PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 920": "OE1" <-> "OE2" Residue "D PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1055": "NH1" <-> "NH2" Residue "D PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1640": "OD1" <-> "OD2" Residue "D GLU 2001": "OE1" <-> "OE2" Residue "D GLU 2079": "OE1" <-> "OE2" Residue "D GLU 2139": "OE1" <-> "OE2" Residue "D ASP 2482": "OD1" <-> "OD2" Residue "D PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2679": "OD1" <-> "OD2" Residue "D ASP 2796": "OD1" <-> "OD2" Residue "D ARG 2886": "NH1" <-> "NH2" Residue "D TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3025": "OD1" <-> "OD2" Residue "D GLU 3650": "OE1" <-> "OE2" Residue "D GLU 3702": "OE1" <-> "OE2" Residue "D TYR 3726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3783": "OE1" <-> "OE2" Residue "D ASP 3832": "OD1" <-> "OD2" Residue "D ASP 3853": "OD1" <-> "OD2" Residue "D GLU 4082": "OE1" <-> "OE2" Residue "D GLU 4146": "OE1" <-> "OE2" Residue "D GLU 4154": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4684": "OE1" <-> "OE2" Residue "D GLU 4838": "OE1" <-> "OE2" Residue "D PHE 4853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4885": "OE1" <-> "OE2" Residue "D GLU 4932": "OE1" <-> "OE2" Time to flip residues: 0.36s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 131656 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "C" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "D" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31353 SG CYS A4888 179.161 204.270 87.586 1.00222.11 S ATOM 31378 SG CYS A4891 181.505 204.459 90.589 1.00227.50 S ATOM 66657 SG CYS B4888 177.973 179.245 87.253 1.00226.33 S ATOM 66682 SG CYS B4891 177.790 181.600 90.249 1.00230.93 S ATOM 98689 SG CYS C4888 203.294 178.131 87.329 1.00254.09 S ATOM 98714 SG CYS C4891 200.933 177.940 90.319 1.00258.25 S ATOM A0NPD SG CYS D4888 204.309 203.813 87.558 1.00244.99 S ATOM A0NQ2 SG CYS D4891 204.491 201.452 90.548 1.00252.16 S Time building chain proxies: 90.06, per 1000 atoms: 0.68 Number of scatterers: 131656 At special positions: 0 Unit cell: (383.337, 383.337, 211.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 876 16.00 P 24 15.00 O 24540 8.00 N 22420 7.00 C 83788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " 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 Time building additional restraints: 38.32 Conformation dependent library (CDL) restraints added in 32.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 30776 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 632 helices and 88 sheets defined 58.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 38.88 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 5.664A pdb=" N SER A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.038A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.326A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.454A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 4.031A pdb=" N LEU A 274 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.731A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.228A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 4.674A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.908A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.815A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.093A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.677A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.617A pdb=" N ILE A 597 " --> pdb=" O HIS A 593 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.699A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.331A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.669A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 removed outlier: 3.869A pdb=" N LEU A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.920A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 4.362A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.635A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.188A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A1235 " --> pdb=" O GLY A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1230 through 1235' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 4.797A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1502 removed outlier: 7.100A pdb=" N ASN A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN A1502 " --> pdb=" O GLN A1498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1497 through 1502' Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.821A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.153A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.610A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.794A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.406A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 5.741A pdb=" N THR A1737 " --> pdb=" O THR A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 4.519A pdb=" N GLN A1777 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR A1778 " --> pdb=" O GLU A1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1773 through 1778' Processing helix chain 'A' and resid 1783 through 1803 removed outlier: 3.706A pdb=" N SER A1803 " --> pdb=" O VAL A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1848 Proline residue: A1848 - end of helix Processing helix chain 'A' and resid 1901 through 1944 removed outlier: 4.092A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1963 removed outlier: 3.944A pdb=" N THR A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA A1959 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A1961 " --> pdb=" O LEU A1957 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 removed outlier: 4.200A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.644A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.741A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 4.783A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.606A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2159 Proline residue: A2159 - end of helix Processing helix chain 'A' and resid 2160 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.992A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.955A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.060A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.679A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 4.203A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.711A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2412 Proline residue: A2404 - end of helix removed outlier: 9.343A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2439 removed outlier: 5.386A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.922A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 4.882A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 3.676A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 3.736A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.287A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 5.441A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP A2546 " --> pdb=" O ALA A2542 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 3.881A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2593 removed outlier: 4.615A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A2590 " --> pdb=" O GLN A2586 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.505A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2656 removed outlier: 6.232A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS A2656 " --> pdb=" O LEU A2652 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2690 through 2696 removed outlier: 4.389A pdb=" N SER A2694 " --> pdb=" O GLU A2690 " (cutoff:3.500A) Processing helix chain 'A' and resid 2714 through 2740 Processing helix chain 'A' and resid 2765 through 2786 removed outlier: 4.329A pdb=" N GLU A2769 " --> pdb=" O GLU A2765 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) Proline residue: A2774 - end of helix removed outlier: 3.825A pdb=" N TRP A2785 " --> pdb=" O THR A2781 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 4.300A pdb=" N ASP A2796 " --> pdb=" O THR A2792 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A2799 " --> pdb=" O GLY A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2880 through 2899 removed outlier: 4.381A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A2888 " --> pdb=" O LYS A2884 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A2892 " --> pdb=" O LYS A2888 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU A2893 " --> pdb=" O ALA A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2945 removed outlier: 4.095A pdb=" N GLY A2945 " --> pdb=" O LEU A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 5.996A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 5.307A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.700A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) Processing helix chain 'A' and resid 3042 through 3048 removed outlier: 4.095A pdb=" N MET A3046 " --> pdb=" O ALA A3042 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3078 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.268A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3599 through 3605 removed outlier: 4.956A pdb=" N MET A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 5.320A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.487A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.579A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.905A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.605A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.744A pdb=" N LEU A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.164A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 4.197A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A3837 " --> pdb=" O ASP A3833 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.576A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.607A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 4.971A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3962 removed outlier: 4.192A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A3957 " --> pdb=" O HIS A3953 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.503A pdb=" N LEU A3986 " --> pdb=" O LEU A3982 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4030 removed outlier: 3.916A pdb=" N PHE A4020 " --> pdb=" O PHE A4016 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP A4030 " --> pdb=" O LEU A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4031 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.610A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4070 Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.715A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 4.363A pdb=" N ASP A4093 " --> pdb=" O GLU A4089 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A4094 " --> pdb=" O PRO A4090 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 Processing helix chain 'A' and resid 4124 through 4134 Proline residue: A4131 - end of helix removed outlier: 5.629A pdb=" N GLY A4134 " --> pdb=" O GLN A4130 " (cutoff:3.500A) Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4182 through 4208 removed outlier: 4.611A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4258 removed outlier: 3.853A pdb=" N THR A4254 " --> pdb=" O TYR A4250 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A4255 " --> pdb=" O ASN A4251 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) Processing helix chain 'A' and resid 4262 through 4272 removed outlier: 3.908A pdb=" N LYS A4266 " --> pdb=" O LYS A4262 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.920A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.322A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 4.436A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.892A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 3.897A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 3.829A pdb=" N VAL A4697 " --> pdb=" O SER A4693 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP A4702 " --> pdb=" O LEU A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4717 removed outlier: 5.449A pdb=" N ASN A4717 " --> pdb=" O VAL A4713 " (cutoff:3.500A) Processing helix chain 'A' and resid 4718 through 4735 removed outlier: 3.675A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.646A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.762A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 5.317A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 3.640A pdb=" N GLY A4820 " --> pdb=" O HIS A4816 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.088A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.992A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.349A pdb=" N PHE A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 4.509A pdb=" N ILE A2382 " --> pdb=" O ASP A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2533 through 2538 removed outlier: 3.725A pdb=" N GLY A2537 " --> pdb=" O LEU A2534 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A2538 " --> pdb=" O PHE A2535 " (cutoff:3.500A) Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 51 through 56 removed outlier: 5.663A pdb=" N SER B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.039A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.327A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TRP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.454A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.031A pdb=" N LEU B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.732A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.228A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 4.674A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.908A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.814A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.093A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 589 removed outlier: 3.678A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.617A pdb=" N ILE B 597 " --> pdb=" O HIS B 593 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.699A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.331A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 875 through 901 removed outlier: 4.669A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 946 removed outlier: 3.869A pdb=" N LEU B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 3.920A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 4.363A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.636A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.188A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B1235 " --> pdb=" O GLY B1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1230 through 1235' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 4.797A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1497 through 1502 removed outlier: 7.100A pdb=" N ASN B1501 " --> pdb=" O GLY B1497 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN B1502 " --> pdb=" O GLN B1498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1497 through 1502' Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.821A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.153A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.611A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.794A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.407A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1737 removed outlier: 5.741A pdb=" N THR B1737 " --> pdb=" O THR B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1773 through 1778 removed outlier: 4.519A pdb=" N GLN B1777 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR B1778 " --> pdb=" O GLU B1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1773 through 1778' Processing helix chain 'B' and resid 1783 through 1803 removed outlier: 3.706A pdb=" N SER B1803 " --> pdb=" O VAL B1799 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1848 Proline residue: B1848 - end of helix Processing helix chain 'B' and resid 1901 through 1944 removed outlier: 4.093A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1963 removed outlier: 3.944A pdb=" N THR B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA B1959 " --> pdb=" O ALA B1955 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS B1961 " --> pdb=" O LEU B1957 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 removed outlier: 4.200A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.643A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.741A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 4.783A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.606A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2154 through 2159 Proline residue: B2159 - end of helix Processing helix chain 'B' and resid 2160 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.991A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.954A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.060A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.678A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 4.203A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B2298 " --> pdb=" O GLU B2294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.710A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2412 Proline residue: B2404 - end of helix removed outlier: 9.342A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2439 removed outlier: 5.386A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.922A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 4.881A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 3.675A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 3.736A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.286A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 5.440A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B2546 " --> pdb=" O ALA B2542 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 3.881A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2583 through 2593 removed outlier: 4.615A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B2590 " --> pdb=" O GLN B2586 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.505A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2656 removed outlier: 6.233A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS B2656 " --> pdb=" O LEU B2652 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2690 through 2696 removed outlier: 4.390A pdb=" N SER B2694 " --> pdb=" O GLU B2690 " (cutoff:3.500A) Processing helix chain 'B' and resid 2714 through 2740 Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 4.329A pdb=" N GLU B2769 " --> pdb=" O GLU B2765 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) Proline residue: B2774 - end of helix removed outlier: 3.824A pdb=" N TRP B2785 " --> pdb=" O THR B2781 " (cutoff:3.500A) Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 4.300A pdb=" N ASP B2796 " --> pdb=" O THR B2792 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B2799 " --> pdb=" O GLY B2795 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2880 through 2899 removed outlier: 4.380A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B2888 " --> pdb=" O LYS B2884 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B2892 " --> pdb=" O LYS B2888 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B2893 " --> pdb=" O ALA B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2945 removed outlier: 4.095A pdb=" N GLY B2945 " --> pdb=" O LEU B2941 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 5.997A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 5.306A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.699A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) Processing helix chain 'B' and resid 3042 through 3048 removed outlier: 4.095A pdb=" N MET B3046 " --> pdb=" O ALA B3042 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3078 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.269A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3599 through 3605 removed outlier: 4.955A pdb=" N MET B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 5.320A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.487A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.578A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.906A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.604A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.743A pdb=" N LEU B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.164A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 4.198A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B3837 " --> pdb=" O ASP B3833 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.576A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.608A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 4.971A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3962 removed outlier: 4.192A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B3957 " --> pdb=" O HIS B3953 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.503A pdb=" N LEU B3986 " --> pdb=" O LEU B3982 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4030 removed outlier: 3.916A pdb=" N PHE B4020 " --> pdb=" O PHE B4016 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASP B4030 " --> pdb=" O LEU B4026 " (cutoff:3.500A) Processing helix chain 'B' and resid 4031 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.610A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4070 Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.715A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 4.365A pdb=" N ASP B4093 " --> pdb=" O GLU B4089 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B4094 " --> pdb=" O PRO B4090 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 Processing helix chain 'B' and resid 4124 through 4134 Proline residue: B4131 - end of helix removed outlier: 5.630A pdb=" N GLY B4134 " --> pdb=" O GLN B4130 " (cutoff:3.500A) Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4182 through 4208 removed outlier: 4.611A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4258 removed outlier: 3.852A pdb=" N THR B4254 " --> pdb=" O TYR B4250 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B4255 " --> pdb=" O ASN B4251 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) Processing helix chain 'B' and resid 4262 through 4272 removed outlier: 3.908A pdb=" N LYS B4266 " --> pdb=" O LYS B4262 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.920A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.322A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 4.437A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.893A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 3.897A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 3.828A pdb=" N VAL B4697 " --> pdb=" O SER B4693 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B4702 " --> pdb=" O LEU B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4717 removed outlier: 5.450A pdb=" N ASN B4717 " --> pdb=" O VAL B4713 " (cutoff:3.500A) Processing helix chain 'B' and resid 4718 through 4735 removed outlier: 3.675A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.646A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.762A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 5.317A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 3.641A pdb=" N GLY B4820 " --> pdb=" O HIS B4816 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.089A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.993A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.349A pdb=" N PHE B 862 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 2377 through 2382 removed outlier: 4.510A pdb=" N ILE B2382 " --> pdb=" O ASP B2379 " (cutoff:3.500A) Processing helix chain 'B' and resid 2533 through 2538 removed outlier: 3.725A pdb=" N GLY B2537 " --> pdb=" O LEU B2534 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B2538 " --> pdb=" O PHE B2535 " (cutoff:3.500A) Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 51 through 56 removed outlier: 5.664A pdb=" N SER C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.039A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.326A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.454A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 275 removed outlier: 4.031A pdb=" N LEU C 274 " --> pdb=" O HIS C 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 275' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.731A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.229A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.674A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.908A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.815A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.093A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 589 removed outlier: 3.677A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.617A pdb=" N ILE C 597 " --> pdb=" O HIS C 593 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 598 " --> pdb=" O ILE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.699A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.331A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.669A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 946 removed outlier: 3.869A pdb=" N LEU C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 3.919A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 4.362A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.635A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.188A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C1235 " --> pdb=" O GLY C1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1230 through 1235' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 4.797A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1497 through 1502 removed outlier: 7.100A pdb=" N ASN C1501 " --> pdb=" O GLY C1497 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN C1502 " --> pdb=" O GLN C1498 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1497 through 1502' Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.820A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.153A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.610A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.794A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.407A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1737 removed outlier: 5.741A pdb=" N THR C1737 " --> pdb=" O THR C1733 " (cutoff:3.500A) Processing helix chain 'C' and resid 1773 through 1778 removed outlier: 4.520A pdb=" N GLN C1777 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR C1778 " --> pdb=" O GLU C1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1773 through 1778' Processing helix chain 'C' and resid 1783 through 1803 removed outlier: 3.706A pdb=" N SER C1803 " --> pdb=" O VAL C1799 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1848 Proline residue: C1848 - end of helix Processing helix chain 'C' and resid 1901 through 1944 removed outlier: 4.091A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1963 removed outlier: 3.944A pdb=" N THR C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA C1959 " --> pdb=" O ALA C1955 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS C1961 " --> pdb=" O LEU C1957 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 removed outlier: 4.200A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.643A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.741A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 4.783A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.606A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2154 through 2159 Proline residue: C2159 - end of helix Processing helix chain 'C' and resid 2160 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.992A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.956A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.060A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.678A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 4.203A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C2298 " --> pdb=" O GLU C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.709A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2412 Proline residue: C2404 - end of helix removed outlier: 9.343A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2439 removed outlier: 5.386A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.922A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 4.882A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 3.676A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 3.737A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.286A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 5.440A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP C2546 " --> pdb=" O ALA C2542 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 3.881A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2583 through 2593 removed outlier: 4.615A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C2590 " --> pdb=" O GLN C2586 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.506A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2656 removed outlier: 6.233A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS C2656 " --> pdb=" O LEU C2652 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2690 through 2696 removed outlier: 4.390A pdb=" N SER C2694 " --> pdb=" O GLU C2690 " (cutoff:3.500A) Processing helix chain 'C' and resid 2714 through 2740 Processing helix chain 'C' and resid 2765 through 2786 removed outlier: 4.329A pdb=" N GLU C2769 " --> pdb=" O GLU C2765 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) Proline residue: C2774 - end of helix removed outlier: 3.823A pdb=" N TRP C2785 " --> pdb=" O THR C2781 " (cutoff:3.500A) Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 4.300A pdb=" N ASP C2796 " --> pdb=" O THR C2792 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C2799 " --> pdb=" O GLY C2795 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2880 through 2899 removed outlier: 4.381A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C2888 " --> pdb=" O LYS C2884 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C2892 " --> pdb=" O LYS C2888 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU C2893 " --> pdb=" O ALA C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2945 removed outlier: 4.095A pdb=" N GLY C2945 " --> pdb=" O LEU C2941 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 5.997A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 5.307A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.700A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) Processing helix chain 'C' and resid 3042 through 3048 removed outlier: 4.095A pdb=" N MET C3046 " --> pdb=" O ALA C3042 " (cutoff:3.500A) Processing helix chain 'C' and resid 3050 through 3078 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.268A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3599 through 3605 removed outlier: 4.955A pdb=" N MET C3605 " --> pdb=" O ALA C3601 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 5.320A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.487A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.578A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.905A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.605A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.743A pdb=" N LEU C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.164A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 4.197A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C3837 " --> pdb=" O ASP C3833 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.576A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.607A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 4.970A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3962 removed outlier: 4.192A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C3957 " --> pdb=" O HIS C3953 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.503A pdb=" N LEU C3986 " --> pdb=" O LEU C3982 " (cutoff:3.500A) Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4030 removed outlier: 3.915A pdb=" N PHE C4020 " --> pdb=" O PHE C4016 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP C4030 " --> pdb=" O LEU C4026 " (cutoff:3.500A) Processing helix chain 'C' and resid 4031 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.610A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4070 Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.715A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 4.364A pdb=" N ASP C4093 " --> pdb=" O GLU C4089 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE C4094 " --> pdb=" O PRO C4090 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 Processing helix chain 'C' and resid 4124 through 4134 Proline residue: C4131 - end of helix removed outlier: 5.629A pdb=" N GLY C4134 " --> pdb=" O GLN C4130 " (cutoff:3.500A) Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4182 through 4208 removed outlier: 4.611A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4258 removed outlier: 3.852A pdb=" N THR C4254 " --> pdb=" O TYR C4250 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C4255 " --> pdb=" O ASN C4251 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) Processing helix chain 'C' and resid 4262 through 4272 removed outlier: 3.908A pdb=" N LYS C4266 " --> pdb=" O LYS C4262 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.920A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.322A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 4.437A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.893A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 3.897A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 3.829A pdb=" N VAL C4697 " --> pdb=" O SER C4693 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP C4702 " --> pdb=" O LEU C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4717 removed outlier: 5.450A pdb=" N ASN C4717 " --> pdb=" O VAL C4713 " (cutoff:3.500A) Processing helix chain 'C' and resid 4718 through 4735 removed outlier: 3.676A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.646A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.762A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 5.317A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 3.641A pdb=" N GLY C4820 " --> pdb=" O HIS C4816 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.088A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.992A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.349A pdb=" N PHE C 862 " --> pdb=" O GLN C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2382 removed outlier: 4.509A pdb=" N ILE C2382 " --> pdb=" O ASP C2379 " (cutoff:3.500A) Processing helix chain 'C' and resid 2533 through 2538 removed outlier: 3.726A pdb=" N GLY C2537 " --> pdb=" O LEU C2534 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C2538 " --> pdb=" O PHE C2535 " (cutoff:3.500A) Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 51 through 56 removed outlier: 5.663A pdb=" N SER D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.038A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 155 through 160 removed outlier: 4.326A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TRP D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.454A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 275 removed outlier: 4.030A pdb=" N LEU D 274 " --> pdb=" O HIS D 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 275' Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.732A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.229A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 4.674A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.907A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.815A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.094A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 589 removed outlier: 3.678A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.617A pdb=" N ILE D 597 " --> pdb=" O HIS D 593 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 598 " --> pdb=" O ILE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.699A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.331A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.669A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 946 removed outlier: 3.869A pdb=" N LEU D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 3.920A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 4.363A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.635A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.188A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D1235 " --> pdb=" O GLY D1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1230 through 1235' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 4.796A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1497 through 1502 removed outlier: 7.101A pdb=" N ASN D1501 " --> pdb=" O GLY D1497 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN D1502 " --> pdb=" O GLN D1498 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1497 through 1502' Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.820A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.153A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.610A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.793A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.407A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1737 removed outlier: 5.740A pdb=" N THR D1737 " --> pdb=" O THR D1733 " (cutoff:3.500A) Processing helix chain 'D' and resid 1773 through 1778 removed outlier: 4.519A pdb=" N GLN D1777 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR D1778 " --> pdb=" O GLU D1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1773 through 1778' Processing helix chain 'D' and resid 1783 through 1803 removed outlier: 3.706A pdb=" N SER D1803 " --> pdb=" O VAL D1799 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1848 Proline residue: D1848 - end of helix Processing helix chain 'D' and resid 1901 through 1944 removed outlier: 4.092A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1954 through 1963 removed outlier: 3.944A pdb=" N THR D1958 " --> pdb=" O SER D1954 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA D1959 " --> pdb=" O ALA D1955 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS D1961 " --> pdb=" O LEU D1957 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 removed outlier: 4.200A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.643A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.742A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 4.783A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.606A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2154 through 2159 Proline residue: D2159 - end of helix Processing helix chain 'D' and resid 2160 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.992A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.956A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.061A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.678A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 4.203A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D2298 " --> pdb=" O GLU D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.710A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2412 Proline residue: D2404 - end of helix removed outlier: 9.343A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2439 removed outlier: 5.385A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.922A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 4.881A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 3.676A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 3.736A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.286A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 5.441A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP D2546 " --> pdb=" O ALA D2542 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 3.881A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2583 through 2593 removed outlier: 4.615A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG D2590 " --> pdb=" O GLN D2586 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.505A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2656 removed outlier: 6.233A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS D2656 " --> pdb=" O LEU D2652 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2690 through 2696 removed outlier: 4.390A pdb=" N SER D2694 " --> pdb=" O GLU D2690 " (cutoff:3.500A) Processing helix chain 'D' and resid 2714 through 2740 Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 4.329A pdb=" N GLU D2769 " --> pdb=" O GLU D2765 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) Proline residue: D2774 - end of helix removed outlier: 3.823A pdb=" N TRP D2785 " --> pdb=" O THR D2781 " (cutoff:3.500A) Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 4.301A pdb=" N ASP D2796 " --> pdb=" O THR D2792 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D2799 " --> pdb=" O GLY D2795 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2880 through 2899 removed outlier: 4.381A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D2888 " --> pdb=" O LYS D2884 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE D2892 " --> pdb=" O LYS D2888 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU D2893 " --> pdb=" O ALA D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2945 removed outlier: 4.095A pdb=" N GLY D2945 " --> pdb=" O LEU D2941 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 5.997A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 5.307A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.699A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) Processing helix chain 'D' and resid 3042 through 3048 removed outlier: 4.095A pdb=" N MET D3046 " --> pdb=" O ALA D3042 " (cutoff:3.500A) Processing helix chain 'D' and resid 3050 through 3078 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.268A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3599 through 3605 removed outlier: 4.955A pdb=" N MET D3605 " --> pdb=" O ALA D3601 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 5.319A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.487A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.579A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.905A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.605A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.744A pdb=" N LEU D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.164A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 4.197A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS D3837 " --> pdb=" O ASP D3833 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.576A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.607A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 4.971A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3962 removed outlier: 4.193A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D3957 " --> pdb=" O HIS D3953 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.503A pdb=" N LEU D3986 " --> pdb=" O LEU D3982 " (cutoff:3.500A) Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4030 removed outlier: 3.916A pdb=" N PHE D4020 " --> pdb=" O PHE D4016 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP D4030 " --> pdb=" O LEU D4026 " (cutoff:3.500A) Processing helix chain 'D' and resid 4031 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.610A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4070 Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.715A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 4.364A pdb=" N ASP D4093 " --> pdb=" O GLU D4089 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE D4094 " --> pdb=" O PRO D4090 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 Processing helix chain 'D' and resid 4124 through 4134 Proline residue: D4131 - end of helix removed outlier: 5.630A pdb=" N GLY D4134 " --> pdb=" O GLN D4130 " (cutoff:3.500A) Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4182 through 4208 removed outlier: 4.611A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4258 removed outlier: 3.852A pdb=" N THR D4254 " --> pdb=" O TYR D4250 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D4255 " --> pdb=" O ASN D4251 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) Processing helix chain 'D' and resid 4262 through 4272 removed outlier: 3.908A pdb=" N LYS D4266 " --> pdb=" O LYS D4262 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.920A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.321A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 4.437A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.892A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 3.896A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 3.828A pdb=" N VAL D4697 " --> pdb=" O SER D4693 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP D4702 " --> pdb=" O LEU D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4717 removed outlier: 5.449A pdb=" N ASN D4717 " --> pdb=" O VAL D4713 " (cutoff:3.500A) Processing helix chain 'D' and resid 4718 through 4735 removed outlier: 3.675A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.645A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.762A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 5.317A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 3.641A pdb=" N GLY D4820 " --> pdb=" O HIS D4816 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.088A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.993A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.351A pdb=" N PHE D 862 " --> pdb=" O GLN D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 2377 through 2382 removed outlier: 4.509A pdb=" N ILE D2382 " --> pdb=" O ASP D2379 " (cutoff:3.500A) Processing helix chain 'D' and resid 2533 through 2538 removed outlier: 3.725A pdb=" N GLY D2537 " --> pdb=" O LEU D2534 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR D2538 " --> pdb=" O PHE D2535 " (cutoff:3.500A) Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.787A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.685A pdb=" N MET E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.525A pdb=" N ALA E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 83' Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.787A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 3.685A pdb=" N MET F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.525A pdb=" N ALA F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 83' Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.787A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.685A pdb=" N MET G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.525A pdb=" N ALA G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 78 through 83' Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.786A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 3.685A pdb=" N MET H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.525A pdb=" N ALA H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 78 through 83' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.692A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU A 121 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET A 128 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= 4, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.813A pdb=" N HIS A 202 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 236 through 239 removed outlier: 5.376A pdb=" N LEU A 236 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 276 through 279 removed outlier: 14.435A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 317 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 307 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 329 through 332 removed outlier: 3.574A pdb=" N TYR A 362 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 9, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.550A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.831A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A1617 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A1620 " --> pdb=" O ASP A1607 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A1607 " --> pdb=" O GLN A1620 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 12, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.439A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1108 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 948 through 952 removed outlier: 4.261A pdb=" N HIS A 949 " --> pdb=" O GLU A1065 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 7.513A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 7.324A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A1208 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A1253 " --> pdb=" O LEU A1595 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.572A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 3.504A pdb=" N CYS A1310 " --> pdb=" O THR A1537 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2741 through 2744 Processing sheet with id= 19, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 3.717A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 4135 through 4139 Processing sheet with id= 21, first strand: chain 'A' and resid 4521 through 4524 removed outlier: 3.530A pdb=" N HIS A4558 " --> pdb=" O SER A4523 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 47 through 50 Processing sheet with id= 23, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.692A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= 25, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.813A pdb=" N HIS B 202 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 236 through 239 removed outlier: 5.377A pdb=" N LEU B 236 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 276 through 279 removed outlier: 14.434A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 317 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 307 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 329 through 332 removed outlier: 3.574A pdb=" N TYR B 362 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 30, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.550A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.831A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B1617 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B1620 " --> pdb=" O ASP B1607 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B1607 " --> pdb=" O GLN B1620 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 33, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.438A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B1108 " --> pdb=" O VAL B1212 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 948 through 952 removed outlier: 4.259A pdb=" N HIS B 949 " --> pdb=" O GLU B1065 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 7.513A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 7.324A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B1208 " --> pdb=" O ASP B1112 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B1253 " --> pdb=" O LEU B1595 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.573A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 3.504A pdb=" N CYS B1310 " --> pdb=" O THR B1537 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 2741 through 2744 Processing sheet with id= 40, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 3.716A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 4135 through 4139 Processing sheet with id= 42, first strand: chain 'B' and resid 4521 through 4524 removed outlier: 3.530A pdb=" N HIS B4558 " --> pdb=" O SER B4523 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= 44, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.692A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU C 121 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET C 128 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= 46, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.813A pdb=" N HIS C 202 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 236 through 239 removed outlier: 5.376A pdb=" N LEU C 236 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 276 through 279 removed outlier: 14.435A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET C 317 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 307 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.574A pdb=" N TYR C 362 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 51, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.550A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.832A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C1617 " --> pdb=" O PHE C 802 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C1620 " --> pdb=" O ASP C1607 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP C1607 " --> pdb=" O GLN C1620 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 54, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.438A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C1108 " --> pdb=" O VAL C1212 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 948 through 952 removed outlier: 4.260A pdb=" N HIS C 949 " --> pdb=" O GLU C1065 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 7.513A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 7.324A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C1208 " --> pdb=" O ASP C1112 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C1253 " --> pdb=" O LEU C1595 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.572A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 3.504A pdb=" N CYS C1310 " --> pdb=" O THR C1537 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 2741 through 2744 Processing sheet with id= 61, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 3.717A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 4135 through 4139 Processing sheet with id= 63, first strand: chain 'C' and resid 4521 through 4524 removed outlier: 3.529A pdb=" N HIS C4558 " --> pdb=" O SER C4523 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 47 through 50 Processing sheet with id= 65, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.692A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= 67, first strand: chain 'D' and resid 193 through 196 removed outlier: 3.813A pdb=" N HIS D 202 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 236 through 239 removed outlier: 5.377A pdb=" N LEU D 236 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 276 through 279 removed outlier: 14.434A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 317 " --> pdb=" O TYR D 305 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 307 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 329 through 332 removed outlier: 3.574A pdb=" N TYR D 362 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 72, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.550A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.831A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D1617 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D1620 " --> pdb=" O ASP D1607 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D1607 " --> pdb=" O GLN D1620 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 75, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.438A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D1108 " --> pdb=" O VAL D1212 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 948 through 952 removed outlier: 4.260A pdb=" N HIS D 949 " --> pdb=" O GLU D1065 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 7.513A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 7.324A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D1208 " --> pdb=" O ASP D1112 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D1253 " --> pdb=" O LEU D1595 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.573A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 3.504A pdb=" N CYS D1310 " --> pdb=" O THR D1537 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 2741 through 2744 Processing sheet with id= 82, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 3.717A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'D' and resid 4135 through 4139 Processing sheet with id= 84, first strand: chain 'D' and resid 4521 through 4524 removed outlier: 3.529A pdb=" N HIS D4558 " --> pdb=" O SER D4523 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.566A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.566A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.565A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.566A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 6900 hydrogen bonds defined for protein. 20524 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: 92.35 Time building geometry restraints manager: 42.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 38721 1.34 - 1.46: 35353 1.46 - 1.59: 59021 1.59 - 1.72: 25 1.72 - 1.85: 1416 Bond restraints: 134536 Sorted by residual: bond pdb=" CG ARG B1960 " pdb=" CD ARG B1960 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" CG ARG C1960 " pdb=" CD ARG C1960 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.46e+01 bond pdb=" CG ARG A1960 " pdb=" CD ARG A1960 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.43e+01 bond pdb=" CG ARG D1960 " pdb=" CD ARG D1960 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.42e+01 bond pdb=" CB TRP B2787 " pdb=" CG TRP B2787 " ideal model delta sigma weight residual 1.498 1.390 0.108 3.10e-02 1.04e+03 1.21e+01 ... (remaining 134531 not shown) Histogram of bond angle deviations from ideal: 93.58 - 103.79: 1836 103.79 - 114.00: 77068 114.00 - 124.21: 99926 124.21 - 134.41: 2902 134.41 - 144.62: 20 Bond angle restraints: 181752 Sorted by residual: angle pdb=" CB MET A2279 " pdb=" CG MET A2279 " pdb=" SD MET A2279 " ideal model delta sigma weight residual 112.70 144.62 -31.92 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CB MET C2279 " pdb=" CG MET C2279 " pdb=" SD MET C2279 " ideal model delta sigma weight residual 112.70 144.61 -31.91 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CB MET B2279 " pdb=" CG MET B2279 " pdb=" SD MET B2279 " ideal model delta sigma weight residual 112.70 144.60 -31.90 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CB MET D2279 " pdb=" CG MET D2279 " pdb=" SD MET D2279 " ideal model delta sigma weight residual 112.70 144.58 -31.88 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CB ARG C2788 " pdb=" CG ARG C2788 " pdb=" CD ARG C2788 " ideal model delta sigma weight residual 111.30 131.96 -20.66 2.30e+00 1.89e-01 8.07e+01 ... (remaining 181747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 72328 17.69 - 35.38: 6888 35.38 - 53.07: 1271 53.07 - 70.76: 420 70.76 - 88.45: 113 Dihedral angle restraints: 81020 sinusoidal: 33260 harmonic: 47760 Sorted by residual: dihedral pdb=" CA HIS B 398 " pdb=" C HIS B 398 " pdb=" N MET B 399 " pdb=" CA MET B 399 " ideal model delta harmonic sigma weight residual 180.00 146.10 33.90 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA HIS A 398 " pdb=" C HIS A 398 " pdb=" N MET A 399 " pdb=" CA MET A 399 " ideal model delta harmonic sigma weight residual 180.00 146.15 33.85 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CA HIS C 398 " pdb=" C HIS C 398 " pdb=" N MET C 399 " pdb=" CA MET C 399 " ideal model delta harmonic sigma weight residual 180.00 146.18 33.82 0 5.00e+00 4.00e-02 4.57e+01 ... (remaining 81017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 19406 0.105 - 0.211: 438 0.211 - 0.316: 31 0.316 - 0.421: 5 0.421 - 0.527: 4 Chirality restraints: 19884 Sorted by residual: chirality pdb=" CG LEU D2783 " pdb=" CB LEU D2783 " pdb=" CD1 LEU D2783 " pdb=" CD2 LEU D2783 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CG LEU B2783 " pdb=" CB LEU B2783 " pdb=" CD1 LEU B2783 " pdb=" CD2 LEU B2783 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CG LEU A2783 " pdb=" CB LEU A2783 " pdb=" CD1 LEU A2783 " pdb=" CD2 LEU A2783 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 19881 not shown) Planarity restraints: 23364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D2788 " 0.779 9.50e-02 1.11e+02 3.49e-01 7.49e+01 pdb=" NE ARG D2788 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG D2788 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D2788 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D2788 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2788 " 0.779 9.50e-02 1.11e+02 3.49e-01 7.48e+01 pdb=" NE ARG A2788 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A2788 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A2788 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A2788 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B2788 " 0.779 9.50e-02 1.11e+02 3.49e-01 7.48e+01 pdb=" NE ARG B2788 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG B2788 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B2788 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B2788 " 0.018 2.00e-02 2.50e+03 ... (remaining 23361 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1791 2.65 - 3.21: 127897 3.21 - 3.78: 214950 3.78 - 4.34: 292479 4.34 - 4.90: 464358 Nonbonded interactions: 1101475 Sorted by model distance: nonbonded pdb=" OG1 THR B2832 " pdb=" O THR C1548 " model vdw 2.090 2.440 nonbonded pdb=" OG1 THR C2832 " pdb=" O THR D1548 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR A4580 " pdb=" NE2 HIS A4733 " model vdw 2.106 2.520 nonbonded pdb=" OG1 THR B4580 " pdb=" NE2 HIS B4733 " model vdw 2.106 2.520 nonbonded pdb=" OG1 THR C4580 " pdb=" NE2 HIS C4733 " model vdw 2.106 2.520 ... (remaining 1101470 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 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.350 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: 0.100 Extract box with map and model: 30.670 Check model and map are aligned: 1.430 Set scattering table: 0.960 Process input model: 411.320 Find NCS groups from input model: 6.680 Set up NCS constraints: 0.850 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: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 461.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 134536 Z= 0.244 Angle : 0.854 31.921 181752 Z= 0.468 Chirality : 0.044 0.527 19884 Planarity : 0.008 0.349 23364 Dihedral : 14.902 88.447 50232 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 0.84 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.06), residues: 16332 helix: 1.03 (0.06), residues: 8468 sheet: -0.15 (0.13), residues: 1572 loop : -0.80 (0.07), residues: 6292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 893 HIS 0.017 0.001 HIS A 398 PHE 0.047 0.002 PHE A2963 TYR 0.032 0.002 TYR D1703 ARG 0.039 0.001 ARG B2886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 768 time to evaluate : 11.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7496 (ppp) REVERT: A 393 MET cc_start: 0.7020 (mmm) cc_final: 0.6780 (tpt) REVERT: A 935 MET cc_start: 0.9386 (ppp) cc_final: 0.9146 (ppp) REVERT: A 1975 MET cc_start: 0.8116 (mtm) cc_final: 0.7727 (mtm) REVERT: A 2214 MET cc_start: 0.8871 (tpt) cc_final: 0.8583 (mmm) REVERT: A 2456 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7410 (mmt) REVERT: A 2652 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 2681 MET cc_start: 0.8278 (mmp) cc_final: 0.7942 (mmp) REVERT: A 2689 MET cc_start: 0.4491 (OUTLIER) cc_final: 0.4162 (ppp) REVERT: A 2719 TYR cc_start: 0.8172 (t80) cc_final: 0.7852 (t80) REVERT: A 2840 MET cc_start: 0.8801 (mmt) cc_final: 0.8368 (mmt) REVERT: A 2843 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8353 (ppp) REVERT: A 2886 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8142 (ptm160) REVERT: A 2897 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8881 (pp30) REVERT: A 2982 PHE cc_start: 0.8641 (m-80) cc_final: 0.8172 (m-80) REVERT: A 3605 MET cc_start: 0.5078 (mmp) cc_final: 0.4800 (mmm) REVERT: A 4052 MET cc_start: 0.8512 (mmm) cc_final: 0.8270 (mmm) REVERT: A 4208 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: A 4728 MET cc_start: 0.8153 (mmm) cc_final: 0.7946 (mmm) REVERT: F 6 GLU cc_start: 0.7612 (pp20) cc_final: 0.6872 (pp20) REVERT: B 678 MET cc_start: 0.8482 (tpt) cc_final: 0.8119 (tpt) REVERT: B 935 MET cc_start: 0.9355 (ppp) cc_final: 0.9142 (ppp) REVERT: B 1975 MET cc_start: 0.8114 (mtm) cc_final: 0.7713 (mtm) REVERT: B 2580 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8535 (tp) REVERT: B 2652 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 2681 MET cc_start: 0.8217 (mmp) cc_final: 0.7842 (mmp) REVERT: B 2695 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8174 (ppp) REVERT: B 2719 TYR cc_start: 0.8592 (t80) cc_final: 0.8028 (t80) REVERT: B 2772 ARG cc_start: 0.9265 (mpt180) cc_final: 0.8937 (mmt180) REVERT: B 2848 TYR cc_start: 0.8383 (m-80) cc_final: 0.7943 (m-80) REVERT: B 2893 LEU cc_start: 0.9641 (pp) cc_final: 0.9331 (pp) REVERT: B 3605 MET cc_start: 0.5459 (mmp) cc_final: 0.5186 (mmm) REVERT: B 4208 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: B 4707 MET cc_start: 0.8679 (ttp) cc_final: 0.8253 (ttp) REVERT: C 935 MET cc_start: 0.9329 (ppp) cc_final: 0.9114 (ppp) REVERT: C 1487 MET cc_start: 0.8198 (mtt) cc_final: 0.7946 (mtt) REVERT: C 1975 MET cc_start: 0.7967 (mtm) cc_final: 0.7567 (mtm) REVERT: C 2468 MET cc_start: 0.8556 (mmp) cc_final: 0.8353 (mmm) REVERT: C 2580 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8487 (tp) REVERT: C 2584 MET cc_start: 0.8181 (mmp) cc_final: 0.7965 (mmm) REVERT: C 2681 MET cc_start: 0.8112 (mmp) cc_final: 0.7721 (mmp) REVERT: C 2719 TYR cc_start: 0.8513 (t80) cc_final: 0.7968 (t80) REVERT: C 2848 TYR cc_start: 0.8369 (m-80) cc_final: 0.7885 (m-10) REVERT: C 2886 ARG cc_start: 0.8529 (mtm180) cc_final: 0.8095 (ptp-170) REVERT: C 3605 MET cc_start: 0.5388 (mmp) cc_final: 0.5143 (mmm) REVERT: C 3739 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8894 (ttp) REVERT: C 4052 MET cc_start: 0.8531 (mmm) cc_final: 0.8241 (mmm) REVERT: C 4208 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: C 4726 MET cc_start: 0.8247 (tpt) cc_final: 0.7757 (tmm) REVERT: D 317 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7447 (ppp) REVERT: D 393 MET cc_start: 0.7105 (mmm) cc_final: 0.6871 (tpt) REVERT: D 399 MET cc_start: 0.7744 (tmm) cc_final: 0.7499 (tmm) REVERT: D 935 MET cc_start: 0.9435 (ppp) cc_final: 0.9128 (ppp) REVERT: D 1165 MET cc_start: 0.7995 (mtm) cc_final: 0.7790 (mtm) REVERT: D 1249 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8091 (mpp) REVERT: D 1487 MET cc_start: 0.7950 (mtt) cc_final: 0.7691 (mtt) REVERT: D 1975 MET cc_start: 0.8059 (mtm) cc_final: 0.7691 (mtm) REVERT: D 2248 MET cc_start: 0.7745 (ttm) cc_final: 0.7517 (ttm) REVERT: D 2456 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7182 (mmt) REVERT: D 2580 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7706 (tt) REVERT: D 2652 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9108 (tp) REVERT: D 2689 MET cc_start: 0.3980 (OUTLIER) cc_final: 0.3280 (ttp) REVERT: D 2719 TYR cc_start: 0.8092 (t80) cc_final: 0.7800 (t80) REVERT: D 2757 MET cc_start: 0.6813 (mmt) cc_final: 0.6375 (mmt) REVERT: D 2840 MET cc_start: 0.8333 (mmt) cc_final: 0.7809 (mmt) REVERT: D 2843 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8295 (ppp) REVERT: D 2960 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8897 (pt) REVERT: D 2982 PHE cc_start: 0.8508 (m-80) cc_final: 0.7893 (m-80) REVERT: D 3605 MET cc_start: 0.5421 (mmp) cc_final: 0.5087 (mmm) REVERT: D 4258 MET cc_start: 0.2756 (ptt) cc_final: 0.2537 (mtt) REVERT: D 4728 MET cc_start: 0.8487 (mmm) cc_final: 0.8281 (mmt) outliers start: 228 outliers final: 37 residues processed: 859 average time/residue: 1.1412 time to fit residues: 1713.9491 Evaluate side-chains 755 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 696 time to evaluate : 11.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 1953 MET Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2652 LEU Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2788 ARG Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 2897 GLN Chi-restraints excluded: chain A residue 2960 ILE Chi-restraints excluded: chain A residue 3051 GLU Chi-restraints excluded: chain A residue 4046 ARG Chi-restraints excluded: chain A residue 4208 GLU Chi-restraints excluded: chain A residue 4718 SER Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 1960 ARG Chi-restraints excluded: chain B residue 2530 ARG Chi-restraints excluded: chain B residue 2580 LEU Chi-restraints excluded: chain B residue 2652 LEU Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2788 ARG Chi-restraints excluded: chain B residue 3051 GLU Chi-restraints excluded: chain B residue 4046 ARG Chi-restraints excluded: chain B residue 4208 GLU Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4817 MET Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1960 ARG Chi-restraints excluded: chain C residue 2530 ARG Chi-restraints excluded: chain C residue 2580 LEU Chi-restraints excluded: chain C residue 2788 ARG Chi-restraints excluded: chain C residue 3051 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 4046 ARG Chi-restraints excluded: chain C residue 4208 GLU Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4791 LYS Chi-restraints excluded: chain C residue 4817 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1960 ARG Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2580 LEU Chi-restraints excluded: chain D residue 2652 LEU Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 2793 ARG Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2960 ILE Chi-restraints excluded: chain D residue 3051 GLU Chi-restraints excluded: chain D residue 4046 ARG Chi-restraints excluded: chain D residue 4208 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1384 optimal weight: 6.9990 chunk 1243 optimal weight: 0.0030 chunk 689 optimal weight: 20.0000 chunk 424 optimal weight: 0.8980 chunk 838 optimal weight: 8.9990 chunk 664 optimal weight: 9.9990 chunk 1285 optimal weight: 9.9990 chunk 497 optimal weight: 10.0000 chunk 781 optimal weight: 10.0000 chunk 956 optimal weight: 1.9990 chunk 1489 optimal weight: 10.0000 overall best weight: 3.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 HIS ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1945 ASN A2158 HIS ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2897 GLN ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 HIS ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1265 HIS ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2158 HIS ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 HIS ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN C1029 ASN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1265 HIS ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2158 HIS ** C2613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS D 971 GLN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1265 HIS ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4794 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 134536 Z= 0.280 Angle : 0.661 14.364 181752 Z= 0.340 Chirality : 0.042 0.248 19884 Planarity : 0.005 0.126 23364 Dihedral : 6.876 99.201 18248 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.71 % Favored : 97.19 % Rotamer: Outliers : 0.45 % Allowed : 4.03 % Favored : 95.52 % 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: 0.63 (0.07), residues: 16332 helix: 1.37 (0.06), residues: 8512 sheet: -0.21 (0.12), residues: 1872 loop : -0.71 (0.08), residues: 5948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B2787 HIS 0.013 0.001 HIS D2613 PHE 0.036 0.002 PHE A2963 TYR 0.038 0.002 TYR B1703 ARG 0.022 0.001 ARG A2788 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 760 time to evaluate : 11.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.7852 (pmm) cc_final: 0.7646 (pmm) REVERT: A 349 MET cc_start: 0.7883 (mmm) cc_final: 0.7086 (mmm) REVERT: A 935 MET cc_start: 0.9426 (ppp) cc_final: 0.9169 (ppp) REVERT: A 1103 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7192 (t80) REVERT: A 1487 MET cc_start: 0.8452 (mtt) cc_final: 0.8158 (mtp) REVERT: A 1975 MET cc_start: 0.8201 (mtm) cc_final: 0.7777 (mtm) REVERT: A 2607 LEU cc_start: 0.9159 (mt) cc_final: 0.8602 (tt) REVERT: A 2652 LEU cc_start: 0.9023 (tp) cc_final: 0.8619 (tp) REVERT: A 2669 LEU cc_start: 0.9559 (mt) cc_final: 0.9310 (mt) REVERT: A 2681 MET cc_start: 0.8493 (mmp) cc_final: 0.8155 (mmp) REVERT: A 2695 MET cc_start: 0.8247 (ptm) cc_final: 0.8037 (ppp) REVERT: A 2719 TYR cc_start: 0.8332 (t80) cc_final: 0.7921 (t80) REVERT: A 2773 TRP cc_start: 0.8607 (m100) cc_final: 0.8252 (m100) REVERT: A 2843 MET cc_start: 0.8674 (ptp) cc_final: 0.8386 (mmm) REVERT: A 2847 ASN cc_start: 0.8847 (t0) cc_final: 0.8426 (m-40) REVERT: A 2886 ARG cc_start: 0.8652 (mtm180) cc_final: 0.8354 (ptm160) REVERT: A 2982 PHE cc_start: 0.8735 (m-80) cc_final: 0.8317 (m-80) REVERT: A 3605 MET cc_start: 0.5098 (mmp) cc_final: 0.4857 (mmm) REVERT: A 3981 MET cc_start: 0.8832 (tmm) cc_final: 0.8105 (ttp) REVERT: A 4292 MET cc_start: 0.8101 (mmt) cc_final: 0.7875 (mmt) REVERT: A 4728 MET cc_start: 0.8210 (mmm) cc_final: 0.8000 (mmm) REVERT: A 4804 MET cc_start: 0.7846 (mmm) cc_final: 0.7578 (mmm) REVERT: B 317 MET cc_start: 0.8310 (ptt) cc_final: 0.8074 (ptm) REVERT: B 935 MET cc_start: 0.9374 (ppp) cc_final: 0.9153 (ppp) REVERT: B 1487 MET cc_start: 0.8513 (mtt) cc_final: 0.7985 (mtp) REVERT: B 1948 MET cc_start: 0.8747 (tpp) cc_final: 0.8512 (mmm) REVERT: B 1975 MET cc_start: 0.8073 (mtm) cc_final: 0.7656 (mtm) REVERT: B 2279 MET cc_start: 0.8058 (ppp) cc_final: 0.7594 (tmm) REVERT: B 2652 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8816 (tp) REVERT: B 2681 MET cc_start: 0.8366 (mmp) cc_final: 0.7949 (mmp) REVERT: B 2695 MET cc_start: 0.8477 (ptm) cc_final: 0.8176 (ppp) REVERT: B 2719 TYR cc_start: 0.8647 (t80) cc_final: 0.7931 (t80) REVERT: B 2769 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8875 (pm20) REVERT: B 2840 MET cc_start: 0.9027 (mmt) cc_final: 0.8787 (mmt) REVERT: B 2847 ASN cc_start: 0.9339 (t0) cc_final: 0.9029 (t0) REVERT: B 2990 LEU cc_start: 0.8311 (mt) cc_final: 0.8087 (mt) REVERT: B 3605 MET cc_start: 0.5227 (mmp) cc_final: 0.5017 (mmm) REVERT: B 4019 MET cc_start: 0.8070 (mtt) cc_final: 0.7790 (mtm) REVERT: B 4279 MET cc_start: 0.7805 (ttt) cc_final: 0.7170 (ppp) REVERT: B 4804 MET cc_start: 0.7898 (mmm) cc_final: 0.7697 (mmm) REVERT: C 349 MET cc_start: 0.8374 (mmm) cc_final: 0.8168 (mmm) REVERT: C 393 MET cc_start: 0.7288 (mmm) cc_final: 0.7081 (mmm) REVERT: C 395 HIS cc_start: 0.9089 (t-90) cc_final: 0.8832 (t-90) REVERT: C 935 MET cc_start: 0.9339 (ppp) cc_final: 0.9129 (ppp) REVERT: C 1300 MET cc_start: 0.8511 (mmp) cc_final: 0.8274 (mmt) REVERT: C 1487 MET cc_start: 0.8307 (mtt) cc_final: 0.8012 (mtp) REVERT: C 1628 MET cc_start: 0.8625 (ttt) cc_final: 0.8414 (mtp) REVERT: C 1975 MET cc_start: 0.8000 (mtm) cc_final: 0.7612 (mtm) REVERT: C 2279 MET cc_start: 0.8191 (ppp) cc_final: 0.7629 (tmm) REVERT: C 2584 MET cc_start: 0.8235 (mmp) cc_final: 0.7966 (mmm) REVERT: C 2652 LEU cc_start: 0.9313 (mp) cc_final: 0.8885 (tp) REVERT: C 2719 TYR cc_start: 0.8600 (t80) cc_final: 0.8104 (t80) REVERT: C 2773 TRP cc_start: 0.8468 (m100) cc_final: 0.8062 (m100) REVERT: C 2847 ASN cc_start: 0.9259 (t0) cc_final: 0.9033 (t0) REVERT: C 2848 TYR cc_start: 0.8538 (m-80) cc_final: 0.7976 (m-80) REVERT: C 3981 MET cc_start: 0.8840 (tmm) cc_final: 0.8168 (ttp) REVERT: C 4052 MET cc_start: 0.8618 (mmm) cc_final: 0.8409 (mmm) REVERT: C 4555 ILE cc_start: 0.4199 (OUTLIER) cc_final: 0.3810 (mt) REVERT: C 4728 MET cc_start: 0.8452 (mmm) cc_final: 0.8159 (mmt) REVERT: C 4804 MET cc_start: 0.7952 (mmm) cc_final: 0.7739 (mmm) REVERT: D 241 MET cc_start: 0.7882 (pmm) cc_final: 0.7679 (pmm) REVERT: D 349 MET cc_start: 0.7765 (mmm) cc_final: 0.7400 (mmm) REVERT: D 393 MET cc_start: 0.6857 (mmm) cc_final: 0.6576 (mmm) REVERT: D 935 MET cc_start: 0.9369 (ppp) cc_final: 0.9164 (ppp) REVERT: D 1103 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7423 (t80) REVERT: D 1165 MET cc_start: 0.8091 (mtm) cc_final: 0.7786 (mtm) REVERT: D 1174 MET cc_start: 0.7899 (mpp) cc_final: 0.7593 (pmm) REVERT: D 1487 MET cc_start: 0.8187 (mtt) cc_final: 0.7872 (mtt) REVERT: D 1975 MET cc_start: 0.8052 (mtm) cc_final: 0.7795 (mtm) REVERT: D 2167 MET cc_start: 0.7495 (ttm) cc_final: 0.7276 (ttp) REVERT: D 2607 LEU cc_start: 0.9055 (mt) cc_final: 0.8501 (tt) REVERT: D 2652 LEU cc_start: 0.9361 (tp) cc_final: 0.9055 (tp) REVERT: D 2719 TYR cc_start: 0.8362 (t80) cc_final: 0.7877 (t80) REVERT: D 2773 TRP cc_start: 0.8354 (m100) cc_final: 0.7733 (m100) REVERT: D 2843 MET cc_start: 0.8689 (ptp) cc_final: 0.8204 (ptm) REVERT: D 2847 ASN cc_start: 0.8985 (t0) cc_final: 0.8445 (m110) REVERT: D 2848 TYR cc_start: 0.8125 (m-80) cc_final: 0.7744 (m-80) REVERT: D 2982 PHE cc_start: 0.8643 (m-80) cc_final: 0.8393 (m-80) REVERT: D 3605 MET cc_start: 0.5274 (mmp) cc_final: 0.4986 (mmm) REVERT: D 4052 MET cc_start: 0.8200 (mmm) cc_final: 0.7893 (mmm) REVERT: D 4258 MET cc_start: 0.2923 (ptt) cc_final: 0.2642 (mtt) REVERT: D 4726 MET cc_start: 0.8207 (tpt) cc_final: 0.7972 (tpp) REVERT: D 4728 MET cc_start: 0.8606 (mmm) cc_final: 0.8389 (mmt) outliers start: 65 outliers final: 12 residues processed: 783 average time/residue: 1.1312 time to fit residues: 1561.1739 Evaluate side-chains 722 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 706 time to evaluate : 11.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1729 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2652 LEU Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1174 MET Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain D residue 1103 PHE Chi-restraints excluded: chain D residue 2953 HIS Chi-restraints excluded: chain D residue 4502 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 827 optimal weight: 0.3980 chunk 462 optimal weight: 9.9990 chunk 1239 optimal weight: 0.9980 chunk 1014 optimal weight: 6.9990 chunk 410 optimal weight: 10.0000 chunk 1491 optimal weight: 40.0000 chunk 1611 optimal weight: 8.9990 chunk 1328 optimal weight: 7.9990 chunk 1479 optimal weight: 2.9990 chunk 508 optimal weight: 9.9990 chunk 1196 optimal weight: 7.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 HIS A1952 ASN ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2927 GLN ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4049 HIS ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1656 HIS ** B2195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1656 HIS ** C2195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2613 HIS ** C2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2927 GLN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1656 HIS ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 134536 Z= 0.269 Angle : 0.614 16.215 181752 Z= 0.315 Chirality : 0.040 0.288 19884 Planarity : 0.005 0.127 23364 Dihedral : 6.142 86.855 18085 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 0.39 % Allowed : 5.57 % Favored : 94.04 % 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: 0.88 (0.07), residues: 16332 helix: 1.64 (0.06), residues: 8512 sheet: -0.28 (0.12), residues: 1816 loop : -0.62 (0.08), residues: 6004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D2852 HIS 0.009 0.001 HIS D4057 PHE 0.026 0.002 PHE B 985 TYR 0.042 0.002 TYR C2939 ARG 0.029 0.001 ARG D2793 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 738 time to evaluate : 10.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7740 (ttp) REVERT: A 349 MET cc_start: 0.7774 (mmm) cc_final: 0.7097 (mmm) REVERT: A 935 MET cc_start: 0.9396 (ppp) cc_final: 0.9168 (ppp) REVERT: A 1113 MET cc_start: 0.7859 (mtt) cc_final: 0.7494 (mtt) REVERT: A 1942 PHE cc_start: 0.8649 (t80) cc_final: 0.8447 (t80) REVERT: A 1975 MET cc_start: 0.8185 (mtm) cc_final: 0.7737 (mtm) REVERT: A 2389 MET cc_start: 0.8314 (mtp) cc_final: 0.8049 (mtm) REVERT: A 2652 LEU cc_start: 0.9019 (tp) cc_final: 0.8579 (tp) REVERT: A 2681 MET cc_start: 0.8382 (mmp) cc_final: 0.8035 (mmp) REVERT: A 2719 TYR cc_start: 0.8555 (t80) cc_final: 0.8004 (t80) REVERT: A 2773 TRP cc_start: 0.8594 (m100) cc_final: 0.8286 (m100) REVERT: A 2843 MET cc_start: 0.8733 (ptp) cc_final: 0.8374 (mmm) REVERT: A 2847 ASN cc_start: 0.8851 (t0) cc_final: 0.8549 (m110) REVERT: A 2886 ARG cc_start: 0.8815 (mtm180) cc_final: 0.8200 (ptp-170) REVERT: A 2927 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8578 (mm-40) REVERT: A 2982 PHE cc_start: 0.8785 (m-80) cc_final: 0.8387 (m-80) REVERT: A 3003 MET cc_start: 0.9412 (mpp) cc_final: 0.9120 (ptp) REVERT: A 3981 MET cc_start: 0.8876 (tmm) cc_final: 0.8111 (ttp) REVERT: A 4804 MET cc_start: 0.7859 (mmm) cc_final: 0.7440 (mmm) REVERT: A 4943 MET cc_start: 0.8523 (mtt) cc_final: 0.8055 (mtp) REVERT: H 6 GLU cc_start: 0.7596 (pp20) cc_final: 0.7346 (pp20) REVERT: B 349 MET cc_start: 0.8222 (mmm) cc_final: 0.7588 (mmm) REVERT: B 395 HIS cc_start: 0.9009 (t-90) cc_final: 0.8797 (t-90) REVERT: B 935 MET cc_start: 0.9402 (ppp) cc_final: 0.9154 (ppp) REVERT: B 1975 MET cc_start: 0.8073 (mtm) cc_final: 0.7657 (mtm) REVERT: B 2652 LEU cc_start: 0.9211 (tp) cc_final: 0.8799 (tp) REVERT: B 2681 MET cc_start: 0.8328 (mmp) cc_final: 0.7909 (mmp) REVERT: B 2695 MET cc_start: 0.8507 (ptm) cc_final: 0.8274 (ppp) REVERT: B 2719 TYR cc_start: 0.8849 (t80) cc_final: 0.8296 (t80) REVERT: B 2840 MET cc_start: 0.9033 (mmt) cc_final: 0.8710 (mmt) REVERT: B 2877 LEU cc_start: 0.8653 (tp) cc_final: 0.8281 (tt) REVERT: B 2886 ARG cc_start: 0.8776 (ptm160) cc_final: 0.8352 (mpp80) REVERT: B 3739 MET cc_start: 0.8983 (ttp) cc_final: 0.8682 (ttp) REVERT: B 3978 MET cc_start: 0.8825 (ttt) cc_final: 0.8509 (ttp) REVERT: B 4019 MET cc_start: 0.8056 (mtt) cc_final: 0.7780 (mtm) REVERT: B 4726 MET cc_start: 0.8231 (mmm) cc_final: 0.7676 (tpp) REVERT: B 4943 MET cc_start: 0.8844 (mmm) cc_final: 0.8302 (mtp) REVERT: C 349 MET cc_start: 0.8260 (mmm) cc_final: 0.8038 (mmm) REVERT: C 395 HIS cc_start: 0.9078 (t-90) cc_final: 0.8822 (t-90) REVERT: C 935 MET cc_start: 0.9352 (ppp) cc_final: 0.9146 (ppp) REVERT: C 1300 MET cc_start: 0.8480 (mmp) cc_final: 0.8253 (mmt) REVERT: C 1487 MET cc_start: 0.8401 (mtt) cc_final: 0.8035 (mtp) REVERT: C 1975 MET cc_start: 0.7958 (mtm) cc_final: 0.7559 (mtm) REVERT: C 2580 LEU cc_start: 0.8926 (tp) cc_final: 0.8649 (tp) REVERT: C 2584 MET cc_start: 0.8273 (mmp) cc_final: 0.7905 (mmm) REVERT: C 2652 LEU cc_start: 0.9274 (mp) cc_final: 0.8815 (tp) REVERT: C 2681 MET cc_start: 0.8193 (mmp) cc_final: 0.7706 (mmp) REVERT: C 2701 PHE cc_start: 0.7415 (t80) cc_final: 0.6964 (t80) REVERT: C 2719 TYR cc_start: 0.8800 (t80) cc_final: 0.8350 (t80) REVERT: C 2772 ARG cc_start: 0.9322 (mpt180) cc_final: 0.8878 (mpt180) REVERT: C 2773 TRP cc_start: 0.8413 (m100) cc_final: 0.7966 (m100) REVERT: C 2848 TYR cc_start: 0.8549 (m-80) cc_final: 0.8249 (m-80) REVERT: C 3981 MET cc_start: 0.8897 (tmm) cc_final: 0.8147 (ttp) REVERT: C 4052 MET cc_start: 0.8659 (mmm) cc_final: 0.8453 (mmm) REVERT: C 4555 ILE cc_start: 0.4202 (OUTLIER) cc_final: 0.3770 (mt) REVERT: C 4728 MET cc_start: 0.8506 (mmm) cc_final: 0.8263 (mmt) REVERT: D 317 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7359 (ttp) REVERT: D 1113 MET cc_start: 0.7532 (mtt) cc_final: 0.7256 (mtt) REVERT: D 1249 MET cc_start: 0.8295 (tpp) cc_final: 0.7951 (tpp) REVERT: D 1487 MET cc_start: 0.8309 (mtt) cc_final: 0.7951 (mtp) REVERT: D 1975 MET cc_start: 0.8032 (mtm) cc_final: 0.7771 (mtm) REVERT: D 2607 LEU cc_start: 0.9036 (mt) cc_final: 0.8426 (tp) REVERT: D 2652 LEU cc_start: 0.9317 (tp) cc_final: 0.8974 (tp) REVERT: D 2719 TYR cc_start: 0.8536 (t80) cc_final: 0.8152 (t80) REVERT: D 2773 TRP cc_start: 0.8287 (m100) cc_final: 0.8021 (m100) REVERT: D 2843 MET cc_start: 0.8811 (ptp) cc_final: 0.8223 (ptm) REVERT: D 2847 ASN cc_start: 0.9025 (t0) cc_final: 0.8536 (m110) REVERT: D 2939 TYR cc_start: 0.9041 (m-10) cc_final: 0.8839 (m-80) REVERT: D 2982 PHE cc_start: 0.8727 (m-80) cc_final: 0.8262 (m-80) REVERT: D 3605 MET cc_start: 0.5367 (mmp) cc_final: 0.5094 (mmm) REVERT: D 3739 MET cc_start: 0.8965 (ttp) cc_final: 0.8722 (ttp) REVERT: D 3978 MET cc_start: 0.8925 (tmm) cc_final: 0.8689 (ttt) REVERT: D 4258 MET cc_start: 0.2878 (ptt) cc_final: 0.2631 (mtt) REVERT: D 4306 PHE cc_start: 0.7776 (m-10) cc_final: 0.7357 (t80) REVERT: D 4728 MET cc_start: 0.8607 (mmm) cc_final: 0.8365 (mmt) outliers start: 56 outliers final: 22 residues processed: 769 average time/residue: 1.1178 time to fit residues: 1519.5744 Evaluate side-chains 731 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 705 time to evaluate : 11.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 2279 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1174 MET Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4718 SER Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2801 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1474 optimal weight: 8.9990 chunk 1121 optimal weight: 50.0000 chunk 774 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 712 optimal weight: 10.0000 chunk 1001 optimal weight: 9.9990 chunk 1497 optimal weight: 5.9990 chunk 1585 optimal weight: 8.9990 chunk 782 optimal weight: 10.0000 chunk 1419 optimal weight: 6.9990 chunk 427 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 238 HIS ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 HIS ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1835 HIS A2177 ASN ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2927 GLN ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 238 HIS ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 HIS B 635 ASN ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1945 ASN B2177 ASN ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN C 238 HIS ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1835 HIS C1945 ASN C2177 ASN C2195 ASN ** C2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4620 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 238 HIS ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 HIS ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 HIS D 635 ASN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1945 ASN D2386 ASN ** D2579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4620 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 134536 Z= 0.495 Angle : 0.712 19.081 181752 Z= 0.367 Chirality : 0.044 0.338 19884 Planarity : 0.005 0.154 23364 Dihedral : 6.216 87.391 18083 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 0.66 % Allowed : 6.79 % Favored : 92.55 % 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: 0.74 (0.07), residues: 16332 helix: 1.54 (0.06), residues: 8544 sheet: -0.44 (0.12), residues: 1800 loop : -0.69 (0.08), residues: 5988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 893 HIS 0.012 0.002 HIS D1656 PHE 0.033 0.002 PHE D4870 TYR 0.034 0.002 TYR C1703 ARG 0.016 0.001 ARG C2835 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 742 time to evaluate : 11.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.7920 (mmm) cc_final: 0.7244 (mmm) REVERT: A 393 MET cc_start: 0.7371 (mmm) cc_final: 0.7160 (mmm) REVERT: A 935 MET cc_start: 0.9427 (ppp) cc_final: 0.9226 (ppp) REVERT: A 1729 MET cc_start: 0.8233 (tpp) cc_final: 0.7902 (mmt) REVERT: A 1975 MET cc_start: 0.8168 (mtm) cc_final: 0.7697 (mtm) REVERT: A 2389 MET cc_start: 0.8454 (mtp) cc_final: 0.8189 (mtm) REVERT: A 2530 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8343 (ptp90) REVERT: A 2607 LEU cc_start: 0.9219 (mt) cc_final: 0.8637 (tt) REVERT: A 2652 LEU cc_start: 0.9102 (tp) cc_final: 0.8669 (tp) REVERT: A 2669 LEU cc_start: 0.9619 (mt) cc_final: 0.9374 (mt) REVERT: A 2681 MET cc_start: 0.8452 (mmp) cc_final: 0.8105 (mmp) REVERT: A 2719 TYR cc_start: 0.8732 (t80) cc_final: 0.8240 (t80) REVERT: A 2773 TRP cc_start: 0.8657 (m100) cc_final: 0.8375 (m100) REVERT: A 2847 ASN cc_start: 0.8954 (t0) cc_final: 0.8606 (m110) REVERT: A 3981 MET cc_start: 0.8846 (tmm) cc_final: 0.8194 (ttp) REVERT: A 4292 MET cc_start: 0.8507 (tpp) cc_final: 0.8175 (mpp) REVERT: A 4520 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7533 (m-10) REVERT: A 4726 MET cc_start: 0.8153 (tpt) cc_final: 0.7796 (tpp) REVERT: A 4804 MET cc_start: 0.7965 (mmm) cc_final: 0.7687 (mmm) REVERT: G 6 GLU cc_start: 0.7567 (pp20) cc_final: 0.7295 (pp20) REVERT: B 935 MET cc_start: 0.9459 (ppp) cc_final: 0.9254 (ppp) REVERT: B 1113 MET cc_start: 0.7975 (mtt) cc_final: 0.7754 (mtm) REVERT: B 1794 MET cc_start: 0.8872 (mtm) cc_final: 0.8626 (mtp) REVERT: B 1975 MET cc_start: 0.8101 (mtm) cc_final: 0.7667 (mtm) REVERT: B 2389 MET cc_start: 0.8517 (mtp) cc_final: 0.8279 (mtm) REVERT: B 2652 LEU cc_start: 0.9246 (tp) cc_final: 0.8839 (tp) REVERT: B 2681 MET cc_start: 0.8447 (mmp) cc_final: 0.8018 (mmp) REVERT: B 2695 MET cc_start: 0.8538 (ptm) cc_final: 0.8291 (ppp) REVERT: B 2719 TYR cc_start: 0.8948 (t80) cc_final: 0.8426 (t80) REVERT: B 2772 ARG cc_start: 0.9487 (mpt180) cc_final: 0.8945 (mpt180) REVERT: B 2847 ASN cc_start: 0.9106 (t0) cc_final: 0.8831 (m110) REVERT: B 2877 LEU cc_start: 0.8786 (tp) cc_final: 0.8580 (tp) REVERT: B 2886 ARG cc_start: 0.8855 (ptm160) cc_final: 0.8423 (mpp80) REVERT: B 3739 MET cc_start: 0.8948 (ttp) cc_final: 0.8685 (ttp) REVERT: B 3954 MET cc_start: 0.8790 (mmm) cc_final: 0.8325 (tpp) REVERT: B 4019 MET cc_start: 0.8243 (mtt) cc_final: 0.7961 (mtm) REVERT: B 4292 MET cc_start: 0.8220 (mmt) cc_final: 0.7811 (mmp) REVERT: B 4726 MET cc_start: 0.8362 (mmm) cc_final: 0.7667 (tpt) REVERT: B 4728 MET cc_start: 0.8553 (mmm) cc_final: 0.8347 (mmp) REVERT: B 4804 MET cc_start: 0.7911 (mmm) cc_final: 0.7651 (mmm) REVERT: C 395 HIS cc_start: 0.9098 (t-90) cc_final: 0.8871 (t-90) REVERT: C 778 MET cc_start: 0.8629 (ptp) cc_final: 0.8256 (ptm) REVERT: C 1103 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 1487 MET cc_start: 0.8514 (mtt) cc_final: 0.8192 (mtp) REVERT: C 1975 MET cc_start: 0.7966 (mtm) cc_final: 0.7569 (mtm) REVERT: C 2580 LEU cc_start: 0.9047 (tp) cc_final: 0.8631 (tp) REVERT: C 2584 MET cc_start: 0.8525 (mmp) cc_final: 0.8099 (mmm) REVERT: C 2652 LEU cc_start: 0.9306 (mp) cc_final: 0.8882 (tp) REVERT: C 2681 MET cc_start: 0.8282 (mmp) cc_final: 0.7698 (mmp) REVERT: C 2719 TYR cc_start: 0.8880 (t80) cc_final: 0.8415 (t80) REVERT: C 2848 TYR cc_start: 0.8649 (m-80) cc_final: 0.8285 (m-80) REVERT: C 2886 ARG cc_start: 0.8712 (mpp80) cc_final: 0.8238 (mpp80) REVERT: C 3605 MET cc_start: 0.4693 (mmm) cc_final: 0.4454 (mmm) REVERT: C 3981 MET cc_start: 0.8821 (tmm) cc_final: 0.8239 (ttp) REVERT: C 4292 MET cc_start: 0.8301 (mmt) cc_final: 0.7901 (mpp) REVERT: C 4520 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7511 (m-10) REVERT: C 4555 ILE cc_start: 0.4428 (OUTLIER) cc_final: 0.3989 (mt) REVERT: C 4726 MET cc_start: 0.8415 (mmm) cc_final: 0.7849 (tpp) REVERT: C 4728 MET cc_start: 0.8612 (mmm) cc_final: 0.8396 (mmt) REVERT: C 4804 MET cc_start: 0.7991 (mmm) cc_final: 0.7717 (mmm) REVERT: C 4817 MET cc_start: 0.8710 (mmm) cc_final: 0.8488 (mmm) REVERT: D 655 MET cc_start: 0.8852 (mmp) cc_final: 0.8518 (mmm) REVERT: D 1249 MET cc_start: 0.8323 (tpp) cc_final: 0.8017 (tpp) REVERT: D 1487 MET cc_start: 0.8485 (mtt) cc_final: 0.8159 (mtp) REVERT: D 1975 MET cc_start: 0.7920 (mtm) cc_final: 0.7601 (mtm) REVERT: D 2580 LEU cc_start: 0.8497 (tp) cc_final: 0.8108 (tp) REVERT: D 2607 LEU cc_start: 0.9148 (mt) cc_final: 0.8620 (tt) REVERT: D 2652 LEU cc_start: 0.9301 (tp) cc_final: 0.8954 (tp) REVERT: D 2719 TYR cc_start: 0.8653 (t80) cc_final: 0.8255 (t80) REVERT: D 2772 ARG cc_start: 0.9282 (mpt180) cc_final: 0.8935 (mpt180) REVERT: D 2773 TRP cc_start: 0.8374 (m100) cc_final: 0.7981 (m100) REVERT: D 2843 MET cc_start: 0.8778 (ptp) cc_final: 0.8261 (ptm) REVERT: D 2847 ASN cc_start: 0.9129 (t0) cc_final: 0.8685 (m110) REVERT: D 2848 TYR cc_start: 0.8293 (m-80) cc_final: 0.7959 (m-80) REVERT: D 2939 TYR cc_start: 0.9012 (m-10) cc_final: 0.8790 (m-80) REVERT: D 2982 PHE cc_start: 0.8934 (m-80) cc_final: 0.8488 (m-80) REVERT: D 3605 MET cc_start: 0.5120 (mmp) cc_final: 0.4833 (mmm) REVERT: D 3739 MET cc_start: 0.8973 (ttp) cc_final: 0.8687 (ttp) REVERT: D 3954 MET cc_start: 0.8712 (mmm) cc_final: 0.7995 (tpp) REVERT: D 4258 MET cc_start: 0.2541 (ptt) cc_final: 0.2271 (mtt) REVERT: D 4728 MET cc_start: 0.8550 (mmm) cc_final: 0.8318 (mmt) REVERT: D 4817 MET cc_start: 0.8696 (mmm) cc_final: 0.8454 (mmm) outliers start: 95 outliers final: 38 residues processed: 796 average time/residue: 1.1190 time to fit residues: 1582.5211 Evaluate side-chains 753 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 710 time to evaluate : 11.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 2530 ARG Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 3702 GLU Chi-restraints excluded: chain A residue 4520 TYR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2843 MET Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1174 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 3702 GLU Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1103 PHE Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1957 LEU Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2801 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1320 optimal weight: 0.8980 chunk 899 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 1180 optimal weight: 7.9990 chunk 654 optimal weight: 0.0370 chunk 1352 optimal weight: 5.9990 chunk 1095 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 809 optimal weight: 10.0000 chunk 1422 optimal weight: 10.0000 chunk 400 optimal weight: 5.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3038 GLN ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2927 GLN ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2927 GLN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 134536 Z= 0.224 Angle : 0.602 16.248 181752 Z= 0.306 Chirality : 0.040 0.249 19884 Planarity : 0.004 0.128 23364 Dihedral : 6.011 87.812 18083 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 0.62 % Allowed : 7.57 % Favored : 91.80 % 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: 0.98 (0.07), residues: 16332 helix: 1.76 (0.06), residues: 8580 sheet: -0.37 (0.12), residues: 1796 loop : -0.61 (0.08), residues: 5956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D2852 HIS 0.008 0.001 HIS A3700 PHE 0.034 0.001 PHE B2720 TYR 0.064 0.001 TYR C2939 ARG 0.007 0.000 ARG D4046 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 726 time to evaluate : 11.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.7893 (mmm) cc_final: 0.7248 (mmm) REVERT: A 935 MET cc_start: 0.9395 (ppp) cc_final: 0.9189 (ppp) REVERT: A 1729 MET cc_start: 0.8130 (tpp) cc_final: 0.7680 (mmt) REVERT: A 1896 MET cc_start: 0.8515 (ttt) cc_final: 0.8308 (ttp) REVERT: A 1975 MET cc_start: 0.8132 (mtm) cc_final: 0.7661 (mtm) REVERT: A 2389 MET cc_start: 0.8382 (mtp) cc_final: 0.8117 (mtm) REVERT: A 2652 LEU cc_start: 0.9058 (tp) cc_final: 0.8598 (tp) REVERT: A 2681 MET cc_start: 0.8342 (mmp) cc_final: 0.8003 (mmp) REVERT: A 2719 TYR cc_start: 0.8664 (t80) cc_final: 0.8103 (t80) REVERT: A 2773 TRP cc_start: 0.8620 (m100) cc_final: 0.8370 (m100) REVERT: A 2840 MET cc_start: 0.8615 (mmt) cc_final: 0.8357 (mmt) REVERT: A 2843 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: A 2847 ASN cc_start: 0.8896 (t0) cc_final: 0.8550 (m110) REVERT: A 3954 MET cc_start: 0.8785 (mmm) cc_final: 0.8148 (tpp) REVERT: A 3981 MET cc_start: 0.8844 (tmm) cc_final: 0.8611 (ttp) REVERT: A 3985 MET cc_start: 0.9159 (mmm) cc_final: 0.8923 (tpp) REVERT: A 4292 MET cc_start: 0.8495 (tpp) cc_final: 0.8145 (mpp) REVERT: A 4804 MET cc_start: 0.8094 (mmm) cc_final: 0.7689 (mmm) REVERT: A 4817 MET cc_start: 0.8714 (tpt) cc_final: 0.8381 (mmm) REVERT: A 4943 MET cc_start: 0.8680 (mtt) cc_final: 0.8388 (mtt) REVERT: F 58 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8861 (mtpp) REVERT: B 393 MET cc_start: 0.7430 (mmm) cc_final: 0.6813 (mmm) REVERT: B 1113 MET cc_start: 0.7786 (mtt) cc_final: 0.7527 (mtm) REVERT: B 1564 MET cc_start: 0.8583 (mmm) cc_final: 0.8340 (mmm) REVERT: B 1975 MET cc_start: 0.8040 (mtm) cc_final: 0.7618 (mtm) REVERT: B 2389 MET cc_start: 0.8445 (mtp) cc_final: 0.8244 (mtm) REVERT: B 2442 MET cc_start: 0.8618 (tpp) cc_final: 0.8350 (tpt) REVERT: B 2652 LEU cc_start: 0.9224 (tp) cc_final: 0.8789 (tp) REVERT: B 2681 MET cc_start: 0.8242 (mmp) cc_final: 0.7796 (mmp) REVERT: B 2695 MET cc_start: 0.8481 (ptm) cc_final: 0.8239 (ppp) REVERT: B 2719 TYR cc_start: 0.8939 (t80) cc_final: 0.8433 (t80) REVERT: B 2720 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: B 2847 ASN cc_start: 0.9071 (t0) cc_final: 0.8787 (m110) REVERT: B 2877 LEU cc_start: 0.8770 (tp) cc_final: 0.8536 (tp) REVERT: B 2886 ARG cc_start: 0.8818 (ptm160) cc_final: 0.8338 (mpp80) REVERT: B 3739 MET cc_start: 0.8910 (ttp) cc_final: 0.8686 (ttp) REVERT: B 3954 MET cc_start: 0.8769 (mmm) cc_final: 0.8302 (tpp) REVERT: B 4019 MET cc_start: 0.8170 (mtt) cc_final: 0.7901 (mtm) REVERT: B 4502 MET cc_start: 0.7955 (mtp) cc_final: 0.7753 (mtm) REVERT: B 4726 MET cc_start: 0.8277 (mmm) cc_final: 0.7559 (tpt) REVERT: B 4728 MET cc_start: 0.8543 (mmm) cc_final: 0.8338 (mmp) REVERT: B 4804 MET cc_start: 0.8006 (mmm) cc_final: 0.7772 (mmm) REVERT: C 395 HIS cc_start: 0.9088 (t-90) cc_final: 0.8870 (t-90) REVERT: C 1103 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7156 (t80) REVERT: C 1113 MET cc_start: 0.7698 (mtt) cc_final: 0.7448 (mtm) REVERT: C 1487 MET cc_start: 0.8471 (mtt) cc_final: 0.8138 (mtp) REVERT: C 1975 MET cc_start: 0.7938 (mtm) cc_final: 0.7540 (mtm) REVERT: C 2580 LEU cc_start: 0.8990 (tp) cc_final: 0.8505 (tp) REVERT: C 2584 MET cc_start: 0.8372 (mmp) cc_final: 0.7968 (mmm) REVERT: C 2681 MET cc_start: 0.8172 (mmp) cc_final: 0.7613 (mmp) REVERT: C 2688 MET cc_start: 0.4334 (pmm) cc_final: 0.4119 (pmm) REVERT: C 2719 TYR cc_start: 0.8842 (t80) cc_final: 0.8454 (t80) REVERT: C 2773 TRP cc_start: 0.8487 (m100) cc_final: 0.8053 (m100) REVERT: C 2835 ARG cc_start: 0.8694 (tpp-160) cc_final: 0.8451 (tpm170) REVERT: C 2840 MET cc_start: 0.8752 (mmt) cc_final: 0.8475 (mmt) REVERT: C 2848 TYR cc_start: 0.8578 (m-80) cc_final: 0.8343 (m-80) REVERT: C 2874 TYR cc_start: 0.7768 (t80) cc_final: 0.7518 (t80) REVERT: C 2886 ARG cc_start: 0.8734 (mpp80) cc_final: 0.8253 (mpp80) REVERT: C 3954 MET cc_start: 0.8804 (mmm) cc_final: 0.8161 (tpp) REVERT: C 3981 MET cc_start: 0.8818 (tmm) cc_final: 0.8587 (ttp) REVERT: C 4292 MET cc_start: 0.8321 (mmt) cc_final: 0.7884 (mpp) REVERT: C 4520 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: C 4555 ILE cc_start: 0.4462 (OUTLIER) cc_final: 0.4013 (mt) REVERT: C 4726 MET cc_start: 0.8393 (mmm) cc_final: 0.7688 (tpt) REVERT: C 4804 MET cc_start: 0.8029 (mmm) cc_final: 0.7767 (mmm) REVERT: C 4817 MET cc_start: 0.8653 (mmm) cc_final: 0.8406 (mmm) REVERT: D 1249 MET cc_start: 0.8268 (tpp) cc_final: 0.8012 (tpp) REVERT: D 1487 MET cc_start: 0.8448 (mtt) cc_final: 0.8125 (mtp) REVERT: D 1975 MET cc_start: 0.7937 (mtm) cc_final: 0.7661 (mtm) REVERT: D 2214 MET cc_start: 0.8916 (tpp) cc_final: 0.8623 (mmm) REVERT: D 2456 MET cc_start: 0.8695 (mmm) cc_final: 0.8324 (tpp) REVERT: D 2580 LEU cc_start: 0.8502 (tp) cc_final: 0.8138 (tp) REVERT: D 2607 LEU cc_start: 0.9102 (mt) cc_final: 0.8603 (tp) REVERT: D 2652 LEU cc_start: 0.9263 (tp) cc_final: 0.8892 (tp) REVERT: D 2719 TYR cc_start: 0.8591 (t80) cc_final: 0.8241 (t80) REVERT: D 2773 TRP cc_start: 0.8339 (m100) cc_final: 0.7955 (m100) REVERT: D 2840 MET cc_start: 0.7938 (mmt) cc_final: 0.7605 (mmt) REVERT: D 2843 MET cc_start: 0.8758 (ptp) cc_final: 0.8231 (ptm) REVERT: D 2847 ASN cc_start: 0.9081 (t0) cc_final: 0.8668 (m110) REVERT: D 2939 TYR cc_start: 0.9019 (m-10) cc_final: 0.8819 (m-80) REVERT: D 2982 PHE cc_start: 0.8907 (m-80) cc_final: 0.8415 (m-80) REVERT: D 3605 MET cc_start: 0.5206 (mmp) cc_final: 0.4955 (mmm) REVERT: D 3739 MET cc_start: 0.8952 (ttp) cc_final: 0.8711 (ttp) REVERT: D 3954 MET cc_start: 0.8739 (mmm) cc_final: 0.7997 (tpp) REVERT: D 4258 MET cc_start: 0.2509 (ptt) cc_final: 0.2257 (mtt) REVERT: D 4306 PHE cc_start: 0.7849 (m-10) cc_final: 0.7412 (t80) REVERT: D 4728 MET cc_start: 0.8561 (mmm) cc_final: 0.8332 (mmt) REVERT: D 4817 MET cc_start: 0.8656 (mmm) cc_final: 0.8378 (mmm) outliers start: 90 outliers final: 48 residues processed: 790 average time/residue: 1.1290 time to fit residues: 1581.5172 Evaluate side-chains 762 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 709 time to evaluate : 11.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 3702 GLU Chi-restraints excluded: chain A residue 4666 ILE Chi-restraints excluded: chain A residue 4752 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2720 PHE Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2843 MET Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3702 GLU Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4666 ILE Chi-restraints excluded: chain B residue 4718 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1644 LEU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2777 GLU Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2927 GLN Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3702 GLU Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4666 ILE Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 3077 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 533 optimal weight: 7.9990 chunk 1427 optimal weight: 6.9990 chunk 313 optimal weight: 1.9990 chunk 930 optimal weight: 10.0000 chunk 391 optimal weight: 5.9990 chunk 1586 optimal weight: 5.9990 chunk 1317 optimal weight: 0.7980 chunk 734 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 524 optimal weight: 20.0000 chunk 833 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2158 HIS ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2927 GLN ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2158 HIS ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2158 HIS ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 134536 Z= 0.297 Angle : 0.616 16.096 181752 Z= 0.313 Chirality : 0.040 0.232 19884 Planarity : 0.004 0.128 23364 Dihedral : 5.933 88.602 18083 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Rotamer: Outliers : 0.68 % Allowed : 8.12 % Favored : 91.20 % 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: 1.02 (0.07), residues: 16332 helix: 1.81 (0.06), residues: 8556 sheet: -0.40 (0.12), residues: 1800 loop : -0.60 (0.08), residues: 5976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 893 HIS 0.007 0.001 HIS C1656 PHE 0.031 0.002 PHE C1942 TYR 0.060 0.002 TYR C2939 ARG 0.007 0.001 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 725 time to evaluate : 11.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.7920 (mmm) cc_final: 0.7266 (mmm) REVERT: A 778 MET cc_start: 0.8655 (ptm) cc_final: 0.8391 (ptp) REVERT: A 986 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5131 (pt) REVERT: A 1113 MET cc_start: 0.7905 (mtt) cc_final: 0.7657 (mtm) REVERT: A 1975 MET cc_start: 0.8145 (mtm) cc_final: 0.7668 (mtm) REVERT: A 2389 MET cc_start: 0.8472 (mtp) cc_final: 0.8221 (mtm) REVERT: A 2652 LEU cc_start: 0.9081 (tp) cc_final: 0.8628 (tp) REVERT: A 2669 LEU cc_start: 0.9606 (mt) cc_final: 0.9362 (mt) REVERT: A 2681 MET cc_start: 0.8411 (mmp) cc_final: 0.8090 (mmp) REVERT: A 2719 TYR cc_start: 0.8705 (t80) cc_final: 0.8228 (t80) REVERT: A 2720 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: A 2843 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8291 (mmm) REVERT: A 2847 ASN cc_start: 0.8908 (t0) cc_final: 0.8566 (m110) REVERT: A 2897 GLN cc_start: 0.9166 (pt0) cc_final: 0.8921 (pp30) REVERT: A 3954 MET cc_start: 0.8740 (mmm) cc_final: 0.8071 (tpp) REVERT: A 3981 MET cc_start: 0.8863 (tmm) cc_final: 0.8617 (ttp) REVERT: A 3985 MET cc_start: 0.9143 (mmm) cc_final: 0.8919 (tpp) REVERT: A 4292 MET cc_start: 0.8564 (tpp) cc_final: 0.8152 (mpp) REVERT: A 4804 MET cc_start: 0.8107 (mmm) cc_final: 0.7775 (mmm) REVERT: A 4817 MET cc_start: 0.8756 (tpt) cc_final: 0.8382 (mmm) REVERT: A 4943 MET cc_start: 0.8685 (mtt) cc_final: 0.8227 (mtp) REVERT: F 58 LYS cc_start: 0.9140 (ttmt) cc_final: 0.8872 (mtpp) REVERT: B 317 MET cc_start: 0.8476 (ptt) cc_final: 0.8195 (ptm) REVERT: B 393 MET cc_start: 0.7451 (mmm) cc_final: 0.6964 (mmm) REVERT: B 1050 LEU cc_start: 0.9434 (tp) cc_final: 0.9221 (tt) REVERT: B 1975 MET cc_start: 0.8038 (mtm) cc_final: 0.7592 (mtm) REVERT: B 2652 LEU cc_start: 0.9238 (tp) cc_final: 0.8805 (tp) REVERT: B 2681 MET cc_start: 0.8304 (mmp) cc_final: 0.7905 (mmp) REVERT: B 2695 MET cc_start: 0.8496 (ptm) cc_final: 0.8267 (ppp) REVERT: B 2719 TYR cc_start: 0.8935 (t80) cc_final: 0.8518 (t80) REVERT: B 2773 TRP cc_start: 0.8734 (m100) cc_final: 0.8492 (m100) REVERT: B 2847 ASN cc_start: 0.9069 (t0) cc_final: 0.8818 (m110) REVERT: B 2877 LEU cc_start: 0.8775 (tp) cc_final: 0.8531 (tp) REVERT: B 2886 ARG cc_start: 0.8910 (ptm160) cc_final: 0.8361 (mpp80) REVERT: B 3739 MET cc_start: 0.8937 (ttp) cc_final: 0.8682 (ttp) REVERT: B 3954 MET cc_start: 0.8735 (mmm) cc_final: 0.8212 (tpp) REVERT: B 4019 MET cc_start: 0.8199 (mtt) cc_final: 0.7933 (mtm) REVERT: B 4726 MET cc_start: 0.8327 (mmm) cc_final: 0.7608 (tpt) REVERT: B 4728 MET cc_start: 0.8555 (mmm) cc_final: 0.8343 (mmp) REVERT: B 4804 MET cc_start: 0.7900 (mmm) cc_final: 0.7623 (mmm) REVERT: C 309 MET cc_start: 0.7728 (mmm) cc_final: 0.7426 (mmp) REVERT: C 393 MET cc_start: 0.7466 (mmm) cc_final: 0.7040 (mmm) REVERT: C 395 HIS cc_start: 0.9095 (t-90) cc_final: 0.8887 (t-90) REVERT: C 921 PHE cc_start: 0.8462 (m-80) cc_final: 0.8248 (m-10) REVERT: C 1103 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7123 (t80) REVERT: C 1487 MET cc_start: 0.8493 (mtt) cc_final: 0.8126 (mtp) REVERT: C 1906 MET cc_start: 0.8397 (mmm) cc_final: 0.8189 (mmm) REVERT: C 1975 MET cc_start: 0.7944 (mtm) cc_final: 0.7538 (mtm) REVERT: C 2580 LEU cc_start: 0.8956 (tp) cc_final: 0.8484 (tp) REVERT: C 2584 MET cc_start: 0.8457 (mmp) cc_final: 0.8096 (mmm) REVERT: C 2652 LEU cc_start: 0.9208 (mt) cc_final: 0.8792 (tp) REVERT: C 2681 MET cc_start: 0.8188 (mmp) cc_final: 0.7632 (mmp) REVERT: C 2719 TYR cc_start: 0.8880 (t80) cc_final: 0.8570 (t80) REVERT: C 2720 PHE cc_start: 0.8372 (m-80) cc_final: 0.7868 (m-10) REVERT: C 2848 TYR cc_start: 0.8574 (m-80) cc_final: 0.8244 (m-80) REVERT: C 2886 ARG cc_start: 0.8732 (mpp80) cc_final: 0.8384 (mpp80) REVERT: C 3605 MET cc_start: 0.4667 (mmm) cc_final: 0.4409 (mmm) REVERT: C 3954 MET cc_start: 0.8759 (mmm) cc_final: 0.8091 (tpp) REVERT: C 3981 MET cc_start: 0.8839 (tmm) cc_final: 0.8173 (ttp) REVERT: C 4292 MET cc_start: 0.8419 (mmt) cc_final: 0.7909 (mpp) REVERT: C 4520 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: C 4555 ILE cc_start: 0.4432 (OUTLIER) cc_final: 0.3970 (mt) REVERT: C 4728 MET cc_start: 0.8587 (mmm) cc_final: 0.8358 (mmp) REVERT: C 4804 MET cc_start: 0.7987 (mmm) cc_final: 0.7719 (mmm) REVERT: C 4817 MET cc_start: 0.8687 (mmm) cc_final: 0.8415 (mmm) REVERT: D 393 MET cc_start: 0.7274 (mmm) cc_final: 0.6884 (mmm) REVERT: D 778 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8408 (ptm) REVERT: D 1113 MET cc_start: 0.7919 (mtt) cc_final: 0.7681 (mtm) REVERT: D 1249 MET cc_start: 0.8161 (tpp) cc_final: 0.7898 (tpp) REVERT: D 1487 MET cc_start: 0.8469 (mtt) cc_final: 0.8111 (mtp) REVERT: D 1906 MET cc_start: 0.8426 (mmm) cc_final: 0.8214 (mmm) REVERT: D 1975 MET cc_start: 0.7947 (mtm) cc_final: 0.7697 (mtm) REVERT: D 2214 MET cc_start: 0.8903 (tpp) cc_final: 0.8622 (mmm) REVERT: D 2580 LEU cc_start: 0.8604 (tp) cc_final: 0.8236 (tp) REVERT: D 2607 LEU cc_start: 0.9117 (mt) cc_final: 0.8633 (tp) REVERT: D 2652 LEU cc_start: 0.9249 (tp) cc_final: 0.8895 (tp) REVERT: D 2719 TYR cc_start: 0.8629 (t80) cc_final: 0.8345 (t80) REVERT: D 2720 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8379 (m-10) REVERT: D 2773 TRP cc_start: 0.8356 (m100) cc_final: 0.7987 (m100) REVERT: D 2843 MET cc_start: 0.8789 (ptp) cc_final: 0.8243 (ptm) REVERT: D 2847 ASN cc_start: 0.9026 (t0) cc_final: 0.8586 (m110) REVERT: D 2848 TYR cc_start: 0.8165 (m-80) cc_final: 0.7900 (m-80) REVERT: D 2939 TYR cc_start: 0.9034 (m-10) cc_final: 0.8831 (m-80) REVERT: D 2982 PHE cc_start: 0.8902 (m-80) cc_final: 0.8405 (m-80) REVERT: D 3605 MET cc_start: 0.5165 (mmp) cc_final: 0.4880 (mmm) REVERT: D 3739 MET cc_start: 0.8947 (ttp) cc_final: 0.8743 (ttt) REVERT: D 3978 MET cc_start: 0.8934 (ttp) cc_final: 0.8660 (ttt) REVERT: D 4139 MET cc_start: 0.8452 (tpt) cc_final: 0.8112 (tpp) REVERT: D 4258 MET cc_start: 0.2328 (ptt) cc_final: 0.2078 (mtt) REVERT: D 4306 PHE cc_start: 0.7882 (m-10) cc_final: 0.7436 (t80) REVERT: D 4728 MET cc_start: 0.8558 (mmm) cc_final: 0.8341 (mmt) REVERT: D 4814 MET cc_start: 0.8054 (tpp) cc_final: 0.7753 (mmm) REVERT: D 4817 MET cc_start: 0.8647 (mmm) cc_final: 0.8365 (mmm) outliers start: 98 outliers final: 58 residues processed: 797 average time/residue: 1.1455 time to fit residues: 1628.0027 Evaluate side-chains 781 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 715 time to evaluate : 11.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2720 PHE Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 4666 ILE Chi-restraints excluded: chain A residue 4752 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1644 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3702 GLU Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4666 ILE Chi-restraints excluded: chain B residue 4718 SER Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1644 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3702 GLU Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4666 ILE Chi-restraints excluded: chain C residue 4718 SER Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2720 PHE Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 2914 THR Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 4752 THR Chi-restraints excluded: chain D residue 4870 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1529 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 904 optimal weight: 6.9990 chunk 1158 optimal weight: 3.9990 chunk 897 optimal weight: 3.9990 chunk 1335 optimal weight: 8.9990 chunk 886 optimal weight: 10.0000 chunk 1580 optimal weight: 8.9990 chunk 989 optimal weight: 10.0000 chunk 963 optimal weight: 0.0270 chunk 729 optimal weight: 7.9990 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2867 ASN C2927 GLN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2847 ASN ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 134536 Z= 0.226 Angle : 0.601 16.109 181752 Z= 0.304 Chirality : 0.039 0.232 19884 Planarity : 0.004 0.128 23364 Dihedral : 5.829 89.757 18083 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 0.63 % Allowed : 8.44 % Favored : 90.93 % 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: 1.10 (0.07), residues: 16332 helix: 1.87 (0.06), residues: 8556 sheet: -0.36 (0.12), residues: 1808 loop : -0.56 (0.08), residues: 5968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 893 HIS 0.010 0.001 HIS B 890 PHE 0.029 0.001 PHE C4870 TYR 0.057 0.001 TYR C2939 ARG 0.006 0.000 ARG D1051 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 710 time to evaluate : 11.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.7924 (mmm) cc_final: 0.7276 (mmm) REVERT: A 935 MET cc_start: 0.9406 (ppp) cc_final: 0.9204 (ppp) REVERT: A 1113 MET cc_start: 0.7859 (mtt) cc_final: 0.7606 (mtm) REVERT: A 1975 MET cc_start: 0.8131 (mtm) cc_final: 0.7657 (mtm) REVERT: A 2652 LEU cc_start: 0.9077 (tp) cc_final: 0.8624 (tp) REVERT: A 2681 MET cc_start: 0.8393 (mmp) cc_final: 0.8049 (mmp) REVERT: A 2719 TYR cc_start: 0.8699 (t80) cc_final: 0.8272 (t80) REVERT: A 2720 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: A 2840 MET cc_start: 0.8560 (mmt) cc_final: 0.8345 (mmt) REVERT: A 2843 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8311 (mmm) REVERT: A 2847 ASN cc_start: 0.8893 (t0) cc_final: 0.8555 (m-40) REVERT: A 3954 MET cc_start: 0.8733 (mmm) cc_final: 0.8039 (tpp) REVERT: A 3981 MET cc_start: 0.8869 (tmm) cc_final: 0.8561 (ttp) REVERT: A 4139 MET cc_start: 0.8608 (tpt) cc_final: 0.8309 (tpp) REVERT: A 4292 MET cc_start: 0.8555 (tpp) cc_final: 0.8128 (mpp) REVERT: A 4804 MET cc_start: 0.8130 (mmm) cc_final: 0.7786 (mmm) REVERT: A 4817 MET cc_start: 0.8736 (tpt) cc_final: 0.8379 (mmm) REVERT: A 4943 MET cc_start: 0.8663 (mtt) cc_final: 0.8347 (mtt) REVERT: F 58 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8854 (mtpp) REVERT: H 108 GLU cc_start: 0.8315 (pm20) cc_final: 0.8086 (pm20) REVERT: B 393 MET cc_start: 0.7472 (mmm) cc_final: 0.7052 (mmm) REVERT: B 594 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9164 (mt) REVERT: B 1050 LEU cc_start: 0.9424 (tp) cc_final: 0.9207 (tt) REVERT: B 1113 MET cc_start: 0.7774 (mtt) cc_final: 0.7525 (mtm) REVERT: B 1564 MET cc_start: 0.8549 (mmm) cc_final: 0.8341 (mmm) REVERT: B 1975 MET cc_start: 0.8047 (mtm) cc_final: 0.7615 (mtm) REVERT: B 2652 LEU cc_start: 0.9234 (tp) cc_final: 0.8787 (tp) REVERT: B 2681 MET cc_start: 0.8243 (mmp) cc_final: 0.7838 (mmp) REVERT: B 2695 MET cc_start: 0.8471 (ptm) cc_final: 0.8232 (ppp) REVERT: B 2719 TYR cc_start: 0.8933 (t80) cc_final: 0.8558 (t80) REVERT: B 2720 PHE cc_start: 0.8260 (m-80) cc_final: 0.7719 (m-80) REVERT: B 2773 TRP cc_start: 0.8731 (m100) cc_final: 0.8468 (m100) REVERT: B 2840 MET cc_start: 0.8987 (mmt) cc_final: 0.8767 (mmt) REVERT: B 2847 ASN cc_start: 0.9044 (t0) cc_final: 0.8794 (m110) REVERT: B 2877 LEU cc_start: 0.8781 (tp) cc_final: 0.8522 (tp) REVERT: B 2886 ARG cc_start: 0.8925 (ptm160) cc_final: 0.8452 (mpp80) REVERT: B 3689 MET cc_start: 0.8139 (mpp) cc_final: 0.7841 (mpp) REVERT: B 3954 MET cc_start: 0.8700 (mmm) cc_final: 0.8191 (tpp) REVERT: B 4019 MET cc_start: 0.8188 (mtt) cc_final: 0.7922 (mtm) REVERT: B 4520 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: B 4726 MET cc_start: 0.8318 (mmm) cc_final: 0.7977 (tpt) REVERT: B 4728 MET cc_start: 0.8540 (mmm) cc_final: 0.8339 (mmp) REVERT: B 4804 MET cc_start: 0.7909 (mmm) cc_final: 0.7631 (mmm) REVERT: C 395 HIS cc_start: 0.9088 (t-90) cc_final: 0.8885 (t-90) REVERT: C 594 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9166 (mt) REVERT: C 1103 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7125 (t80) REVERT: C 1487 MET cc_start: 0.8476 (mtt) cc_final: 0.8106 (mtp) REVERT: C 1896 MET cc_start: 0.8554 (ttt) cc_final: 0.8354 (ttp) REVERT: C 1906 MET cc_start: 0.8361 (mmm) cc_final: 0.8151 (mmm) REVERT: C 1975 MET cc_start: 0.7931 (mtm) cc_final: 0.7530 (mtm) REVERT: C 2142 MET cc_start: 0.8592 (mmp) cc_final: 0.8271 (mmp) REVERT: C 2192 MET cc_start: 0.8631 (tpp) cc_final: 0.8420 (tpp) REVERT: C 2584 MET cc_start: 0.8427 (mmp) cc_final: 0.8134 (mmm) REVERT: C 2652 LEU cc_start: 0.9192 (mt) cc_final: 0.8752 (tp) REVERT: C 2681 MET cc_start: 0.8168 (mmp) cc_final: 0.7625 (mmp) REVERT: C 2719 TYR cc_start: 0.8865 (t80) cc_final: 0.8566 (t80) REVERT: C 2720 PHE cc_start: 0.8308 (m-80) cc_final: 0.7881 (m-80) REVERT: C 2773 TRP cc_start: 0.8522 (m100) cc_final: 0.8215 (m100) REVERT: C 2840 MET cc_start: 0.8600 (mmt) cc_final: 0.8369 (mmt) REVERT: C 2848 TYR cc_start: 0.8528 (m-80) cc_final: 0.8322 (m-80) REVERT: C 2886 ARG cc_start: 0.8736 (mpp80) cc_final: 0.8371 (mpp80) REVERT: C 3605 MET cc_start: 0.4951 (mmm) cc_final: 0.4717 (mmm) REVERT: C 3954 MET cc_start: 0.8748 (mmm) cc_final: 0.8054 (tpp) REVERT: C 3981 MET cc_start: 0.8822 (tmm) cc_final: 0.8140 (ttp) REVERT: C 4139 MET cc_start: 0.8529 (tpt) cc_final: 0.8184 (tpp) REVERT: C 4292 MET cc_start: 0.8442 (mmt) cc_final: 0.7929 (mpp) REVERT: C 4555 ILE cc_start: 0.4409 (OUTLIER) cc_final: 0.3935 (mt) REVERT: C 4728 MET cc_start: 0.8602 (mmm) cc_final: 0.8390 (mmp) REVERT: C 4804 MET cc_start: 0.8018 (mmm) cc_final: 0.7739 (mmm) REVERT: C 4817 MET cc_start: 0.8690 (mmm) cc_final: 0.8386 (mmm) REVERT: D 393 MET cc_start: 0.7314 (mmm) cc_final: 0.6960 (mmm) REVERT: D 594 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9182 (mt) REVERT: D 778 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8381 (ptm) REVERT: D 1487 MET cc_start: 0.8451 (mtt) cc_final: 0.8084 (mtp) REVERT: D 1906 MET cc_start: 0.8370 (mmm) cc_final: 0.8146 (mmm) REVERT: D 1975 MET cc_start: 0.7936 (mtm) cc_final: 0.7509 (mtm) REVERT: D 2580 LEU cc_start: 0.8629 (tp) cc_final: 0.8247 (tp) REVERT: D 2607 LEU cc_start: 0.9103 (mt) cc_final: 0.8619 (tp) REVERT: D 2652 LEU cc_start: 0.9237 (tp) cc_final: 0.8869 (tp) REVERT: D 2681 MET cc_start: 0.7686 (mmp) cc_final: 0.7256 (mmp) REVERT: D 2719 TYR cc_start: 0.8625 (t80) cc_final: 0.8357 (t80) REVERT: D 2720 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: D 2773 TRP cc_start: 0.8346 (m100) cc_final: 0.7980 (m100) REVERT: D 2840 MET cc_start: 0.7804 (mmt) cc_final: 0.7475 (mmt) REVERT: D 2843 MET cc_start: 0.8731 (ptp) cc_final: 0.8242 (ptm) REVERT: D 2847 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8470 (m110) REVERT: D 2848 TYR cc_start: 0.8093 (m-80) cc_final: 0.7819 (m-80) REVERT: D 2939 TYR cc_start: 0.9013 (m-10) cc_final: 0.8801 (m-80) REVERT: D 2982 PHE cc_start: 0.8884 (m-80) cc_final: 0.8383 (m-80) REVERT: D 3003 MET cc_start: 0.9228 (pmm) cc_final: 0.8791 (pmm) REVERT: D 3605 MET cc_start: 0.5145 (mmp) cc_final: 0.4880 (mmm) REVERT: D 3954 MET cc_start: 0.8883 (tpp) cc_final: 0.8248 (tpp) REVERT: D 3978 MET cc_start: 0.8924 (ttp) cc_final: 0.8672 (ttt) REVERT: D 4139 MET cc_start: 0.8447 (tpt) cc_final: 0.8116 (tpp) REVERT: D 4258 MET cc_start: 0.2288 (ptt) cc_final: 0.2052 (mtt) REVERT: D 4306 PHE cc_start: 0.7843 (m-10) cc_final: 0.7397 (t80) REVERT: D 4728 MET cc_start: 0.8555 (mmm) cc_final: 0.8340 (mmt) REVERT: D 4814 MET cc_start: 0.8046 (tpp) cc_final: 0.7732 (mmm) REVERT: D 4817 MET cc_start: 0.8632 (mmm) cc_final: 0.8368 (mmm) outliers start: 91 outliers final: 63 residues processed: 781 average time/residue: 1.1255 time to fit residues: 1559.6047 Evaluate side-chains 779 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 705 time to evaluate : 11.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2720 PHE Chi-restraints excluded: chain A residue 2724 TYR Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 4666 ILE Chi-restraints excluded: chain A residue 4752 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 1051 ARG Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2843 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3702 GLU Chi-restraints excluded: chain B residue 4520 TYR Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4666 ILE Chi-restraints excluded: chain B residue 4718 SER Chi-restraints excluded: chain B residue 4861 ILE Chi-restraints excluded: chain B residue 4870 PHE Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 1051 ARG Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3702 GLU Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4666 ILE Chi-restraints excluded: chain C residue 4861 ILE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1051 ARG Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2720 PHE Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2847 ASN Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 2914 THR Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 4752 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 977 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 944 optimal weight: 9.9990 chunk 476 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 1004 optimal weight: 4.9990 chunk 1076 optimal weight: 9.9990 chunk 781 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 1242 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 836 HIS ** D 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 134536 Z= 0.329 Angle : 0.632 16.752 181752 Z= 0.321 Chirality : 0.040 0.285 19884 Planarity : 0.005 0.127 23364 Dihedral : 5.794 89.804 18083 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.32 % Favored : 96.58 % Rotamer: Outliers : 0.62 % Allowed : 8.66 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.07), residues: 16332 helix: 1.87 (0.06), residues: 8544 sheet: -0.39 (0.12), residues: 1808 loop : -0.56 (0.08), residues: 5980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 893 HIS 0.010 0.001 HIS B 890 PHE 0.032 0.002 PHE C4870 TYR 0.054 0.002 TYR C2939 ARG 0.010 0.001 ARG A2530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 711 time to evaluate : 11.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9181 (mt) REVERT: A 655 MET cc_start: 0.8728 (mmm) cc_final: 0.8196 (mmp) REVERT: A 890 HIS cc_start: 0.9275 (OUTLIER) cc_final: 0.8839 (p-80) REVERT: A 935 MET cc_start: 0.9391 (ppp) cc_final: 0.9189 (ppp) REVERT: A 986 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.5315 (pt) REVERT: A 1564 MET cc_start: 0.8532 (mmm) cc_final: 0.8312 (mmm) REVERT: A 1975 MET cc_start: 0.8162 (mtm) cc_final: 0.7683 (mtm) REVERT: A 2389 MET cc_start: 0.8537 (mtp) cc_final: 0.8316 (mtm) REVERT: A 2652 LEU cc_start: 0.9103 (tp) cc_final: 0.8661 (tp) REVERT: A 2681 MET cc_start: 0.8451 (mmp) cc_final: 0.8111 (mmp) REVERT: A 2719 TYR cc_start: 0.8744 (t80) cc_final: 0.8363 (t80) REVERT: A 2720 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: A 2777 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8708 (mm-30) REVERT: A 2843 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8291 (mmm) REVERT: A 2847 ASN cc_start: 0.8910 (t0) cc_final: 0.8558 (m-40) REVERT: A 3954 MET cc_start: 0.8736 (mmm) cc_final: 0.8047 (tpp) REVERT: A 3981 MET cc_start: 0.8846 (tmm) cc_final: 0.8603 (ttp) REVERT: A 4053 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8583 (mm-30) REVERT: A 4292 MET cc_start: 0.8589 (tpp) cc_final: 0.8157 (mpp) REVERT: A 4804 MET cc_start: 0.8137 (mmm) cc_final: 0.7929 (mmm) REVERT: A 4817 MET cc_start: 0.8790 (tpt) cc_final: 0.8419 (mmm) REVERT: A 4943 MET cc_start: 0.8679 (mtt) cc_final: 0.8414 (mtt) REVERT: E 58 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8865 (mtpp) REVERT: F 58 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8854 (mtpp) REVERT: H 108 GLU cc_start: 0.8261 (pm20) cc_final: 0.7975 (pm20) REVERT: B 393 MET cc_start: 0.7499 (mmm) cc_final: 0.7082 (mmm) REVERT: B 594 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9190 (mt) REVERT: B 890 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.8255 (p-80) REVERT: B 1050 LEU cc_start: 0.9442 (tp) cc_final: 0.9237 (tt) REVERT: B 1113 MET cc_start: 0.7899 (mtt) cc_final: 0.7641 (mtm) REVERT: B 1975 MET cc_start: 0.8037 (mtm) cc_final: 0.7583 (mtm) REVERT: B 2456 MET cc_start: 0.8702 (mmm) cc_final: 0.8364 (tpp) REVERT: B 2652 LEU cc_start: 0.9249 (tp) cc_final: 0.8807 (tp) REVERT: B 2681 MET cc_start: 0.8313 (mmp) cc_final: 0.7919 (mmp) REVERT: B 2695 MET cc_start: 0.8469 (ptm) cc_final: 0.8244 (ppp) REVERT: B 2719 TYR cc_start: 0.8953 (t80) cc_final: 0.8538 (t80) REVERT: B 2720 PHE cc_start: 0.8337 (m-80) cc_final: 0.7759 (m-80) REVERT: B 2840 MET cc_start: 0.8980 (mmt) cc_final: 0.8703 (mmt) REVERT: B 2847 ASN cc_start: 0.9056 (t0) cc_final: 0.8812 (m110) REVERT: B 2877 LEU cc_start: 0.8783 (tp) cc_final: 0.8513 (tp) REVERT: B 2886 ARG cc_start: 0.8939 (ptm160) cc_final: 0.8486 (mpp80) REVERT: B 3739 MET cc_start: 0.8930 (ttp) cc_final: 0.8662 (ttt) REVERT: B 3954 MET cc_start: 0.8685 (mmm) cc_final: 0.8180 (tpp) REVERT: B 4019 MET cc_start: 0.8189 (mtt) cc_final: 0.7932 (mtm) REVERT: B 4520 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7621 (m-10) REVERT: B 4726 MET cc_start: 0.8385 (mmm) cc_final: 0.8029 (tpt) REVERT: B 4728 MET cc_start: 0.8550 (mmm) cc_final: 0.8339 (mmp) REVERT: B 4804 MET cc_start: 0.7896 (mmm) cc_final: 0.7620 (mmm) REVERT: C 395 HIS cc_start: 0.9097 (t-90) cc_final: 0.8893 (t-90) REVERT: C 594 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9196 (mt) REVERT: C 890 HIS cc_start: 0.9263 (OUTLIER) cc_final: 0.8836 (p-80) REVERT: C 1103 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7136 (t80) REVERT: C 1113 MET cc_start: 0.7852 (mtt) cc_final: 0.7578 (mtm) REVERT: C 1487 MET cc_start: 0.8507 (mtt) cc_final: 0.8143 (mtp) REVERT: C 1906 MET cc_start: 0.8436 (mmm) cc_final: 0.8204 (mmm) REVERT: C 1975 MET cc_start: 0.7950 (mtm) cc_final: 0.7527 (mtm) REVERT: C 2142 MET cc_start: 0.8692 (mmp) cc_final: 0.8354 (mmp) REVERT: C 2192 MET cc_start: 0.8506 (tpp) cc_final: 0.8083 (tpp) REVERT: C 2584 MET cc_start: 0.8509 (mmp) cc_final: 0.8199 (mmm) REVERT: C 2652 LEU cc_start: 0.9201 (mt) cc_final: 0.8739 (tp) REVERT: C 2681 MET cc_start: 0.8222 (mmp) cc_final: 0.7670 (mmp) REVERT: C 2719 TYR cc_start: 0.8891 (t80) cc_final: 0.8606 (t80) REVERT: C 2720 PHE cc_start: 0.8367 (m-80) cc_final: 0.7958 (m-80) REVERT: C 2773 TRP cc_start: 0.8542 (m100) cc_final: 0.8173 (m100) REVERT: C 2840 MET cc_start: 0.8614 (mmt) cc_final: 0.8381 (mmt) REVERT: C 2848 TYR cc_start: 0.8503 (m-80) cc_final: 0.8239 (m-80) REVERT: C 2858 MET cc_start: 0.8453 (ptp) cc_final: 0.8244 (ppp) REVERT: C 2886 ARG cc_start: 0.8737 (mpp80) cc_final: 0.8377 (mpp80) REVERT: C 3954 MET cc_start: 0.8751 (mmm) cc_final: 0.8037 (tpp) REVERT: C 3981 MET cc_start: 0.8841 (tmm) cc_final: 0.8170 (ttp) REVERT: C 4053 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: C 4139 MET cc_start: 0.8521 (tpt) cc_final: 0.8184 (tpp) REVERT: C 4555 ILE cc_start: 0.4321 (OUTLIER) cc_final: 0.3841 (mt) REVERT: C 4728 MET cc_start: 0.8614 (mmm) cc_final: 0.8398 (mmp) REVERT: C 4804 MET cc_start: 0.8011 (mmm) cc_final: 0.7745 (mmm) REVERT: C 4817 MET cc_start: 0.8710 (mmm) cc_final: 0.8418 (mmm) REVERT: D 393 MET cc_start: 0.7371 (mmm) cc_final: 0.7033 (mmm) REVERT: D 594 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9216 (mt) REVERT: D 778 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8406 (ptm) REVERT: D 1487 MET cc_start: 0.8478 (mtt) cc_final: 0.8118 (mtp) REVERT: D 1906 MET cc_start: 0.8448 (mmm) cc_final: 0.8208 (mmm) REVERT: D 2580 LEU cc_start: 0.8714 (tp) cc_final: 0.8340 (tp) REVERT: D 2607 LEU cc_start: 0.9123 (mt) cc_final: 0.8636 (tp) REVERT: D 2652 LEU cc_start: 0.9243 (tp) cc_final: 0.8887 (tp) REVERT: D 2681 MET cc_start: 0.7711 (mmp) cc_final: 0.7252 (mmp) REVERT: D 2719 TYR cc_start: 0.8623 (t80) cc_final: 0.8379 (t80) REVERT: D 2720 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8305 (m-10) REVERT: D 2840 MET cc_start: 0.7876 (mmt) cc_final: 0.7504 (mmt) REVERT: D 2843 MET cc_start: 0.8739 (ptp) cc_final: 0.8362 (ptm) REVERT: D 2848 TYR cc_start: 0.8114 (m-80) cc_final: 0.7881 (m-80) REVERT: D 2939 TYR cc_start: 0.9007 (m-10) cc_final: 0.8805 (m-80) REVERT: D 2982 PHE cc_start: 0.8911 (m-80) cc_final: 0.8438 (m-80) REVERT: D 3003 MET cc_start: 0.9250 (pmm) cc_final: 0.8860 (pmm) REVERT: D 3605 MET cc_start: 0.5171 (mmp) cc_final: 0.4897 (mmm) REVERT: D 3739 MET cc_start: 0.8944 (ttp) cc_final: 0.8679 (ttt) REVERT: D 3978 MET cc_start: 0.8906 (ttp) cc_final: 0.8654 (ttt) REVERT: D 4139 MET cc_start: 0.8484 (tpt) cc_final: 0.8138 (tpp) REVERT: D 4306 PHE cc_start: 0.7886 (m-10) cc_final: 0.7426 (t80) REVERT: D 4726 MET cc_start: 0.8396 (tpp) cc_final: 0.7994 (tpp) REVERT: D 4728 MET cc_start: 0.8551 (mmm) cc_final: 0.8341 (mmt) REVERT: D 4814 MET cc_start: 0.8075 (tpp) cc_final: 0.7733 (mpp) REVERT: D 4817 MET cc_start: 0.8644 (mmm) cc_final: 0.8348 (mmm) outliers start: 90 outliers final: 61 residues processed: 781 average time/residue: 1.1151 time to fit residues: 1550.7363 Evaluate side-chains 786 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 707 time to evaluate : 13.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1051 ARG Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2720 PHE Chi-restraints excluded: chain A residue 2724 TYR Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 4053 GLU Chi-restraints excluded: chain A residue 4666 ILE Chi-restraints excluded: chain A residue 4752 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2843 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3702 GLU Chi-restraints excluded: chain B residue 4520 TYR Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4666 ILE Chi-restraints excluded: chain B residue 4718 SER Chi-restraints excluded: chain B residue 4752 THR Chi-restraints excluded: chain B residue 4861 ILE Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3702 GLU Chi-restraints excluded: chain C residue 4053 GLU Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4666 ILE Chi-restraints excluded: chain C residue 4718 SER Chi-restraints excluded: chain C residue 4861 ILE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1051 ARG Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2720 PHE Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 2914 THR Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 4752 THR Chi-restraints excluded: chain D residue 4870 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1437 optimal weight: 2.9990 chunk 1514 optimal weight: 20.0000 chunk 1381 optimal weight: 7.9990 chunk 1473 optimal weight: 20.0000 chunk 1513 optimal weight: 3.9990 chunk 886 optimal weight: 9.9990 chunk 641 optimal weight: 2.9990 chunk 1156 optimal weight: 5.9990 chunk 452 optimal weight: 8.9990 chunk 1331 optimal weight: 0.0970 chunk 1393 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2867 ASN B3931 ASN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 134536 Z= 0.236 Angle : 0.608 17.273 181752 Z= 0.307 Chirality : 0.039 0.299 19884 Planarity : 0.004 0.127 23364 Dihedral : 5.681 89.448 18083 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 0.67 % Allowed : 8.69 % Favored : 90.63 % 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: 1.16 (0.07), residues: 16332 helix: 1.92 (0.06), residues: 8552 sheet: -0.35 (0.12), residues: 1816 loop : -0.52 (0.08), residues: 5964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 893 HIS 0.007 0.001 HIS C3700 PHE 0.032 0.001 PHE C4870 TYR 0.052 0.001 TYR C2939 ARG 0.006 0.000 ARG B1960 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 706 time to evaluate : 14.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 MET cc_start: 0.8691 (mmm) cc_final: 0.8197 (mmp) REVERT: A 890 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.8820 (p-80) REVERT: A 986 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5310 (pt) REVERT: A 1113 MET cc_start: 0.7833 (mtt) cc_final: 0.7566 (mtm) REVERT: A 1564 MET cc_start: 0.8516 (mmm) cc_final: 0.8301 (mmm) REVERT: A 1975 MET cc_start: 0.8076 (mtm) cc_final: 0.7605 (mtm) REVERT: A 2389 MET cc_start: 0.8516 (mtp) cc_final: 0.8298 (mtm) REVERT: A 2652 LEU cc_start: 0.9091 (tp) cc_final: 0.8634 (tp) REVERT: A 2681 MET cc_start: 0.8415 (mmp) cc_final: 0.8072 (mmp) REVERT: A 2719 TYR cc_start: 0.8698 (t80) cc_final: 0.8338 (t80) REVERT: A 2720 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: A 2777 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8748 (mm-30) REVERT: A 2843 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8278 (mmm) REVERT: A 2847 ASN cc_start: 0.8844 (t0) cc_final: 0.8526 (m-40) REVERT: A 2886 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8454 (mpp80) REVERT: A 3954 MET cc_start: 0.8711 (mmm) cc_final: 0.8030 (tpp) REVERT: A 3981 MET cc_start: 0.8857 (tmm) cc_final: 0.8545 (ttp) REVERT: A 4053 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8590 (mm-30) REVERT: A 4292 MET cc_start: 0.8570 (tpp) cc_final: 0.8181 (mpp) REVERT: A 4804 MET cc_start: 0.8158 (mmm) cc_final: 0.7790 (mmm) REVERT: A 4817 MET cc_start: 0.8757 (tpt) cc_final: 0.8420 (mmm) REVERT: A 4943 MET cc_start: 0.8659 (mtt) cc_final: 0.8353 (mtt) REVERT: E 58 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8835 (mtpp) REVERT: F 58 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8836 (mtpp) REVERT: G 58 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8872 (mtpp) REVERT: H 58 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8864 (mtpp) REVERT: H 108 GLU cc_start: 0.8182 (pm20) cc_final: 0.7922 (pm20) REVERT: B 393 MET cc_start: 0.7512 (mmm) cc_final: 0.7112 (mmm) REVERT: B 594 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9168 (mt) REVERT: B 655 MET cc_start: 0.8824 (mmp) cc_final: 0.8557 (mmm) REVERT: B 890 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8221 (p-80) REVERT: B 986 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6518 (pt) REVERT: B 1050 LEU cc_start: 0.9418 (tp) cc_final: 0.9202 (tt) REVERT: B 1113 MET cc_start: 0.7797 (mtt) cc_final: 0.7539 (mtm) REVERT: B 1975 MET cc_start: 0.8044 (mtm) cc_final: 0.7605 (mtm) REVERT: B 2456 MET cc_start: 0.8674 (mmm) cc_final: 0.8336 (tpp) REVERT: B 2652 LEU cc_start: 0.9239 (tp) cc_final: 0.8785 (tp) REVERT: B 2681 MET cc_start: 0.8269 (mmp) cc_final: 0.7879 (mmp) REVERT: B 2688 MET cc_start: 0.4474 (pmm) cc_final: 0.3929 (ppp) REVERT: B 2695 MET cc_start: 0.8430 (ptm) cc_final: 0.8207 (ppp) REVERT: B 2719 TYR cc_start: 0.8909 (t80) cc_final: 0.8527 (t80) REVERT: B 2720 PHE cc_start: 0.8278 (m-80) cc_final: 0.7713 (m-80) REVERT: B 2840 MET cc_start: 0.8957 (mmt) cc_final: 0.8642 (mmt) REVERT: B 2847 ASN cc_start: 0.9013 (t0) cc_final: 0.8771 (m110) REVERT: B 2877 LEU cc_start: 0.8753 (tp) cc_final: 0.8484 (tp) REVERT: B 2886 ARG cc_start: 0.8935 (ptm160) cc_final: 0.8489 (mpp80) REVERT: B 3003 MET cc_start: 0.9444 (mpp) cc_final: 0.8995 (pmm) REVERT: B 3689 MET cc_start: 0.8148 (mpp) cc_final: 0.7820 (mpp) REVERT: B 3739 MET cc_start: 0.8909 (ttp) cc_final: 0.8653 (ttt) REVERT: B 3954 MET cc_start: 0.8665 (mmm) cc_final: 0.8190 (tpp) REVERT: B 4019 MET cc_start: 0.8170 (mtt) cc_final: 0.7909 (mtm) REVERT: B 4053 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: B 4520 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: B 4726 MET cc_start: 0.8345 (mmm) cc_final: 0.8002 (tpt) REVERT: B 4804 MET cc_start: 0.7911 (mmm) cc_final: 0.7636 (mmm) REVERT: C 309 MET cc_start: 0.7764 (mmm) cc_final: 0.7451 (mmp) REVERT: C 594 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9172 (mt) REVERT: C 890 HIS cc_start: 0.9269 (OUTLIER) cc_final: 0.8871 (p-80) REVERT: C 1103 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7203 (t80) REVERT: C 1113 MET cc_start: 0.7756 (mtt) cc_final: 0.7480 (mtm) REVERT: C 1487 MET cc_start: 0.8480 (mtt) cc_final: 0.8117 (mtp) REVERT: C 1906 MET cc_start: 0.8397 (mmm) cc_final: 0.8171 (mmm) REVERT: C 1975 MET cc_start: 0.7953 (mtm) cc_final: 0.7542 (mtm) REVERT: C 2142 MET cc_start: 0.8682 (mmp) cc_final: 0.8387 (mmp) REVERT: C 2192 MET cc_start: 0.8490 (tpp) cc_final: 0.8036 (tpp) REVERT: C 2214 MET cc_start: 0.8952 (mmm) cc_final: 0.8695 (mmm) REVERT: C 2584 MET cc_start: 0.8475 (mmp) cc_final: 0.8171 (mmm) REVERT: C 2652 LEU cc_start: 0.9178 (mt) cc_final: 0.8686 (tp) REVERT: C 2681 MET cc_start: 0.8181 (mmp) cc_final: 0.7641 (mmp) REVERT: C 2719 TYR cc_start: 0.8840 (t80) cc_final: 0.8583 (t80) REVERT: C 2720 PHE cc_start: 0.8273 (m-80) cc_final: 0.7868 (m-80) REVERT: C 2773 TRP cc_start: 0.8548 (m100) cc_final: 0.8176 (m100) REVERT: C 2840 MET cc_start: 0.8544 (mmt) cc_final: 0.8138 (mmt) REVERT: C 2843 MET cc_start: 0.8916 (ptp) cc_final: 0.8666 (mpp) REVERT: C 2848 TYR cc_start: 0.8425 (m-80) cc_final: 0.8166 (m-80) REVERT: C 2886 ARG cc_start: 0.8706 (mpp80) cc_final: 0.8340 (mpp80) REVERT: C 3605 MET cc_start: 0.4564 (mmm) cc_final: 0.4280 (mmm) REVERT: C 3954 MET cc_start: 0.8722 (mmm) cc_final: 0.8042 (tpp) REVERT: C 3981 MET cc_start: 0.8837 (tmm) cc_final: 0.8561 (ttp) REVERT: C 4139 MET cc_start: 0.8532 (tpt) cc_final: 0.8188 (tpp) REVERT: C 4555 ILE cc_start: 0.4531 (OUTLIER) cc_final: 0.3998 (mt) REVERT: C 4728 MET cc_start: 0.8598 (mmm) cc_final: 0.8398 (mmp) REVERT: C 4804 MET cc_start: 0.8021 (mmm) cc_final: 0.7752 (mmm) REVERT: C 4817 MET cc_start: 0.8697 (mmm) cc_final: 0.8382 (mmm) REVERT: D 393 MET cc_start: 0.7381 (mmm) cc_final: 0.7023 (mmm) REVERT: D 395 HIS cc_start: 0.9146 (t-90) cc_final: 0.8945 (t-90) REVERT: D 594 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9184 (mt) REVERT: D 778 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8395 (ptm) REVERT: D 890 HIS cc_start: 0.9694 (OUTLIER) cc_final: 0.9433 (p-80) REVERT: D 1113 MET cc_start: 0.7818 (mtt) cc_final: 0.7550 (mtm) REVERT: D 1487 MET cc_start: 0.8457 (mtt) cc_final: 0.8087 (mtp) REVERT: D 1906 MET cc_start: 0.8408 (mmm) cc_final: 0.8178 (mmm) REVERT: D 2580 LEU cc_start: 0.8734 (tp) cc_final: 0.8362 (tp) REVERT: D 2652 LEU cc_start: 0.9215 (tp) cc_final: 0.8827 (tp) REVERT: D 2719 TYR cc_start: 0.8578 (t80) cc_final: 0.8272 (t80) REVERT: D 2720 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8254 (m-10) REVERT: D 2777 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8482 (mm-30) REVERT: D 2848 TYR cc_start: 0.8068 (m-80) cc_final: 0.7842 (m-80) REVERT: D 2886 ARG cc_start: 0.9011 (ptm160) cc_final: 0.8752 (ptm160) REVERT: D 2939 TYR cc_start: 0.8994 (m-10) cc_final: 0.8786 (m-80) REVERT: D 2982 PHE cc_start: 0.8878 (m-80) cc_final: 0.8391 (m-80) REVERT: D 3003 MET cc_start: 0.9227 (pmm) cc_final: 0.8671 (pmm) REVERT: D 3605 MET cc_start: 0.5184 (mmp) cc_final: 0.4917 (mmm) REVERT: D 3739 MET cc_start: 0.8924 (ttp) cc_final: 0.8664 (ttt) REVERT: D 3954 MET cc_start: 0.8921 (tpp) cc_final: 0.8306 (tpp) REVERT: D 3978 MET cc_start: 0.8902 (ttp) cc_final: 0.8684 (ttt) REVERT: D 4139 MET cc_start: 0.8486 (tpt) cc_final: 0.8164 (tpp) REVERT: D 4306 PHE cc_start: 0.7838 (m-10) cc_final: 0.7449 (t80) REVERT: D 4726 MET cc_start: 0.8340 (tpp) cc_final: 0.8013 (tpp) REVERT: D 4728 MET cc_start: 0.8543 (mmm) cc_final: 0.8337 (mmt) REVERT: D 4814 MET cc_start: 0.8041 (tpp) cc_final: 0.7790 (mmm) REVERT: D 4817 MET cc_start: 0.8624 (mmm) cc_final: 0.8368 (mmm) outliers start: 97 outliers final: 65 residues processed: 781 average time/residue: 1.1266 time to fit residues: 1562.6722 Evaluate side-chains 789 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 703 time to evaluate : 11.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1051 ARG Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2720 PHE Chi-restraints excluded: chain A residue 2724 TYR Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 4053 GLU Chi-restraints excluded: chain A residue 4666 ILE Chi-restraints excluded: chain A residue 4752 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 986 ILE Chi-restraints excluded: chain B residue 1051 ARG Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2843 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3702 GLU Chi-restraints excluded: chain B residue 4053 GLU Chi-restraints excluded: chain B residue 4520 TYR Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4666 ILE Chi-restraints excluded: chain B residue 4718 SER Chi-restraints excluded: chain B residue 4752 THR Chi-restraints excluded: chain B residue 4861 ILE Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 1051 ARG Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3702 GLU Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4666 ILE Chi-restraints excluded: chain C residue 4718 SER Chi-restraints excluded: chain C residue 4861 ILE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1051 ARG Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2720 PHE Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2757 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 2914 THR Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 4752 THR Chi-restraints excluded: chain D residue 4870 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1467 optimal weight: 20.0000 chunk 967 optimal weight: 20.0000 chunk 1557 optimal weight: 5.9990 chunk 950 optimal weight: 20.0000 chunk 738 optimal weight: 5.9990 chunk 1082 optimal weight: 30.0000 chunk 1633 optimal weight: 0.0970 chunk 1503 optimal weight: 8.9990 chunk 1301 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 1004 optimal weight: 0.5980 overall best weight: 4.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 HIS A 635 ASN ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 GLN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2410 HIS ** D2579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 134536 Z= 0.295 Angle : 0.630 20.063 181752 Z= 0.318 Chirality : 0.040 0.318 19884 Planarity : 0.004 0.127 23364 Dihedral : 5.628 87.309 18083 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 0.60 % Allowed : 8.88 % Favored : 90.52 % 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: 1.13 (0.07), residues: 16332 helix: 1.89 (0.06), residues: 8568 sheet: -0.37 (0.12), residues: 1816 loop : -0.53 (0.08), residues: 5948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 893 HIS 0.008 0.001 HIS A 890 PHE 0.055 0.002 PHE B2895 TYR 0.051 0.002 TYR C2939 ARG 0.010 0.001 ARG B1960 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 704 time to evaluate : 11.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7902 (ttp) REVERT: A 655 MET cc_start: 0.8752 (mmm) cc_final: 0.8278 (mmp) REVERT: A 778 MET cc_start: 0.8656 (ptm) cc_final: 0.8368 (ptp) REVERT: A 890 HIS cc_start: 0.9276 (OUTLIER) cc_final: 0.8844 (p-80) REVERT: A 986 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5426 (pt) REVERT: A 1113 MET cc_start: 0.7935 (mtt) cc_final: 0.7682 (mtm) REVERT: A 1564 MET cc_start: 0.8523 (mmm) cc_final: 0.8312 (mmm) REVERT: A 1975 MET cc_start: 0.8105 (mtm) cc_final: 0.7617 (mtm) REVERT: A 2389 MET cc_start: 0.8548 (mtp) cc_final: 0.8338 (mtm) REVERT: A 2652 LEU cc_start: 0.9123 (tp) cc_final: 0.8676 (tp) REVERT: A 2681 MET cc_start: 0.8410 (mmp) cc_final: 0.8067 (mmp) REVERT: A 2719 TYR cc_start: 0.8714 (t80) cc_final: 0.8366 (t80) REVERT: A 2720 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: A 2777 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8751 (mm-30) REVERT: A 2843 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8299 (mmm) REVERT: A 2847 ASN cc_start: 0.8834 (t0) cc_final: 0.8542 (m-40) REVERT: A 2886 ARG cc_start: 0.9031 (ptm160) cc_final: 0.8461 (mpp80) REVERT: A 3954 MET cc_start: 0.8706 (mmm) cc_final: 0.8044 (tpp) REVERT: A 3981 MET cc_start: 0.8813 (tmm) cc_final: 0.8122 (ttp) REVERT: A 4053 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: A 4292 MET cc_start: 0.8604 (tpp) cc_final: 0.8155 (mpp) REVERT: A 4804 MET cc_start: 0.8151 (mmm) cc_final: 0.7807 (mmm) REVERT: A 4817 MET cc_start: 0.8792 (tpt) cc_final: 0.8415 (mmm) REVERT: E 58 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8847 (mtpp) REVERT: F 58 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8851 (mtpp) REVERT: G 58 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8884 (mtpp) REVERT: H 58 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8864 (mtpp) REVERT: H 108 GLU cc_start: 0.8130 (pm20) cc_final: 0.7896 (pm20) REVERT: B 393 MET cc_start: 0.7505 (mmm) cc_final: 0.7085 (mmm) REVERT: B 594 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9189 (mt) REVERT: B 890 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8275 (p-80) REVERT: B 986 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6632 (pt) REVERT: B 1050 LEU cc_start: 0.9441 (tp) cc_final: 0.9226 (tt) REVERT: B 1113 MET cc_start: 0.7875 (mtt) cc_final: 0.7633 (mtm) REVERT: B 1306 MET cc_start: 0.8837 (mmm) cc_final: 0.8610 (mmm) REVERT: B 1975 MET cc_start: 0.8029 (mtm) cc_final: 0.7564 (mtm) REVERT: B 2456 MET cc_start: 0.8693 (mmm) cc_final: 0.8349 (tpp) REVERT: B 2652 LEU cc_start: 0.9247 (tp) cc_final: 0.8804 (tp) REVERT: B 2681 MET cc_start: 0.8303 (mmp) cc_final: 0.7909 (mmp) REVERT: B 2688 MET cc_start: 0.4779 (pmm) cc_final: 0.4290 (ppp) REVERT: B 2695 MET cc_start: 0.8437 (ptm) cc_final: 0.8233 (ppp) REVERT: B 2719 TYR cc_start: 0.8915 (t80) cc_final: 0.8505 (t80) REVERT: B 2720 PHE cc_start: 0.8263 (m-80) cc_final: 0.7710 (m-80) REVERT: B 2840 MET cc_start: 0.8932 (mmt) cc_final: 0.8566 (mmt) REVERT: B 2847 ASN cc_start: 0.9031 (t0) cc_final: 0.8786 (m110) REVERT: B 2858 MET cc_start: 0.8483 (pmm) cc_final: 0.8280 (pmm) REVERT: B 2877 LEU cc_start: 0.8767 (tp) cc_final: 0.8495 (tp) REVERT: B 2886 ARG cc_start: 0.8963 (ptm160) cc_final: 0.8490 (mpp80) REVERT: B 3739 MET cc_start: 0.8917 (ttp) cc_final: 0.8656 (ttt) REVERT: B 3954 MET cc_start: 0.8652 (mmm) cc_final: 0.8194 (tpp) REVERT: B 4019 MET cc_start: 0.8185 (mtt) cc_final: 0.7925 (mtm) REVERT: B 4053 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8484 (mm-30) REVERT: B 4520 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7626 (m-10) REVERT: B 4726 MET cc_start: 0.8373 (mmm) cc_final: 0.8028 (tpt) REVERT: B 4804 MET cc_start: 0.7918 (mmm) cc_final: 0.7643 (mmm) REVERT: C 309 MET cc_start: 0.7751 (mmm) cc_final: 0.7441 (mmp) REVERT: C 349 MET cc_start: 0.8166 (mmm) cc_final: 0.7902 (mmp) REVERT: C 594 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9193 (mt) REVERT: C 890 HIS cc_start: 0.9237 (OUTLIER) cc_final: 0.8790 (p-80) REVERT: C 1103 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7116 (t80) REVERT: C 1113 MET cc_start: 0.7829 (mtt) cc_final: 0.7574 (mtm) REVERT: C 1487 MET cc_start: 0.8493 (mtt) cc_final: 0.8127 (mtp) REVERT: C 1906 MET cc_start: 0.8417 (mmm) cc_final: 0.8183 (mmm) REVERT: C 1975 MET cc_start: 0.7955 (mtm) cc_final: 0.7533 (mtm) REVERT: C 2142 MET cc_start: 0.8702 (mmp) cc_final: 0.8422 (mmp) REVERT: C 2192 MET cc_start: 0.8514 (tpp) cc_final: 0.8027 (tpp) REVERT: C 2214 MET cc_start: 0.8930 (mmm) cc_final: 0.8689 (mmm) REVERT: C 2584 MET cc_start: 0.8562 (mmp) cc_final: 0.8241 (mmm) REVERT: C 2652 LEU cc_start: 0.9203 (mt) cc_final: 0.8730 (tp) REVERT: C 2681 MET cc_start: 0.8210 (mmp) cc_final: 0.7668 (mmp) REVERT: C 2719 TYR cc_start: 0.8877 (t80) cc_final: 0.8654 (t80) REVERT: C 2720 PHE cc_start: 0.8331 (m-80) cc_final: 0.7883 (m-80) REVERT: C 2772 ARG cc_start: 0.9168 (ptp-110) cc_final: 0.8601 (ptp-110) REVERT: C 2773 TRP cc_start: 0.8558 (m100) cc_final: 0.8127 (m100) REVERT: C 2840 MET cc_start: 0.8555 (mmt) cc_final: 0.8342 (mmt) REVERT: C 2848 TYR cc_start: 0.8399 (m-80) cc_final: 0.8071 (m-80) REVERT: C 2858 MET cc_start: 0.8405 (ptp) cc_final: 0.8157 (ppp) REVERT: C 2886 ARG cc_start: 0.8735 (mpp80) cc_final: 0.8355 (mpp80) REVERT: C 3605 MET cc_start: 0.4663 (mmm) cc_final: 0.4403 (mmm) REVERT: C 3954 MET cc_start: 0.8718 (mmm) cc_final: 0.8037 (tpp) REVERT: C 3981 MET cc_start: 0.8854 (tmm) cc_final: 0.8084 (ttp) REVERT: C 4139 MET cc_start: 0.8471 (tpt) cc_final: 0.8169 (tpp) REVERT: C 4292 MET cc_start: 0.8462 (mpp) cc_final: 0.8051 (mpp) REVERT: C 4555 ILE cc_start: 0.4689 (OUTLIER) cc_final: 0.4149 (mt) REVERT: C 4728 MET cc_start: 0.8614 (mmm) cc_final: 0.8403 (mmp) REVERT: C 4804 MET cc_start: 0.8029 (mmm) cc_final: 0.7761 (mmm) REVERT: C 4817 MET cc_start: 0.8716 (mmm) cc_final: 0.8426 (mmm) REVERT: D 393 MET cc_start: 0.7391 (mmm) cc_final: 0.7009 (mmm) REVERT: D 395 HIS cc_start: 0.9151 (t-90) cc_final: 0.8951 (t-90) REVERT: D 594 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9205 (mt) REVERT: D 778 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8369 (ptm) REVERT: D 1487 MET cc_start: 0.8475 (mtt) cc_final: 0.8112 (mtp) REVERT: D 1906 MET cc_start: 0.8432 (mmm) cc_final: 0.8193 (mmm) REVERT: D 2580 LEU cc_start: 0.8827 (tp) cc_final: 0.8468 (tp) REVERT: D 2652 LEU cc_start: 0.9223 (tp) cc_final: 0.8844 (tp) REVERT: D 2681 MET cc_start: 0.7676 (mmp) cc_final: 0.7255 (mmp) REVERT: D 2719 TYR cc_start: 0.8594 (t80) cc_final: 0.8307 (t80) REVERT: D 2720 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8262 (m-10) REVERT: D 2777 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8521 (mm-30) REVERT: D 2828 MET cc_start: 0.7271 (tpt) cc_final: 0.6728 (mmm) REVERT: D 2848 TYR cc_start: 0.8088 (m-80) cc_final: 0.7863 (m-80) REVERT: D 2858 MET cc_start: 0.8344 (pmm) cc_final: 0.8058 (pmm) REVERT: D 2886 ARG cc_start: 0.9035 (ptm160) cc_final: 0.8649 (ptm160) REVERT: D 2939 TYR cc_start: 0.9008 (m-10) cc_final: 0.8804 (m-80) REVERT: D 2982 PHE cc_start: 0.8916 (m-80) cc_final: 0.8410 (m-80) REVERT: D 3003 MET cc_start: 0.9237 (pmm) cc_final: 0.8770 (pmm) REVERT: D 3605 MET cc_start: 0.5213 (mmp) cc_final: 0.4949 (mmm) REVERT: D 3739 MET cc_start: 0.8938 (ttp) cc_final: 0.8669 (ttt) REVERT: D 3978 MET cc_start: 0.8911 (ttp) cc_final: 0.8693 (ttt) REVERT: D 4139 MET cc_start: 0.8551 (tpt) cc_final: 0.8200 (tpp) REVERT: D 4306 PHE cc_start: 0.7838 (m-10) cc_final: 0.7465 (t80) REVERT: D 4726 MET cc_start: 0.8378 (tpp) cc_final: 0.8018 (tpp) REVERT: D 4728 MET cc_start: 0.8541 (mmm) cc_final: 0.8336 (mmt) REVERT: D 4814 MET cc_start: 0.8058 (tpp) cc_final: 0.7789 (mmm) REVERT: D 4817 MET cc_start: 0.8634 (mmm) cc_final: 0.8365 (mmm) outliers start: 87 outliers final: 62 residues processed: 772 average time/residue: 1.1529 time to fit residues: 1585.2473 Evaluate side-chains 782 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 700 time to evaluate : 11.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1051 ARG Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2720 PHE Chi-restraints excluded: chain A residue 2724 TYR Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 4053 GLU Chi-restraints excluded: chain A residue 4666 ILE Chi-restraints excluded: chain A residue 4752 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 986 ILE Chi-restraints excluded: chain B residue 1051 ARG Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2843 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3702 GLU Chi-restraints excluded: chain B residue 4053 GLU Chi-restraints excluded: chain B residue 4520 TYR Chi-restraints excluded: chain B residue 4555 ILE Chi-restraints excluded: chain B residue 4666 ILE Chi-restraints excluded: chain B residue 4718 SER Chi-restraints excluded: chain B residue 4752 THR Chi-restraints excluded: chain B residue 4861 ILE Chi-restraints excluded: chain B residue 4923 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3702 GLU Chi-restraints excluded: chain C residue 4555 ILE Chi-restraints excluded: chain C residue 4666 ILE Chi-restraints excluded: chain C residue 4718 SER Chi-restraints excluded: chain C residue 4861 ILE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2720 PHE Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 2914 THR Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 4752 THR Chi-restraints excluded: chain D residue 4870 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 797 optimal weight: 1.9990 chunk 1033 optimal weight: 5.9990 chunk 1385 optimal weight: 10.0000 chunk 398 optimal weight: 7.9990 chunk 1199 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 361 optimal weight: 10.0000 chunk 1303 optimal weight: 9.9990 chunk 545 optimal weight: 10.0000 chunk 1338 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.043129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.031972 restraints weight = 1564791.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.033313 restraints weight = 585531.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.034062 restraints weight = 338351.426| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 134536 Z= 0.219 Angle : 0.614 19.387 181752 Z= 0.309 Chirality : 0.040 0.268 19884 Planarity : 0.004 0.127 23364 Dihedral : 5.533 85.749 18083 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 0.61 % Allowed : 8.89 % Favored : 90.50 % 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: 1.19 (0.07), residues: 16332 helix: 1.93 (0.06), residues: 8576 sheet: -0.33 (0.12), residues: 1816 loop : -0.50 (0.08), residues: 5940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 893 HIS 0.011 0.001 HIS A 890 PHE 0.052 0.001 PHE B2895 TYR 0.051 0.001 TYR C2939 ARG 0.009 0.000 ARG B1960 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29858.76 seconds wall clock time: 526 minutes 21.09 seconds (31581.09 seconds total)