Starting phenix.real_space_refine on Mon Mar 18 23:11:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxf_42762/03_2024/8uxf_42762_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxf_42762/03_2024/8uxf_42762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxf_42762/03_2024/8uxf_42762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxf_42762/03_2024/8uxf_42762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxf_42762/03_2024/8uxf_42762_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxf_42762/03_2024/8uxf_42762_updated.pdb" } resolution = 3.13 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= 0.011 sd= 0.031 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 936 5.16 5 C 88228 2.51 5 N 23588 2.21 5 O 25840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1184": "OD1" <-> "OD2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A ASP 1471": "OD1" <-> "OD2" Residue "A GLU 1634": "OE1" <-> "OE2" Residue "A ASP 1708": "OD1" <-> "OD2" Residue "A TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1946": "OE1" <-> "OE2" Residue "A TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2183": "OE1" <-> "OE2" Residue "A GLU 2329": "OE1" <-> "OE2" Residue "A GLU 2682": "OE1" <-> "OE2" Residue "A GLU 2715": "OE1" <-> "OE2" Residue "A TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2735": "OD1" <-> "OD2" Residue "A PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3025": "OD1" <-> "OD2" Residue "A TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3259": "OE1" <-> "OE2" Residue "A PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3710": "OE1" <-> "OE2" Residue "A ASP 3899": "OD1" <-> "OD2" Residue "A ASP 4038": "OD1" <-> "OD2" Residue "A ASP 4047": "OD1" <-> "OD2" Residue "A TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4123": "OE1" <-> "OE2" Residue "A GLU 4151": "OE1" <-> "OE2" Residue "A GLU 4161": "OE1" <-> "OE2" Residue "A PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4179": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4659": "OE1" <-> "OE2" Residue "A TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4678": "OD1" <-> "OD2" Residue "A ASP 4691": "OD1" <-> "OD2" Residue "A GLU 4797": "OE1" <-> "OE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1184": "OD1" <-> "OD2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1199": "OD1" <-> "OD2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B GLU 1634": "OE1" <-> "OE2" Residue "B ASP 1708": "OD1" <-> "OD2" Residue "B TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1946": "OE1" <-> "OE2" Residue "B TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2183": "OE1" <-> "OE2" Residue "B GLU 2329": "OE1" <-> "OE2" Residue "B GLU 2682": "OE1" <-> "OE2" Residue "B GLU 2715": "OE1" <-> "OE2" Residue "B TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2735": "OD1" <-> "OD2" Residue "B PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3025": "OD1" <-> "OD2" Residue "B TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3259": "OE1" <-> "OE2" Residue "B PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3710": "OE1" <-> "OE2" Residue "B ASP 3899": "OD1" <-> "OD2" Residue "B ASP 4038": "OD1" <-> "OD2" Residue "B ASP 4047": "OD1" <-> "OD2" Residue "B TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4123": "OE1" <-> "OE2" Residue "B GLU 4151": "OE1" <-> "OE2" Residue "B GLU 4161": "OE1" <-> "OE2" Residue "B PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4179": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4659": "OE1" <-> "OE2" Residue "B TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4678": "OD1" <-> "OD2" Residue "B ASP 4691": "OD1" <-> "OD2" Residue "B GLU 4797": "OE1" <-> "OE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1184": "OD1" <-> "OD2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1199": "OD1" <-> "OD2" Residue "C ASP 1471": "OD1" <-> "OD2" Residue "C GLU 1634": "OE1" <-> "OE2" Residue "C ASP 1708": "OD1" <-> "OD2" Residue "C TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1946": "OE1" <-> "OE2" Residue "C TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2183": "OE1" <-> "OE2" Residue "C GLU 2329": "OE1" <-> "OE2" Residue "C GLU 2682": "OE1" <-> "OE2" Residue "C GLU 2715": "OE1" <-> "OE2" Residue "C TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2735": "OD1" <-> "OD2" Residue "C PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3025": "OD1" <-> "OD2" Residue "C TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3259": "OE1" <-> "OE2" Residue "C PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3710": "OE1" <-> "OE2" Residue "C ASP 3899": "OD1" <-> "OD2" Residue "C ASP 4038": "OD1" <-> "OD2" Residue "C ASP 4047": "OD1" <-> "OD2" Residue "C TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4123": "OE1" <-> "OE2" Residue "C GLU 4151": "OE1" <-> "OE2" Residue "C GLU 4161": "OE1" <-> "OE2" Residue "C PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4179": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4659": "OE1" <-> "OE2" Residue "C TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4678": "OD1" <-> "OD2" Residue "C ASP 4691": "OD1" <-> "OD2" Residue "C GLU 4797": "OE1" <-> "OE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1184": "OD1" <-> "OD2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1199": "OD1" <-> "OD2" Residue "D ASP 1471": "OD1" <-> "OD2" Residue "D GLU 1634": "OE1" <-> "OE2" Residue "D ASP 1708": "OD1" <-> "OD2" Residue "D TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1946": "OE1" <-> "OE2" Residue "D TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2183": "OE1" <-> "OE2" Residue "D GLU 2329": "OE1" <-> "OE2" Residue "D GLU 2682": "OE1" <-> "OE2" Residue "D GLU 2715": "OE1" <-> "OE2" Residue "D TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2735": "OD1" <-> "OD2" Residue "D PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3025": "OD1" <-> "OD2" Residue "D TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3259": "OE1" <-> "OE2" Residue "D PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3710": "OE1" <-> "OE2" Residue "D ASP 3899": "OD1" <-> "OD2" Residue "D ASP 4038": "OD1" <-> "OD2" Residue "D ASP 4047": "OD1" <-> "OD2" Residue "D TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4123": "OE1" <-> "OE2" Residue "D GLU 4151": "OE1" <-> "OE2" Residue "D GLU 4161": "OE1" <-> "OE2" Residue "D PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4179": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4659": "OE1" <-> "OE2" Residue "D TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4678": "OD1" <-> "OD2" Residue "D ASP 4691": "OD1" <-> "OD2" Residue "D GLU 4797": "OE1" <-> "OE2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "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: 138620 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 34490 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: "B" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 34490 Chain: "C" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 34490 Chain: "D" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 4224, 33766 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} 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: 34490 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: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33095 SG CYS A4888 178.907 203.804 86.655 1.00 84.91 S ATOM 33120 SG CYS A4891 181.332 203.705 89.560 1.00 85.60 S ATOM 67687 SG CYS B4888 177.313 178.075 86.578 1.00 85.92 S ATOM 67712 SG CYS B4891 177.417 180.497 89.485 1.00 85.25 S ATOM A014L SG CYS C4888 203.111 176.554 86.681 1.00 84.71 S ATOM A015A SG CYS C4891 200.692 176.657 89.590 1.00 85.37 S ATOM A0R6R SG CYS D4888 204.624 202.282 86.671 1.00 84.50 S ATOM A0R7G SG CYS D4891 204.522 199.864 89.582 1.00 85.75 S Time building chain proxies: 92.22, per 1000 atoms: 0.67 Number of scatterers: 138620 At special positions: 0 Unit cell: (382.041, 382.041, 211.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 936 16.00 P 24 15.00 O 25840 8.00 N 23588 7.00 C 88228 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: 38.35 Conformation dependent library (CDL) restraints added in 34.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 8 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32464 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: 688 helices and 84 sheets defined 59.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 44.32 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.880A 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: 4.824A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.878A 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: 4.117A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.681A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.611A 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: 3.632A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.044A 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: 4.806A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.793A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.352A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.228A 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 590 removed outlier: 3.748A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.630A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.609A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.652A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.551A 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 857 through 862 removed outlier: 4.999A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.916A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.069A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 4.107A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 4.534A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.086A pdb=" N ILE A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 987' Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.826A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.099A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.849A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.159A 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 1494 Processing helix chain 'A' and resid 1498 through 1503 removed outlier: 4.563A pdb=" N ASN A1502 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1498 through 1503' Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.767A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.155A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.638A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.879A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.935A 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 1722 removed outlier: 3.696A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.561A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1899 through 1948 removed outlier: 4.253A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1965 removed outlier: 3.805A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 3.837A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.510A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.695A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.580A 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: 3.923A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.406A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.865A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 4.066A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.625A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.315A 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: 4.219A 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: 3.628A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A2301 " --> pdb=" O ARG A2297 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A2302 " --> pdb=" O TYR A2298 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.582A 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: 9.101A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.728A 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: 5.754A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.807A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 3.625A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2532 removed outlier: 3.518A pdb=" N THR A2522 " --> pdb=" O ARG A2518 " (cutoff:3.500A) removed outlier: 5.478A 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: 4.205A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A2546 " --> pdb=" O ALA A2542 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2581 removed outlier: 3.500A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A2581 " --> pdb=" O CYS A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2582 through 2596 removed outlier: 4.445A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.801A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.188A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (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 2691 through 2696 removed outlier: 3.851A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A2696 " --> pdb=" O GLN A2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2691 through 2696' Processing helix chain 'A' and resid 2714 through 2740 removed outlier: 4.104A pdb=" N GLU A2718 " --> pdb=" O PRO A2714 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.460A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 4.481A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.403A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.761A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A2893 " --> pdb=" O ALA A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2921 removed outlier: 4.024A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE A2921 " --> pdb=" O ILE A2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2916 through 2921' Processing helix chain 'A' and resid 2922 through 2947 removed outlier: 3.870A pdb=" N GLY A2945 " --> pdb=" O LEU A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.694A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix removed outlier: 3.541A pdb=" N PHE A2975 " --> pdb=" O ILE A2971 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 5.151A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3048 removed outlier: 3.838A pdb=" N VAL A3045 " --> pdb=" O ASP A3041 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3078 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.010A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.109A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 3.766A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 4.435A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3180' Processing helix chain 'A' and resid 3182 through 3188 Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.858A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 4.550A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 4.206A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3250 removed outlier: 5.152A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix Processing helix chain 'A' and resid 3253 through 3258 Proline residue: A3258 - end of helix Processing helix chain 'A' and resid 3269 through 3291 removed outlier: 4.452A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE A3290 " --> pdb=" O ASN A3286 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP A3291 " --> pdb=" O ASN A3287 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.175A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 6.128A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3329 removed outlier: 5.287A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 4.474A pdb=" N LYS A3329 " --> pdb=" O LYS A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3605 removed outlier: 4.935A pdb=" N MET A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.796A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.197A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.403A 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: 4.576A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.979A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.888A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.545A pdb=" N ILE A3744 " --> pdb=" O VAL A3740 " (cutoff:3.500A) removed outlier: 3.861A 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: 4.672A 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 3826 through 3848 removed outlier: 5.331A pdb=" N LEU A3830 " --> pdb=" O GLY A3826 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A3831 " --> pdb=" O GLU A3827 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP A3832 " --> pdb=" O LYS A3828 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A3833 " --> pdb=" O VAL A3829 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU A3834 " --> pdb=" O LEU A3830 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE A3835 " --> pdb=" O GLN A3831 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.625A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 3.627A pdb=" N VAL A3875 " --> pdb=" O ILE A3871 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A3892 " --> pdb=" O PHE A3888 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 removed outlier: 3.539A pdb=" N ILE A3924 " --> pdb=" O LEU A3920 " (cutoff:3.500A) Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.505A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.704A pdb=" N LYS A3976 " --> pdb=" O MET A3972 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 3.549A pdb=" N PHE A4020 " --> pdb=" O PHE A4016 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.253A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 Proline residue: A4090 - end of helix Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4181 through 4208 removed outlier: 4.910A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4259 removed outlier: 4.323A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4272 removed outlier: 4.491A pdb=" N GLN A4267 " --> pdb=" O SER A4263 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.853A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 3.814A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.206A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4569 through 4612 removed outlier: 3.522A pdb=" N ARG A4573 " --> pdb=" O GLU A4569 " (cutoff:3.500A) removed outlier: 4.117A 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: 3.730A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.780A 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: 4.654A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4701 removed outlier: 3.783A pdb=" N ILE A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.897A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.743A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.885A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.097A 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: 4.507A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 5.177A 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: 3.549A 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: 4.193A 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: 4.054A 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 1772 through 1778 removed outlier: 4.587A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.879A 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: 4.823A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.878A 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: 4.117A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.682A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.611A 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: 3.631A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.045A 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: 4.806A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.794A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.352A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.229A 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 590 removed outlier: 3.748A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.630A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.609A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.651A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.550A 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 857 through 862 removed outlier: 4.999A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 875 through 901 removed outlier: 4.916A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.069A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 4.107A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 4.534A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.086A pdb=" N ILE B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 982 through 987' Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.826A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.099A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.851A 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: 3.848A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.160A 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 1494 Processing helix chain 'B' and resid 1498 through 1503 removed outlier: 4.564A pdb=" N ASN B1502 " --> pdb=" O GLN B1498 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1498 through 1503' Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.767A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.154A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.638A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B1666 " --> pdb=" O SER B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.879A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.936A 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 1722 removed outlier: 3.696A pdb=" N MET B1721 " --> pdb=" O ALA B1717 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.561A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1802 Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1899 through 1948 removed outlier: 4.254A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1965 removed outlier: 3.804A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 3.837A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.510A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.696A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.581A 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: 3.923A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.406A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.865A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 4.066A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.625A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.316A 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: 4.219A 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: 3.629A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B2301 " --> pdb=" O ARG B2297 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B2302 " --> pdb=" O TYR B2298 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.582A 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: 9.101A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.727A 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: 5.754A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.807A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 3.626A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2510 through 2532 removed outlier: 3.517A pdb=" N THR B2522 " --> pdb=" O ARG B2518 " (cutoff:3.500A) removed outlier: 5.479A 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: 4.204A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B2546 " --> pdb=" O ALA B2542 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2581 removed outlier: 3.500A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG B2581 " --> pdb=" O CYS B2577 " (cutoff:3.500A) Processing helix chain 'B' and resid 2582 through 2596 removed outlier: 4.446A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.803A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.189A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (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 2691 through 2696 removed outlier: 3.851A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP B2696 " --> pdb=" O GLN B2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2691 through 2696' Processing helix chain 'B' and resid 2714 through 2740 removed outlier: 4.103A pdb=" N GLU B2718 " --> pdb=" O PRO B2714 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR B2719 " --> pdb=" O GLU B2715 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.459A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 4.482A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.403A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.761A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B2893 " --> pdb=" O ALA B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2921 removed outlier: 4.024A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE B2921 " --> pdb=" O ILE B2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2916 through 2921' Processing helix chain 'B' and resid 2922 through 2947 removed outlier: 3.870A pdb=" N GLY B2945 " --> pdb=" O LEU B2941 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.694A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix removed outlier: 3.541A pdb=" N PHE B2975 " --> pdb=" O ILE B2971 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 5.150A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3048 removed outlier: 3.839A pdb=" N VAL B3045 " --> pdb=" O ASP B3041 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3078 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.010A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.108A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 3.766A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 4.435A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3180' Processing helix chain 'B' and resid 3182 through 3188 Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.858A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 4.550A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 4.207A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3250 removed outlier: 5.152A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix Processing helix chain 'B' and resid 3253 through 3258 Proline residue: B3258 - end of helix Processing helix chain 'B' and resid 3269 through 3291 removed outlier: 4.452A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE B3290 " --> pdb=" O ASN B3286 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP B3291 " --> pdb=" O ASN B3287 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.174A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B3301 " --> pdb=" O LYS B3297 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 6.129A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3329 removed outlier: 5.286A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 4.474A pdb=" N LYS B3329 " --> pdb=" O LYS B3325 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3605 removed outlier: 4.936A pdb=" N MET B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.796A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.198A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.402A 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: 4.576A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.979A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.888A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.545A pdb=" N ILE B3744 " --> pdb=" O VAL B3740 " (cutoff:3.500A) removed outlier: 3.861A 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: 4.671A 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 3826 through 3848 removed outlier: 5.331A pdb=" N LEU B3830 " --> pdb=" O GLY B3826 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B3831 " --> pdb=" O GLU B3827 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B3832 " --> pdb=" O LYS B3828 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B3833 " --> pdb=" O VAL B3829 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU B3834 " --> pdb=" O LEU B3830 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE B3835 " --> pdb=" O GLN B3831 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.624A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 3.627A pdb=" N VAL B3875 " --> pdb=" O ILE B3871 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B3892 " --> pdb=" O PHE B3888 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 removed outlier: 3.539A pdb=" N ILE B3924 " --> pdb=" O LEU B3920 " (cutoff:3.500A) Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.505A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.704A pdb=" N LYS B3976 " --> pdb=" O MET B3972 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 3.549A pdb=" N PHE B4020 " --> pdb=" O PHE B4016 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.253A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 Proline residue: B4090 - end of helix Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4181 through 4208 removed outlier: 4.910A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4259 removed outlier: 4.323A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4272 removed outlier: 4.491A pdb=" N GLN B4267 " --> pdb=" O SER B4263 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.852A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 3.814A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.206A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4569 through 4612 removed outlier: 3.523A pdb=" N ARG B4573 " --> pdb=" O GLU B4569 " (cutoff:3.500A) removed outlier: 4.118A 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: 3.730A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.779A 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: 4.654A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4701 removed outlier: 3.784A pdb=" N ILE B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) Processing helix chain 'B' and resid 4702 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.896A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.743A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.885A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.097A 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: 4.508A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 5.178A 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: 3.549A pdb=" N GLY B4820 " --> pdb=" O HIS B4816 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.194A 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: 4.054A 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 1772 through 1778 removed outlier: 4.586A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.879A 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: 4.824A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.879A 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: 4.116A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.681A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.611A 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: 3.632A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.045A 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: 4.807A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.794A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.352A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.229A 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 590 removed outlier: 3.748A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.631A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.609A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.651A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.551A 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 857 through 862 removed outlier: 4.999A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.916A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.069A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 4.107A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 4.534A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 4.086A pdb=" N ILE C 986 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 987' Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.826A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.098A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.847A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.159A 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 1494 Processing helix chain 'C' and resid 1498 through 1503 removed outlier: 4.564A pdb=" N ASN C1502 " --> pdb=" O GLN C1498 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1498 through 1503' Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.767A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.155A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.638A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C1666 " --> pdb=" O SER C1662 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.879A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.935A 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 1722 removed outlier: 3.697A pdb=" N MET C1721 " --> pdb=" O ALA C1717 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.561A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1899 through 1948 removed outlier: 4.253A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1965 removed outlier: 3.804A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 3.837A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.510A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.695A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.579A 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: 3.923A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.405A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.865A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 4.067A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.626A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.316A 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: 4.219A 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: 3.628A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C2301 " --> pdb=" O ARG C2297 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C2302 " --> pdb=" O TYR C2298 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.582A 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: 9.101A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.728A 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: 5.755A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.807A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 3.625A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2510 through 2532 removed outlier: 3.518A pdb=" N THR C2522 " --> pdb=" O ARG C2518 " (cutoff:3.500A) removed outlier: 5.478A 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: 4.205A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP C2546 " --> pdb=" O ALA C2542 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2581 removed outlier: 5.501A pdb=" N ARG C2581 " --> pdb=" O CYS C2577 " (cutoff:3.500A) Processing helix chain 'C' and resid 2582 through 2596 removed outlier: 4.446A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.802A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.189A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (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 2691 through 2696 removed outlier: 3.851A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C2696 " --> pdb=" O GLN C2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2691 through 2696' Processing helix chain 'C' and resid 2714 through 2740 removed outlier: 4.104A pdb=" N GLU C2718 " --> pdb=" O PRO C2714 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR C2719 " --> pdb=" O GLU C2715 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.459A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 4.481A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.403A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.760A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C2893 " --> pdb=" O ALA C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2921 removed outlier: 4.024A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE C2921 " --> pdb=" O ILE C2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2916 through 2921' Processing helix chain 'C' and resid 2922 through 2947 removed outlier: 3.871A pdb=" N GLY C2945 " --> pdb=" O LEU C2941 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.694A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix removed outlier: 3.541A pdb=" N PHE C2975 " --> pdb=" O ILE C2971 " (cutoff:3.500A) Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 5.151A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3048 removed outlier: 3.838A pdb=" N VAL C3045 " --> pdb=" O ASP C3041 " (cutoff:3.500A) Processing helix chain 'C' and resid 3050 through 3078 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.010A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.109A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 3.765A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 4.436A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3180' Processing helix chain 'C' and resid 3182 through 3188 Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.858A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 4.549A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 4.206A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3250 removed outlier: 5.152A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix Processing helix chain 'C' and resid 3253 through 3258 Proline residue: C3258 - end of helix Processing helix chain 'C' and resid 3269 through 3291 removed outlier: 4.451A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE C3290 " --> pdb=" O ASN C3286 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP C3291 " --> pdb=" O ASN C3287 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.175A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C3301 " --> pdb=" O LYS C3297 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 6.129A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3329 removed outlier: 5.287A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 4.474A pdb=" N LYS C3329 " --> pdb=" O LYS C3325 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3605 removed outlier: 4.936A pdb=" N MET C3605 " --> pdb=" O ALA C3601 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.796A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.198A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.402A 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: 4.576A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.979A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.888A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.544A pdb=" N ILE C3744 " --> pdb=" O VAL C3740 " (cutoff:3.500A) removed outlier: 3.861A 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: 4.672A 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 3826 through 3848 removed outlier: 5.331A pdb=" N LEU C3830 " --> pdb=" O GLY C3826 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C3831 " --> pdb=" O GLU C3827 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP C3832 " --> pdb=" O LYS C3828 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP C3833 " --> pdb=" O VAL C3829 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU C3834 " --> pdb=" O LEU C3830 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE C3835 " --> pdb=" O GLN C3831 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.625A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 3.628A pdb=" N VAL C3875 " --> pdb=" O ILE C3871 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C3892 " --> pdb=" O PHE C3888 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 removed outlier: 3.539A pdb=" N ILE C3924 " --> pdb=" O LEU C3920 " (cutoff:3.500A) Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.505A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.705A pdb=" N LYS C3976 " --> pdb=" O MET C3972 " (cutoff:3.500A) Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 3.550A pdb=" N PHE C4020 " --> pdb=" O PHE C4016 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.253A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 Proline residue: C4090 - end of helix Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4181 through 4208 removed outlier: 4.911A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4259 removed outlier: 4.322A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4272 removed outlier: 4.491A pdb=" N GLN C4267 " --> pdb=" O SER C4263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.852A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 3.813A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.206A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4569 through 4612 removed outlier: 3.523A pdb=" N ARG C4573 " --> pdb=" O GLU C4569 " (cutoff:3.500A) removed outlier: 4.117A 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: 3.730A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.778A 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: 4.653A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4701 removed outlier: 3.783A pdb=" N ILE C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) Processing helix chain 'C' and resid 4702 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.897A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.743A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.885A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.097A 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: 4.509A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 5.177A 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: 3.550A pdb=" N GLY C4820 " --> pdb=" O HIS C4816 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.193A 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: 4.054A 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 1772 through 1778 removed outlier: 4.586A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.879A 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: 4.824A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.878A 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: 4.115A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.681A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.611A 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: 3.631A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.044A 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: 4.807A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.793A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.351A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.229A 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 590 removed outlier: 3.748A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.631A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.609A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.652A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.551A 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 857 through 862 removed outlier: 4.998A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.915A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.069A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 4.106A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 4.534A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.086A pdb=" N ILE D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 987 " --> pdb=" O LEU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 982 through 987' Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.826A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.099A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.851A 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: 3.848A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.159A 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 1494 Processing helix chain 'D' and resid 1498 through 1503 removed outlier: 4.564A pdb=" N ASN D1502 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1498 through 1503' Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.767A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.155A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.638A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D1666 " --> pdb=" O SER D1662 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.879A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.935A 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 1722 removed outlier: 3.696A pdb=" N MET D1721 " --> pdb=" O ALA D1717 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.560A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1802 Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1899 through 1948 removed outlier: 4.253A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1954 through 1965 removed outlier: 3.804A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 3.837A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.511A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.695A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.580A 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: 3.924A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.406A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.865A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 4.066A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.626A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.317A 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: 4.218A 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: 3.629A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D2301 " --> pdb=" O ARG D2297 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D2302 " --> pdb=" O TYR D2298 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.582A 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: 9.100A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.728A 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: 5.754A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.808A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 3.625A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2510 through 2532 removed outlier: 3.518A pdb=" N THR D2522 " --> pdb=" O ARG D2518 " (cutoff:3.500A) removed outlier: 5.478A 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: 4.205A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP D2546 " --> pdb=" O ALA D2542 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2581 removed outlier: 3.500A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG D2581 " --> pdb=" O CYS D2577 " (cutoff:3.500A) Processing helix chain 'D' and resid 2582 through 2596 removed outlier: 4.445A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.802A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.189A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (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 2691 through 2696 removed outlier: 3.850A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D2696 " --> pdb=" O GLN D2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2691 through 2696' Processing helix chain 'D' and resid 2714 through 2740 removed outlier: 4.103A pdb=" N GLU D2718 " --> pdb=" O PRO D2714 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR D2719 " --> pdb=" O GLU D2715 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.459A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 4.482A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.403A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.761A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D2893 " --> pdb=" O ALA D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2921 removed outlier: 4.024A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE D2921 " --> pdb=" O ILE D2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2916 through 2921' Processing helix chain 'D' and resid 2922 through 2947 removed outlier: 3.870A pdb=" N GLY D2945 " --> pdb=" O LEU D2941 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.694A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix removed outlier: 3.541A pdb=" N PHE D2975 " --> pdb=" O ILE D2971 " (cutoff:3.500A) Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 5.150A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3048 removed outlier: 3.839A pdb=" N VAL D3045 " --> pdb=" O ASP D3041 " (cutoff:3.500A) Processing helix chain 'D' and resid 3050 through 3078 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.010A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.109A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 3.766A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 4.436A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3180' Processing helix chain 'D' and resid 3182 through 3188 Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.857A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 4.549A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 4.206A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3250 removed outlier: 5.152A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix Processing helix chain 'D' and resid 3253 through 3258 Proline residue: D3258 - end of helix Processing helix chain 'D' and resid 3269 through 3291 removed outlier: 4.451A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE D3290 " --> pdb=" O ASN D3286 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP D3291 " --> pdb=" O ASN D3287 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.175A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D3301 " --> pdb=" O LYS D3297 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 6.130A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3329 removed outlier: 5.287A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 4.474A pdb=" N LYS D3329 " --> pdb=" O LYS D3325 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3605 removed outlier: 4.935A pdb=" N MET D3605 " --> pdb=" O ALA D3601 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.797A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.197A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.402A 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: 4.576A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.979A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.889A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.544A pdb=" N ILE D3744 " --> pdb=" O VAL D3740 " (cutoff:3.500A) removed outlier: 3.861A 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: 4.671A 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 3826 through 3848 removed outlier: 5.331A pdb=" N LEU D3830 " --> pdb=" O GLY D3826 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN D3831 " --> pdb=" O GLU D3827 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP D3832 " --> pdb=" O LYS D3828 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP D3833 " --> pdb=" O VAL D3829 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU D3834 " --> pdb=" O LEU D3830 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE D3835 " --> pdb=" O GLN D3831 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.624A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 3.628A pdb=" N VAL D3875 " --> pdb=" O ILE D3871 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR D3892 " --> pdb=" O PHE D3888 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 removed outlier: 3.539A pdb=" N ILE D3924 " --> pdb=" O LEU D3920 " (cutoff:3.500A) Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.505A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.705A pdb=" N LYS D3976 " --> pdb=" O MET D3972 " (cutoff:3.500A) Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 3.549A pdb=" N PHE D4020 " --> pdb=" O PHE D4016 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.253A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 Proline residue: D4090 - end of helix Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4181 through 4208 removed outlier: 4.911A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4259 removed outlier: 4.323A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4272 removed outlier: 4.491A pdb=" N GLN D4267 " --> pdb=" O SER D4263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.852A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 3.814A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.206A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4569 through 4612 removed outlier: 3.522A pdb=" N ARG D4573 " --> pdb=" O GLU D4569 " (cutoff:3.500A) removed outlier: 4.118A 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: 3.731A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.779A 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: 4.653A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4701 removed outlier: 3.784A pdb=" N ILE D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) Processing helix chain 'D' and resid 4702 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.897A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.743A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.885A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.096A 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: 4.508A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 5.178A 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: 3.550A pdb=" N GLY D4820 " --> pdb=" O HIS D4816 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.195A 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: 4.055A 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 1772 through 1778 removed outlier: 4.586A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.645A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.158A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.803A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.645A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.158A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.803A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.644A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.158A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.803A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.644A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.157A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.802A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.290A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.022A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.670A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (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 192 through 196 Processing sheet with id= 5, first strand: chain 'A' and resid 260 through 264 removed outlier: 5.285A pdb=" N LEU A 236 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N VAL A 247 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 15.097A pdb=" N LEU A 234 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 7, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 8, first strand: chain 'A' and resid 737 through 740 removed outlier: 5.486A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.888A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 776 through 780 removed outlier: 5.529A pdb=" N GLN A 776 " --> pdb=" O GLY A1470 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A1478 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.377A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 948 through 952 Processing sheet with id= 13, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= 14, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 7.071A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 5.168A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.887A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 4.837A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2741 through 2744 removed outlier: 3.597A pdb=" N GLY A2744 " --> pdb=" O GLN A2754 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 3.806A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.571A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.290A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.022A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.670A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= 24, first strand: chain 'B' and resid 192 through 196 Processing sheet with id= 25, first strand: chain 'B' and resid 260 through 264 removed outlier: 5.284A pdb=" N LEU B 236 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N VAL B 247 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 15.098A pdb=" N LEU B 234 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 27, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 28, first strand: chain 'B' and resid 737 through 740 removed outlier: 5.486A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.888A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 776 through 780 removed outlier: 5.528A pdb=" N GLN B 776 " --> pdb=" O GLY B1470 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B1478 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.378A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 948 through 952 Processing sheet with id= 33, first strand: chain 'B' and resid 1016 through 1019 Processing sheet with id= 34, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 7.071A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 5.167A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.887A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 4.836A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 2741 through 2744 removed outlier: 3.597A pdb=" N GLY B2744 " --> pdb=" O GLN B2754 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 3.806A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.572A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.289A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.022A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.670A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= 44, first strand: chain 'C' and resid 192 through 196 Processing sheet with id= 45, first strand: chain 'C' and resid 260 through 264 removed outlier: 5.284A pdb=" N LEU C 236 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N VAL C 247 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 15.097A pdb=" N LEU C 234 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 47, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 48, first strand: chain 'C' and resid 737 through 740 removed outlier: 5.486A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.888A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 776 through 780 removed outlier: 5.529A pdb=" N GLN C 776 " --> pdb=" O GLY C1470 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C1478 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.378A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 948 through 952 Processing sheet with id= 53, first strand: chain 'C' and resid 1016 through 1019 Processing sheet with id= 54, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 7.072A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 5.168A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.887A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 4.836A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 2741 through 2744 removed outlier: 3.596A pdb=" N GLY C2744 " --> pdb=" O GLN C2754 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 3.807A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.571A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.289A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.023A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.671A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= 64, first strand: chain 'D' and resid 192 through 196 Processing sheet with id= 65, first strand: chain 'D' and resid 260 through 264 removed outlier: 5.285A pdb=" N LEU D 236 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N VAL D 247 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 15.097A pdb=" N LEU D 234 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 67, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 68, first strand: chain 'D' and resid 737 through 740 removed outlier: 5.486A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.887A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 776 through 780 removed outlier: 5.529A pdb=" N GLN D 776 " --> pdb=" O GLY D1470 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D1478 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.378A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 948 through 952 Processing sheet with id= 73, first strand: chain 'D' and resid 1016 through 1019 Processing sheet with id= 74, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 7.071A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 5.168A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.888A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 4.837A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 2741 through 2744 removed outlier: 3.597A pdb=" N GLY D2744 " --> pdb=" O GLN D2754 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 3.807A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.571A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.859A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN E 21 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.858A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN F 21 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.858A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN G 21 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.859A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN H 21 " --> pdb=" O ILE H 51 " (cutoff:3.500A) 7313 hydrogen bonds defined for protein. 21835 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: 105.03 Time building geometry restraints manager: 42.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 45393 1.34 - 1.46: 32745 1.46 - 1.59: 61974 1.59 - 1.71: 24 1.71 - 1.83: 1512 Bond restraints: 141648 Sorted by residual: bond pdb=" CA MET C2234 " pdb=" C MET C2234 " ideal model delta sigma weight residual 1.522 1.488 0.035 1.40e-02 5.10e+03 6.09e+00 bond pdb=" CA MET D2234 " pdb=" C MET D2234 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.40e-02 5.10e+03 5.65e+00 bond pdb=" CA MET B2234 " pdb=" C MET B2234 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.40e-02 5.10e+03 5.51e+00 bond pdb=" CA MET A2234 " pdb=" C MET A2234 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.40e-02 5.10e+03 5.50e+00 bond pdb=" CG LEU C 892 " pdb=" CD2 LEU C 892 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.85e+00 ... (remaining 141643 not shown) Histogram of bond angle deviations from ideal: 94.12 - 103.27: 1621 103.27 - 112.42: 72370 112.42 - 121.56: 87015 121.56 - 130.71: 29618 130.71 - 139.86: 768 Bond angle restraints: 191392 Sorted by residual: angle pdb=" CB MET A3215 " pdb=" CG MET A3215 " pdb=" SD MET A3215 " ideal model delta sigma weight residual 112.70 129.15 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" CB MET C3215 " pdb=" CG MET C3215 " pdb=" SD MET C3215 " ideal model delta sigma weight residual 112.70 129.14 -16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" CB MET B3215 " pdb=" CG MET B3215 " pdb=" SD MET B3215 " ideal model delta sigma weight residual 112.70 129.13 -16.43 3.00e+00 1.11e-01 3.00e+01 angle pdb=" CB MET D3215 " pdb=" CG MET D3215 " pdb=" SD MET D3215 " ideal model delta sigma weight residual 112.70 129.12 -16.42 3.00e+00 1.11e-01 3.00e+01 angle pdb=" C VAL A3310 " pdb=" N LYS A3311 " pdb=" CA LYS A3311 " ideal model delta sigma weight residual 120.68 128.46 -7.78 1.52e+00 4.33e-01 2.62e+01 ... (remaining 191387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 76632 18.01 - 36.02: 7142 36.02 - 54.02: 1085 54.02 - 72.03: 453 72.03 - 90.04: 88 Dihedral angle restraints: 85400 sinusoidal: 35040 harmonic: 50360 Sorted by residual: dihedral pdb=" CA PHE B4640 " pdb=" C PHE B4640 " pdb=" N PRO B4641 " pdb=" CA PRO B4641 " ideal model delta harmonic sigma weight residual 180.00 -137.47 -42.53 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA PHE D4640 " pdb=" C PHE D4640 " pdb=" N PRO D4641 " pdb=" CA PRO D4641 " ideal model delta harmonic sigma weight residual 180.00 -137.48 -42.52 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual 180.00 -137.49 -42.51 0 5.00e+00 4.00e-02 7.23e+01 ... (remaining 85397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 17095 0.052 - 0.104: 3555 0.104 - 0.156: 305 0.156 - 0.208: 25 0.208 - 0.260: 8 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CB ILE A3122 " pdb=" CA ILE A3122 " pdb=" CG1 ILE A3122 " pdb=" CG2 ILE A3122 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE B3122 " pdb=" CA ILE B3122 " pdb=" CG1 ILE B3122 " pdb=" CG2 ILE B3122 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE C3122 " pdb=" CA ILE C3122 " pdb=" CG1 ILE C3122 " pdb=" CG2 ILE C3122 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 20985 not shown) Planarity restraints: 24588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C4640 " 0.097 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO C4641 " -0.258 5.00e-02 4.00e+02 pdb=" CA PRO C4641 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO C4641 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D4640 " 0.097 5.00e-02 4.00e+02 1.49e-01 3.54e+01 pdb=" N PRO D4641 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO D4641 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO D4641 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " 0.097 5.00e-02 4.00e+02 1.49e-01 3.54e+01 pdb=" N PRO A4641 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " 0.076 5.00e-02 4.00e+02 ... (remaining 24585 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 2217 2.68 - 3.24: 140459 3.24 - 3.79: 227736 3.79 - 4.35: 303345 4.35 - 4.90: 489407 Nonbonded interactions: 1163164 Sorted by model distance: nonbonded pdb=" O PHE A1768 " pdb=" OH TYR E 83 " model vdw 2.129 2.440 nonbonded pdb=" O ASP C3025 " pdb=" OG SER C3028 " model vdw 2.141 2.440 nonbonded pdb=" O ASP A3025 " pdb=" OG SER A3028 " model vdw 2.142 2.440 nonbonded pdb=" O ASP D3025 " pdb=" OG SER D3028 " model vdw 2.142 2.440 nonbonded pdb=" O ASP B3025 " pdb=" OG SER B3028 " model vdw 2.143 2.440 ... (remaining 1163159 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 5003)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.710 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: 0.090 Extract box with map and model: 28.280 Check model and map are aligned: 1.380 Set scattering table: 0.840 Process input model: 446.790 Find NCS groups from input model: 7.050 Set up NCS constraints: 1.040 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:2.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 495.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 0.073 141648 Z= 0.265 Angle : 0.697 16.446 191392 Z= 0.396 Chirality : 0.041 0.260 20988 Planarity : 0.005 0.149 24588 Dihedral : 14.669 90.038 52924 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 0.58 % Allowed : 0.56 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.86 (0.06), residues: 17212 helix: 1.47 (0.06), residues: 8964 sheet: 0.19 (0.12), residues: 1708 loop : -0.52 (0.07), residues: 6540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP C 893 HIS 0.016 0.001 HIS D4055 PHE 0.037 0.002 PHE C3854 TYR 0.043 0.001 TYR B4567 ARG 0.013 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1001 time to evaluate : 12.678 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: A 393 MET cc_start: 0.8675 (mmm) cc_final: 0.7723 (tpt) REVERT: A 890 HIS cc_start: 0.9494 (t-90) cc_final: 0.9017 (t-90) REVERT: A 995 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8549 (mmm) REVERT: A 999 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9091 (mm) REVERT: A 1062 TYR cc_start: 0.7507 (m-80) cc_final: 0.7009 (m-80) REVERT: A 1165 MET cc_start: 0.8448 (mtm) cc_final: 0.8235 (mtp) REVERT: A 2442 MET cc_start: 0.8144 (mmm) cc_final: 0.7865 (mmp) REVERT: A 2681 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7345 (mmm) REVERT: A 2695 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7988 (pmm) REVERT: A 2720 PHE cc_start: 0.9002 (t80) cc_final: 0.8506 (t80) REVERT: A 2727 HIS cc_start: 0.8965 (t-90) cc_final: 0.8134 (t-90) REVERT: A 2731 LYS cc_start: 0.9008 (ptpp) cc_final: 0.8468 (pttt) REVERT: A 2732 TRP cc_start: 0.8938 (t60) cc_final: 0.8420 (t60) REVERT: A 2734 MET cc_start: 0.9033 (mmp) cc_final: 0.8510 (mmt) REVERT: A 2772 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8593 (ptt90) REVERT: A 2779 LEU cc_start: 0.9397 (mt) cc_final: 0.9073 (mt) REVERT: A 2844 MET cc_start: 0.8612 (ptm) cc_final: 0.8324 (tmm) REVERT: A 2855 LYS cc_start: 0.9228 (mptt) cc_final: 0.9002 (mmtt) REVERT: A 2877 LEU cc_start: 0.9526 (mt) cc_final: 0.8932 (mt) REVERT: A 3057 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8802 (pp) REVERT: A 3104 MET cc_start: 0.8419 (ptm) cc_final: 0.8007 (ptt) REVERT: A 3137 LEU cc_start: 0.9165 (mt) cc_final: 0.8880 (mp) REVERT: A 3235 MET cc_start: 0.7054 (ptt) cc_final: 0.6335 (ppp) REVERT: A 3242 LEU cc_start: 0.9106 (mt) cc_final: 0.8806 (mt) REVERT: A 3304 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8332 (tp40) REVERT: A 3323 MET cc_start: 0.8683 (mmp) cc_final: 0.8476 (mmm) REVERT: A 4002 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8383 (tmm) REVERT: B 393 MET cc_start: 0.8647 (mmm) cc_final: 0.7785 (tpt) REVERT: B 890 HIS cc_start: 0.9514 (t-90) cc_final: 0.9020 (t-90) REVERT: B 935 MET cc_start: 0.8831 (ppp) cc_final: 0.8593 (ppp) REVERT: B 995 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8482 (mmm) REVERT: B 999 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9038 (mm) REVERT: B 1062 TYR cc_start: 0.7373 (m-80) cc_final: 0.6992 (m-80) REVERT: B 1165 MET cc_start: 0.8410 (mtm) cc_final: 0.8154 (mtp) REVERT: B 2192 MET cc_start: 0.8087 (tpp) cc_final: 0.7777 (tpt) REVERT: B 2442 MET cc_start: 0.8101 (mmm) cc_final: 0.7836 (mmp) REVERT: B 2727 HIS cc_start: 0.8894 (t-90) cc_final: 0.8274 (t-90) REVERT: B 2731 LYS cc_start: 0.9002 (ptpp) cc_final: 0.8598 (pttm) REVERT: B 2734 MET cc_start: 0.9023 (mmp) cc_final: 0.8549 (mmm) REVERT: B 2772 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8478 (ptt90) REVERT: B 2779 LEU cc_start: 0.9452 (mt) cc_final: 0.9198 (mt) REVERT: B 2843 MET cc_start: 0.8800 (mtp) cc_final: 0.8459 (mtp) REVERT: B 2844 MET cc_start: 0.8698 (ptm) cc_final: 0.8457 (tmm) REVERT: B 3057 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8840 (pp) REVERT: B 3104 MET cc_start: 0.8495 (ptm) cc_final: 0.8231 (ptm) REVERT: B 3137 LEU cc_start: 0.9133 (mt) cc_final: 0.8839 (mt) REVERT: B 3304 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8421 (tp-100) REVERT: C 393 MET cc_start: 0.8663 (mmm) cc_final: 0.7715 (tpt) REVERT: C 890 HIS cc_start: 0.9517 (t-90) cc_final: 0.9032 (t-90) REVERT: C 935 MET cc_start: 0.8905 (ppp) cc_final: 0.8650 (ppp) REVERT: C 995 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8340 (mmm) REVERT: C 1062 TYR cc_start: 0.7336 (m-80) cc_final: 0.6951 (m-80) REVERT: C 2442 MET cc_start: 0.8152 (mmm) cc_final: 0.7907 (mmp) REVERT: C 2727 HIS cc_start: 0.8938 (t-90) cc_final: 0.8428 (t-90) REVERT: C 2731 LYS cc_start: 0.8997 (ptpp) cc_final: 0.8624 (pttm) REVERT: C 2734 MET cc_start: 0.9041 (mmp) cc_final: 0.8564 (mmm) REVERT: C 2771 TYR cc_start: 0.9027 (m-10) cc_final: 0.8809 (m-80) REVERT: C 2772 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8538 (ptt90) REVERT: C 2779 LEU cc_start: 0.9469 (mt) cc_final: 0.9209 (mt) REVERT: C 2843 MET cc_start: 0.8786 (mtp) cc_final: 0.8438 (mtp) REVERT: C 3057 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8848 (pp) REVERT: C 3104 MET cc_start: 0.8486 (ptm) cc_final: 0.8248 (ptm) REVERT: C 3137 LEU cc_start: 0.9143 (mt) cc_final: 0.8856 (mt) REVERT: C 3304 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8431 (tp-100) REVERT: C 4002 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8379 (tmm) REVERT: C 4814 MET cc_start: 0.8047 (mmm) cc_final: 0.7762 (mmm) REVERT: D 82 LEU cc_start: 0.9192 (mt) cc_final: 0.8700 (mt) REVERT: D 128 MET cc_start: 0.8864 (mtm) cc_final: 0.8553 (mtm) REVERT: D 393 MET cc_start: 0.8625 (mmm) cc_final: 0.7523 (tpt) REVERT: D 890 HIS cc_start: 0.9512 (t-90) cc_final: 0.9035 (t-90) REVERT: D 935 MET cc_start: 0.8868 (ppp) cc_final: 0.8588 (ppp) REVERT: D 995 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8445 (mmm) REVERT: D 1062 TYR cc_start: 0.7414 (m-80) cc_final: 0.6902 (m-80) REVERT: D 2442 MET cc_start: 0.8177 (mmm) cc_final: 0.7893 (mmm) REVERT: D 2727 HIS cc_start: 0.8957 (t-90) cc_final: 0.8254 (t-90) REVERT: D 2731 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8581 (pttt) REVERT: D 2732 TRP cc_start: 0.8964 (t60) cc_final: 0.8600 (t60) REVERT: D 2734 MET cc_start: 0.9011 (mmp) cc_final: 0.8464 (mmt) REVERT: D 2757 MET cc_start: 0.7949 (mmp) cc_final: 0.7642 (mmm) REVERT: D 2771 TYR cc_start: 0.8968 (m-10) cc_final: 0.8708 (m-10) REVERT: D 2772 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8513 (ptt90) REVERT: D 2779 LEU cc_start: 0.9450 (mt) cc_final: 0.9216 (mt) REVERT: D 3239 LEU cc_start: 0.9201 (mp) cc_final: 0.8954 (tp) REVERT: D 4002 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8302 (tmm) REVERT: H 54 GLN cc_start: 0.8587 (mp10) cc_final: 0.8384 (mp10) outliers start: 88 outliers final: 19 residues processed: 1013 average time/residue: 1.1818 time to fit residues: 2106.9826 Evaluate side-chains 922 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 885 time to evaluate : 11.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 2772 ARG Chi-restraints excluded: chain A residue 3057 LEU Chi-restraints excluded: chain A residue 3190 ARG Chi-restraints excluded: chain A residue 3215 MET Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2681 MET Chi-restraints excluded: chain B residue 2772 ARG Chi-restraints excluded: chain B residue 3057 LEU Chi-restraints excluded: chain B residue 3190 ARG Chi-restraints excluded: chain B residue 3215 MET Chi-restraints excluded: chain B residue 3316 LYS Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 2681 MET Chi-restraints excluded: chain C residue 2772 ARG Chi-restraints excluded: chain C residue 3057 LEU Chi-restraints excluded: chain C residue 3190 ARG Chi-restraints excluded: chain C residue 3215 MET Chi-restraints excluded: chain C residue 3316 LYS Chi-restraints excluded: chain C residue 4002 MET Chi-restraints excluded: chain D residue 995 MET Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2772 ARG Chi-restraints excluded: chain D residue 3190 ARG Chi-restraints excluded: chain D residue 3215 MET Chi-restraints excluded: chain D residue 4002 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 9.9990 chunk 1309 optimal weight: 8.9990 chunk 726 optimal weight: 20.0000 chunk 447 optimal weight: 9.9990 chunk 883 optimal weight: 10.0000 chunk 699 optimal weight: 6.9990 chunk 1354 optimal weight: 4.9990 chunk 524 optimal weight: 6.9990 chunk 823 optimal weight: 9.9990 chunk 1008 optimal weight: 6.9990 chunk 1569 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 604 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 ASN A 914 GLN ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN A2316 ASN ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4736 ASN A4933 HIS E 26 HIS ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN B 914 GLN ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1974 ASN B2316 ASN ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2899 ASN ** B3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4201 GLN B4736 ASN B4903 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 HIS C 604 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN C 914 GLN ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2316 ASN ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2899 ASN ** C3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4736 ASN C4903 HIS ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 HIS D 604 HIS ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 896 ASN D 914 GLN ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2316 ASN ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2899 ASN ** D3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4736 ASN D4903 HIS D4933 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 141648 Z= 0.505 Angle : 0.663 16.777 191392 Z= 0.344 Chirality : 0.044 0.201 20988 Planarity : 0.005 0.142 24588 Dihedral : 6.110 78.464 19140 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.20 % Rotamer: Outliers : 0.38 % Allowed : 4.10 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.94 (0.06), residues: 17212 helix: 1.60 (0.06), residues: 8992 sheet: 0.02 (0.12), residues: 1816 loop : -0.56 (0.08), residues: 6404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D2773 HIS 0.012 0.002 HIS C3700 PHE 0.034 0.002 PHE C3854 TYR 0.033 0.002 TYR A4520 ARG 0.010 0.001 ARG A3730 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 969 time to evaluate : 12.172 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: A 309 MET cc_start: 0.7265 (mmp) cc_final: 0.6998 (mmp) REVERT: A 890 HIS cc_start: 0.9312 (t-90) cc_final: 0.9103 (t-90) REVERT: A 995 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8459 (mmp) REVERT: A 999 LEU cc_start: 0.9374 (mm) cc_final: 0.9077 (mm) REVERT: A 1062 TYR cc_start: 0.7494 (m-80) cc_final: 0.7089 (m-80) REVERT: A 1165 MET cc_start: 0.8554 (mtm) cc_final: 0.8290 (mtp) REVERT: A 1421 MET cc_start: 0.8973 (mmp) cc_final: 0.8744 (mmp) REVERT: A 2442 MET cc_start: 0.8191 (mmm) cc_final: 0.7825 (mmm) REVERT: A 2681 MET cc_start: 0.7799 (tpt) cc_final: 0.7459 (mmp) REVERT: A 2695 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8049 (pmm) REVERT: A 2720 PHE cc_start: 0.8917 (t80) cc_final: 0.8697 (t80) REVERT: A 2727 HIS cc_start: 0.8954 (t-90) cc_final: 0.8053 (t-90) REVERT: A 2731 LYS cc_start: 0.9007 (ptpp) cc_final: 0.8445 (pttt) REVERT: A 2734 MET cc_start: 0.9077 (mmp) cc_final: 0.8725 (mmm) REVERT: A 2779 LEU cc_start: 0.9356 (mt) cc_final: 0.9026 (mt) REVERT: A 2798 MET cc_start: 0.8067 (mmm) cc_final: 0.7804 (mmm) REVERT: A 2840 MET cc_start: 0.8980 (mtp) cc_final: 0.8756 (mmm) REVERT: A 2843 MET cc_start: 0.8788 (mtp) cc_final: 0.8129 (ttm) REVERT: A 2844 MET cc_start: 0.8635 (ptm) cc_final: 0.8255 (tmm) REVERT: A 2877 LEU cc_start: 0.9553 (mt) cc_final: 0.9314 (mt) REVERT: A 2939 TYR cc_start: 0.8526 (m-80) cc_final: 0.8319 (m-80) REVERT: A 3003 MET cc_start: 0.8779 (ptt) cc_final: 0.8398 (ptm) REVERT: A 3057 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8992 (tp) REVERT: A 3104 MET cc_start: 0.8484 (ptm) cc_final: 0.8113 (ptt) REVERT: A 3235 MET cc_start: 0.7378 (ptt) cc_final: 0.6962 (ppp) REVERT: A 3239 LEU cc_start: 0.9264 (mt) cc_final: 0.8670 (pp) REVERT: A 3304 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8311 (tp40) REVERT: A 3323 MET cc_start: 0.8733 (mmp) cc_final: 0.8504 (mmm) REVERT: A 4274 MET cc_start: 0.6717 (mmm) cc_final: 0.6477 (tpt) REVERT: B 890 HIS cc_start: 0.9295 (t-90) cc_final: 0.8988 (t70) REVERT: B 935 MET cc_start: 0.8826 (ppp) cc_final: 0.8626 (ppp) REVERT: B 995 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8398 (mmp) REVERT: B 999 LEU cc_start: 0.9334 (mm) cc_final: 0.9005 (mm) REVERT: B 1062 TYR cc_start: 0.7374 (m-80) cc_final: 0.7107 (m-80) REVERT: B 1165 MET cc_start: 0.8538 (mtm) cc_final: 0.8275 (mtp) REVERT: B 1168 MET cc_start: 0.8406 (ttp) cc_final: 0.8178 (mtp) REVERT: B 2234 MET cc_start: 0.8740 (mtp) cc_final: 0.8532 (mtp) REVERT: B 2442 MET cc_start: 0.8163 (mmm) cc_final: 0.7837 (mmp) REVERT: B 2681 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7512 (mmp) REVERT: B 2727 HIS cc_start: 0.8942 (t-90) cc_final: 0.7925 (t-90) REVERT: B 2731 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8544 (pttt) REVERT: B 2732 TRP cc_start: 0.9105 (t-100) cc_final: 0.8778 (t-100) REVERT: B 2734 MET cc_start: 0.9041 (mmp) cc_final: 0.8663 (mmm) REVERT: B 2775 ILE cc_start: 0.9477 (mt) cc_final: 0.9187 (tt) REVERT: B 2779 LEU cc_start: 0.9412 (mt) cc_final: 0.9103 (mt) REVERT: B 2843 MET cc_start: 0.8825 (mtp) cc_final: 0.8620 (mtp) REVERT: B 2844 MET cc_start: 0.8723 (ptm) cc_final: 0.8419 (tmm) REVERT: B 2939 TYR cc_start: 0.8582 (m-80) cc_final: 0.8330 (m-80) REVERT: B 3003 MET cc_start: 0.8655 (ptm) cc_final: 0.8349 (ptm) REVERT: B 3057 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8968 (pp) REVERT: B 3104 MET cc_start: 0.8537 (ptm) cc_final: 0.8286 (ptm) REVERT: B 3137 LEU cc_start: 0.9229 (mt) cc_final: 0.8903 (mt) REVERT: B 3235 MET cc_start: 0.7157 (ptt) cc_final: 0.6727 (tmm) REVERT: B 3239 LEU cc_start: 0.9304 (mt) cc_final: 0.8993 (pp) REVERT: B 4048 PHE cc_start: 0.8626 (t80) cc_final: 0.8328 (t80) REVERT: C 890 HIS cc_start: 0.9325 (t-90) cc_final: 0.8879 (t70) REVERT: C 935 MET cc_start: 0.8892 (ppp) cc_final: 0.8680 (ppp) REVERT: C 995 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8285 (mmp) REVERT: C 1062 TYR cc_start: 0.7255 (m-80) cc_final: 0.6953 (m-80) REVERT: C 1168 MET cc_start: 0.8320 (ttp) cc_final: 0.8063 (mtp) REVERT: C 2142 MET cc_start: 0.8370 (tpp) cc_final: 0.8095 (tpp) REVERT: C 2442 MET cc_start: 0.8197 (mmm) cc_final: 0.7899 (mmp) REVERT: C 2681 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7464 (mmp) REVERT: C 2727 HIS cc_start: 0.8958 (t-90) cc_final: 0.8246 (t-90) REVERT: C 2731 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8584 (pttt) REVERT: C 2732 TRP cc_start: 0.9141 (t-100) cc_final: 0.8860 (t-100) REVERT: C 2734 MET cc_start: 0.9063 (mmp) cc_final: 0.8689 (mmm) REVERT: C 2775 ILE cc_start: 0.9503 (mt) cc_final: 0.9226 (tt) REVERT: C 2779 LEU cc_start: 0.9411 (mt) cc_final: 0.9131 (mt) REVERT: C 2798 MET cc_start: 0.8259 (mmm) cc_final: 0.7985 (mmm) REVERT: C 2840 MET cc_start: 0.9084 (mtp) cc_final: 0.8716 (mmm) REVERT: C 2939 TYR cc_start: 0.8608 (m-80) cc_final: 0.8348 (m-80) REVERT: C 3003 MET cc_start: 0.8660 (ptm) cc_final: 0.8354 (ptm) REVERT: C 3057 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8981 (pp) REVERT: C 3104 MET cc_start: 0.8532 (ptm) cc_final: 0.8296 (ptm) REVERT: C 3137 LEU cc_start: 0.9253 (mt) cc_final: 0.8949 (mt) REVERT: C 3235 MET cc_start: 0.7116 (ptt) cc_final: 0.6614 (tmm) REVERT: C 3239 LEU cc_start: 0.9282 (mt) cc_final: 0.8978 (pp) REVERT: C 3304 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8417 (tp-100) REVERT: D 890 HIS cc_start: 0.9316 (t-90) cc_final: 0.8986 (t-90) REVERT: D 935 MET cc_start: 0.8855 (ppp) cc_final: 0.8650 (ppp) REVERT: D 995 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8267 (mmp) REVERT: D 1062 TYR cc_start: 0.7285 (m-80) cc_final: 0.6857 (m-80) REVERT: D 1421 MET cc_start: 0.8976 (mmp) cc_final: 0.8769 (mmp) REVERT: D 2442 MET cc_start: 0.8238 (mmm) cc_final: 0.7949 (mmp) REVERT: D 2727 HIS cc_start: 0.8963 (t-90) cc_final: 0.8102 (t-90) REVERT: D 2731 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8579 (pttt) REVERT: D 2734 MET cc_start: 0.9096 (mmp) cc_final: 0.8692 (mmm) REVERT: D 2775 ILE cc_start: 0.9470 (mt) cc_final: 0.9208 (tt) REVERT: D 2779 LEU cc_start: 0.9400 (mt) cc_final: 0.9143 (mt) REVERT: D 2840 MET cc_start: 0.9075 (mtp) cc_final: 0.8809 (mmm) REVERT: D 2939 TYR cc_start: 0.8760 (m-80) cc_final: 0.8525 (m-80) REVERT: D 3003 MET cc_start: 0.8725 (ptm) cc_final: 0.8425 (ptm) REVERT: D 3239 LEU cc_start: 0.9258 (mp) cc_final: 0.8835 (mt) REVERT: G 30 MET cc_start: 0.7894 (mtm) cc_final: 0.7642 (mtm) outliers start: 57 outliers final: 10 residues processed: 980 average time/residue: 1.1736 time to fit residues: 2032.3788 Evaluate side-chains 940 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 920 time to evaluate : 11.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 3057 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2681 MET Chi-restraints excluded: chain B residue 3057 LEU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2681 MET Chi-restraints excluded: chain C residue 3057 LEU Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 995 MET Chi-restraints excluded: chain D residue 1168 MET Chi-restraints excluded: chain D residue 1720 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 9.9990 chunk 487 optimal weight: 0.9990 chunk 1306 optimal weight: 20.0000 chunk 1068 optimal weight: 20.0000 chunk 432 optimal weight: 20.0000 chunk 1572 optimal weight: 5.9990 chunk 1698 optimal weight: 7.9990 chunk 1400 optimal weight: 7.9990 chunk 1558 optimal weight: 20.0000 chunk 535 optimal weight: 9.9990 chunk 1261 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3975 GLN A4488 GLN A4903 HIS ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 HIS ** B 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3024 ASN ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3178 HIS ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3975 GLN B4488 GLN ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 HIS ** C 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1974 ASN ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3024 ASN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 HIS ** C3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3975 GLN C4488 GLN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3024 ASN ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3178 HIS ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3975 GLN D4488 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 141648 Z= 0.352 Angle : 0.600 15.464 191392 Z= 0.308 Chirality : 0.041 0.233 20988 Planarity : 0.005 0.136 24588 Dihedral : 5.555 75.708 19054 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 0.40 % Allowed : 5.41 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.12 (0.06), residues: 17212 helix: 1.81 (0.06), residues: 8944 sheet: -0.07 (0.12), residues: 1828 loop : -0.49 (0.08), residues: 6440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D2773 HIS 0.011 0.001 HIS A3700 PHE 0.035 0.002 PHE D2954 TYR 0.026 0.002 TYR D3228 ARG 0.017 0.001 ARG C2772 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 944 time to evaluate : 11.862 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 393 MET cc_start: 0.8705 (mmm) cc_final: 0.8022 (mmm) REVERT: A 890 HIS cc_start: 0.9253 (t-90) cc_final: 0.8324 (t-90) REVERT: A 995 MET cc_start: 0.8766 (tpp) cc_final: 0.8015 (tpp) REVERT: A 999 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 1062 TYR cc_start: 0.7516 (m-80) cc_final: 0.7082 (m-80) REVERT: A 1165 MET cc_start: 0.8530 (mtm) cc_final: 0.8267 (mtp) REVERT: A 1421 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8715 (mmp) REVERT: A 2192 MET cc_start: 0.8629 (tpp) cc_final: 0.8419 (tpt) REVERT: A 2442 MET cc_start: 0.8225 (mmm) cc_final: 0.7938 (mmp) REVERT: A 2695 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8048 (pmm) REVERT: A 2720 PHE cc_start: 0.9026 (t80) cc_final: 0.8788 (t80) REVERT: A 2727 HIS cc_start: 0.9005 (t-90) cc_final: 0.8058 (t-90) REVERT: A 2731 LYS cc_start: 0.8984 (ptpp) cc_final: 0.8403 (pttt) REVERT: A 2734 MET cc_start: 0.9103 (mmp) cc_final: 0.8770 (mmm) REVERT: A 2772 ARG cc_start: 0.8909 (mtm110) cc_final: 0.8580 (mtm110) REVERT: A 2779 LEU cc_start: 0.9324 (mt) cc_final: 0.9028 (mt) REVERT: A 2798 MET cc_start: 0.8017 (mmm) cc_final: 0.7763 (mmm) REVERT: A 2843 MET cc_start: 0.8813 (mtp) cc_final: 0.8188 (ttm) REVERT: A 2844 MET cc_start: 0.8654 (ptm) cc_final: 0.7581 (tmm) REVERT: A 2877 LEU cc_start: 0.9555 (mt) cc_final: 0.9310 (mt) REVERT: A 2939 TYR cc_start: 0.8495 (m-80) cc_final: 0.8220 (m-80) REVERT: A 3003 MET cc_start: 0.8794 (ptt) cc_final: 0.8448 (ptm) REVERT: A 3057 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8931 (pp) REVERT: A 3104 MET cc_start: 0.8481 (ptm) cc_final: 0.8119 (ptt) REVERT: A 3235 MET cc_start: 0.7266 (ptt) cc_final: 0.6771 (ppp) REVERT: A 3239 LEU cc_start: 0.9265 (mt) cc_final: 0.8913 (pp) REVERT: A 3241 MET cc_start: 0.8547 (tpp) cc_final: 0.8325 (tpp) REVERT: B 393 MET cc_start: 0.8664 (mmm) cc_final: 0.7970 (mmm) REVERT: B 890 HIS cc_start: 0.9265 (t-90) cc_final: 0.8242 (t-90) REVERT: B 995 MET cc_start: 0.8747 (tpp) cc_final: 0.8466 (mmm) REVERT: B 1062 TYR cc_start: 0.7306 (m-80) cc_final: 0.7043 (m-80) REVERT: B 1165 MET cc_start: 0.8526 (mtm) cc_final: 0.8254 (mtp) REVERT: B 1168 MET cc_start: 0.8358 (ttp) cc_final: 0.8104 (mtp) REVERT: B 2234 MET cc_start: 0.8719 (mtp) cc_final: 0.8407 (mtp) REVERT: B 2442 MET cc_start: 0.8164 (mmm) cc_final: 0.7910 (mmm) REVERT: B 2727 HIS cc_start: 0.8916 (t-90) cc_final: 0.7952 (t-90) REVERT: B 2731 LYS cc_start: 0.8934 (ptpp) cc_final: 0.8472 (pttt) REVERT: B 2732 TRP cc_start: 0.9051 (t-100) cc_final: 0.8672 (t-100) REVERT: B 2734 MET cc_start: 0.9028 (mmp) cc_final: 0.8658 (mmp) REVERT: B 2772 ARG cc_start: 0.8914 (mtm110) cc_final: 0.8624 (mtm110) REVERT: B 2775 ILE cc_start: 0.9460 (mt) cc_final: 0.9167 (tt) REVERT: B 2779 LEU cc_start: 0.9361 (mt) cc_final: 0.9098 (mt) REVERT: B 2844 MET cc_start: 0.8745 (ptm) cc_final: 0.7679 (tmm) REVERT: B 2939 TYR cc_start: 0.8536 (m-80) cc_final: 0.8207 (m-80) REVERT: B 3003 MET cc_start: 0.8658 (ptm) cc_final: 0.8307 (ptm) REVERT: B 3072 MET cc_start: 0.8427 (tpp) cc_final: 0.8180 (tpt) REVERT: B 3104 MET cc_start: 0.8529 (ptm) cc_final: 0.8282 (ptm) REVERT: B 3137 LEU cc_start: 0.9257 (mt) cc_final: 0.8987 (mt) REVERT: B 3140 LEU cc_start: 0.9173 (mt) cc_final: 0.8840 (mt) REVERT: B 3235 MET cc_start: 0.7205 (ptt) cc_final: 0.6607 (ppp) REVERT: B 3239 LEU cc_start: 0.9223 (mt) cc_final: 0.8872 (pp) REVERT: B 3242 LEU cc_start: 0.9098 (mp) cc_final: 0.8759 (pt) REVERT: C 309 MET cc_start: 0.7390 (mmp) cc_final: 0.7173 (mmp) REVERT: C 393 MET cc_start: 0.8692 (mmm) cc_final: 0.7984 (mmm) REVERT: C 890 HIS cc_start: 0.9345 (t-90) cc_final: 0.8231 (t-90) REVERT: C 935 MET cc_start: 0.8891 (ppp) cc_final: 0.8679 (ppp) REVERT: C 995 MET cc_start: 0.8740 (tpp) cc_final: 0.8435 (mmm) REVERT: C 1062 TYR cc_start: 0.7311 (m-80) cc_final: 0.6939 (m-80) REVERT: C 1113 MET cc_start: 0.8905 (mtm) cc_final: 0.8689 (mtt) REVERT: C 1168 MET cc_start: 0.8256 (ttp) cc_final: 0.8038 (mtp) REVERT: C 2442 MET cc_start: 0.8182 (mmm) cc_final: 0.7929 (mmm) REVERT: C 2727 HIS cc_start: 0.9015 (t-90) cc_final: 0.8032 (t-90) REVERT: C 2731 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8511 (pttt) REVERT: C 2732 TRP cc_start: 0.9095 (t-100) cc_final: 0.8738 (t-100) REVERT: C 2772 ARG cc_start: 0.8924 (mtm110) cc_final: 0.8639 (mtm110) REVERT: C 2775 ILE cc_start: 0.9471 (mt) cc_final: 0.9140 (tt) REVERT: C 2779 LEU cc_start: 0.9340 (mt) cc_final: 0.9067 (mt) REVERT: C 2798 MET cc_start: 0.8209 (mmm) cc_final: 0.7939 (mmm) REVERT: C 2843 MET cc_start: 0.8745 (mtp) cc_final: 0.8456 (mtp) REVERT: C 2844 MET cc_start: 0.8870 (ptp) cc_final: 0.8298 (ppp) REVERT: C 2939 TYR cc_start: 0.8572 (m-80) cc_final: 0.8231 (m-80) REVERT: C 3003 MET cc_start: 0.8662 (ptm) cc_final: 0.8314 (ptm) REVERT: C 3104 MET cc_start: 0.8530 (ptm) cc_final: 0.8296 (ptm) REVERT: C 3233 HIS cc_start: 0.8103 (m90) cc_final: 0.7764 (m170) REVERT: C 3235 MET cc_start: 0.7152 (ptt) cc_final: 0.6562 (ppp) REVERT: C 3239 LEU cc_start: 0.9228 (mt) cc_final: 0.8916 (pp) REVERT: C 4943 MET cc_start: 0.8640 (mtm) cc_final: 0.8397 (mtp) REVERT: D 393 MET cc_start: 0.8684 (mmm) cc_final: 0.7989 (mmm) REVERT: D 890 HIS cc_start: 0.9318 (t-90) cc_final: 0.8265 (t-90) REVERT: D 935 MET cc_start: 0.8864 (ppp) cc_final: 0.8663 (ppp) REVERT: D 995 MET cc_start: 0.8712 (tpp) cc_final: 0.8100 (tpp) REVERT: D 1062 TYR cc_start: 0.7304 (m-80) cc_final: 0.6877 (m-80) REVERT: D 1113 MET cc_start: 0.8904 (mtm) cc_final: 0.8676 (mtt) REVERT: D 1421 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8708 (mmp) REVERT: D 2442 MET cc_start: 0.8229 (mmm) cc_final: 0.7957 (mmm) REVERT: D 2727 HIS cc_start: 0.9023 (t-90) cc_final: 0.8226 (t-90) REVERT: D 2731 LYS cc_start: 0.8959 (ptpp) cc_final: 0.8503 (pttm) REVERT: D 2732 TRP cc_start: 0.9151 (t-100) cc_final: 0.8914 (t-100) REVERT: D 2734 MET cc_start: 0.9025 (mmp) cc_final: 0.8608 (mmm) REVERT: D 2772 ARG cc_start: 0.8884 (mtm110) cc_final: 0.8605 (mtm110) REVERT: D 2773 TRP cc_start: 0.8735 (t-100) cc_final: 0.8531 (t-100) REVERT: D 2775 ILE cc_start: 0.9445 (mt) cc_final: 0.9174 (tt) REVERT: D 2779 LEU cc_start: 0.9355 (mt) cc_final: 0.9109 (mt) REVERT: D 2840 MET cc_start: 0.9082 (mtp) cc_final: 0.8783 (mmm) REVERT: D 2843 MET cc_start: 0.8650 (mtp) cc_final: 0.8371 (mtp) REVERT: D 2939 TYR cc_start: 0.8712 (m-80) cc_final: 0.8329 (m-80) REVERT: D 3003 MET cc_start: 0.8722 (ptm) cc_final: 0.8510 (ptm) REVERT: D 3131 TYR cc_start: 0.9007 (m-80) cc_final: 0.8566 (m-80) REVERT: D 3239 LEU cc_start: 0.9285 (mp) cc_final: 0.9060 (mt) REVERT: D 4046 ARG cc_start: 0.8858 (mmm160) cc_final: 0.8403 (mmm160) REVERT: D 4814 MET cc_start: 0.7986 (mmm) cc_final: 0.7750 (mmm) REVERT: G 30 MET cc_start: 0.7894 (mtm) cc_final: 0.7691 (mtm) outliers start: 60 outliers final: 32 residues processed: 963 average time/residue: 1.1847 time to fit residues: 2016.8696 Evaluate side-chains 966 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 929 time to evaluate : 11.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 3057 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2777 GLU Chi-restraints excluded: chain B residue 2840 MET Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 3819 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2777 GLU Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1421 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 20.0000 chunk 1181 optimal weight: 0.9990 chunk 815 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 750 optimal weight: 2.9990 chunk 1055 optimal weight: 6.9990 chunk 1577 optimal weight: 40.0000 chunk 1670 optimal weight: 0.2980 chunk 824 optimal weight: 1.9990 chunk 1495 optimal weight: 0.9990 chunk 450 optimal weight: 0.0770 overall best weight: 0.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2729 HIS ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2729 HIS ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS ** D 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 141648 Z= 0.145 Angle : 0.549 16.264 191392 Z= 0.277 Chirality : 0.039 0.169 20988 Planarity : 0.004 0.126 24588 Dihedral : 5.236 88.375 19029 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 0.39 % Allowed : 5.98 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.35 (0.07), residues: 17212 helix: 2.02 (0.06), residues: 8912 sheet: 0.07 (0.12), residues: 1808 loop : -0.43 (0.08), residues: 6492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C2773 HIS 0.011 0.001 HIS A3700 PHE 0.030 0.001 PHE C4305 TYR 0.027 0.001 TYR D4567 ARG 0.009 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 939 time to evaluate : 11.755 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: A 393 MET cc_start: 0.8684 (mmm) cc_final: 0.8079 (mmm) REVERT: A 890 HIS cc_start: 0.9068 (t-90) cc_final: 0.8480 (t-90) REVERT: A 935 MET cc_start: 0.8853 (ppp) cc_final: 0.8491 (ppp) REVERT: A 995 MET cc_start: 0.8717 (tpp) cc_final: 0.8020 (tpp) REVERT: A 999 LEU cc_start: 0.9397 (mm) cc_final: 0.9089 (mm) REVERT: A 1062 TYR cc_start: 0.7534 (m-80) cc_final: 0.7038 (m-80) REVERT: A 1421 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8641 (mmp) REVERT: A 2192 MET cc_start: 0.8586 (tpp) cc_final: 0.8373 (tpt) REVERT: A 2214 MET cc_start: 0.9225 (mmm) cc_final: 0.9019 (mmp) REVERT: A 2234 MET cc_start: 0.8686 (mtp) cc_final: 0.8398 (mtp) REVERT: A 2384 MET cc_start: 0.8886 (mmt) cc_final: 0.8670 (mmt) REVERT: A 2442 MET cc_start: 0.8174 (mmm) cc_final: 0.7817 (mmm) REVERT: A 2720 PHE cc_start: 0.9007 (t80) cc_final: 0.8752 (t80) REVERT: A 2727 HIS cc_start: 0.9028 (t-90) cc_final: 0.8049 (t-90) REVERT: A 2731 LYS cc_start: 0.8956 (ptpp) cc_final: 0.8380 (pttt) REVERT: A 2734 MET cc_start: 0.9082 (mmp) cc_final: 0.8712 (mmt) REVERT: A 2772 ARG cc_start: 0.8902 (mtm110) cc_final: 0.8547 (mtm110) REVERT: A 2779 LEU cc_start: 0.9285 (mt) cc_final: 0.8995 (mt) REVERT: A 2798 MET cc_start: 0.8059 (mmm) cc_final: 0.7774 (mmm) REVERT: A 2843 MET cc_start: 0.8758 (mtp) cc_final: 0.8240 (ttm) REVERT: A 2844 MET cc_start: 0.8603 (ptm) cc_final: 0.6840 (ttp) REVERT: A 2848 TYR cc_start: 0.8013 (m-80) cc_final: 0.7430 (m-80) REVERT: A 2939 TYR cc_start: 0.8511 (m-80) cc_final: 0.8154 (m-80) REVERT: A 3003 MET cc_start: 0.8773 (ptt) cc_final: 0.8437 (ptm) REVERT: A 3057 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8950 (pp) REVERT: A 3104 MET cc_start: 0.8452 (ptm) cc_final: 0.8095 (ptt) REVERT: A 3235 MET cc_start: 0.7015 (ptt) cc_final: 0.6448 (ppp) REVERT: A 3304 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8189 (tp-100) REVERT: A 4046 ARG cc_start: 0.8820 (mmm160) cc_final: 0.8308 (mmp80) REVERT: A 4274 MET cc_start: 0.6082 (tpt) cc_final: 0.5174 (ptt) REVERT: B 393 MET cc_start: 0.8658 (mmm) cc_final: 0.8016 (mmm) REVERT: B 890 HIS cc_start: 0.9064 (t-90) cc_final: 0.8473 (t-90) REVERT: B 995 MET cc_start: 0.8722 (tpp) cc_final: 0.8092 (tpp) REVERT: B 1062 TYR cc_start: 0.7372 (m-80) cc_final: 0.6966 (m-80) REVERT: B 1113 MET cc_start: 0.8828 (mtm) cc_final: 0.8576 (mtt) REVERT: B 1948 MET cc_start: 0.8773 (mmp) cc_final: 0.8552 (tpp) REVERT: B 2066 MET cc_start: 0.8961 (mmp) cc_final: 0.8703 (mmp) REVERT: B 2234 MET cc_start: 0.8650 (mtp) cc_final: 0.8371 (mtp) REVERT: B 2442 MET cc_start: 0.8131 (mmm) cc_final: 0.7926 (mmm) REVERT: B 2727 HIS cc_start: 0.8966 (t-90) cc_final: 0.8543 (t-90) REVERT: B 2732 TRP cc_start: 0.9034 (t-100) cc_final: 0.8655 (t-100) REVERT: B 2772 ARG cc_start: 0.8912 (mtm110) cc_final: 0.8595 (mtm110) REVERT: B 2773 TRP cc_start: 0.8773 (t-100) cc_final: 0.8422 (t-100) REVERT: B 2775 ILE cc_start: 0.9475 (mt) cc_final: 0.9155 (tt) REVERT: B 2777 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: B 2779 LEU cc_start: 0.9333 (mt) cc_final: 0.9069 (mt) REVERT: B 2843 MET cc_start: 0.8694 (mtp) cc_final: 0.8138 (ttm) REVERT: B 2844 MET cc_start: 0.8658 (ptm) cc_final: 0.8349 (ptm) REVERT: B 2848 TYR cc_start: 0.8063 (m-80) cc_final: 0.7861 (m-80) REVERT: B 2939 TYR cc_start: 0.8515 (m-80) cc_final: 0.8193 (m-80) REVERT: B 3003 MET cc_start: 0.8636 (ptm) cc_final: 0.8311 (ptm) REVERT: B 3104 MET cc_start: 0.8487 (ptm) cc_final: 0.8232 (ptm) REVERT: B 3235 MET cc_start: 0.7008 (ptt) cc_final: 0.6625 (tmm) REVERT: B 3239 LEU cc_start: 0.9207 (mt) cc_final: 0.8910 (pp) REVERT: B 3273 MET cc_start: 0.8654 (mtp) cc_final: 0.8390 (mtp) REVERT: B 4046 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8471 (mmm160) REVERT: C 393 MET cc_start: 0.8699 (mmm) cc_final: 0.8047 (mmm) REVERT: C 890 HIS cc_start: 0.9067 (t-90) cc_final: 0.8510 (t-90) REVERT: C 935 MET cc_start: 0.8887 (ppp) cc_final: 0.8673 (ppp) REVERT: C 995 MET cc_start: 0.8679 (tpp) cc_final: 0.8413 (mmm) REVERT: C 1062 TYR cc_start: 0.7390 (m-80) cc_final: 0.6889 (m-80) REVERT: C 1113 MET cc_start: 0.8782 (mtm) cc_final: 0.8571 (mtt) REVERT: C 2214 MET cc_start: 0.9219 (mmm) cc_final: 0.9006 (mmp) REVERT: C 2234 MET cc_start: 0.8668 (mtp) cc_final: 0.8375 (mtp) REVERT: C 2442 MET cc_start: 0.8152 (mmm) cc_final: 0.7906 (mmm) REVERT: C 2727 HIS cc_start: 0.8926 (t-90) cc_final: 0.8608 (t-90) REVERT: C 2732 TRP cc_start: 0.9065 (t-100) cc_final: 0.8684 (t-100) REVERT: C 2772 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8588 (mtm110) REVERT: C 2775 ILE cc_start: 0.9474 (mt) cc_final: 0.9131 (tt) REVERT: C 2777 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: C 2779 LEU cc_start: 0.9326 (mt) cc_final: 0.9074 (mt) REVERT: C 2840 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8369 (mmm) REVERT: C 2843 MET cc_start: 0.8641 (mtp) cc_final: 0.8171 (ttm) REVERT: C 2844 MET cc_start: 0.8755 (ptp) cc_final: 0.8544 (ptp) REVERT: C 2848 TYR cc_start: 0.8046 (m-80) cc_final: 0.7725 (m-80) REVERT: C 2871 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9340 (mm) REVERT: C 2939 TYR cc_start: 0.8556 (m-80) cc_final: 0.8205 (m-80) REVERT: C 3003 MET cc_start: 0.8638 (ptm) cc_final: 0.8320 (ptm) REVERT: C 3104 MET cc_start: 0.8498 (ptm) cc_final: 0.8250 (ptm) REVERT: C 3131 TYR cc_start: 0.8972 (m-80) cc_final: 0.8607 (m-80) REVERT: C 3233 HIS cc_start: 0.8000 (m90) cc_final: 0.7630 (m170) REVERT: C 3235 MET cc_start: 0.6963 (ptt) cc_final: 0.6591 (tmm) REVERT: C 3239 LEU cc_start: 0.9208 (mt) cc_final: 0.8876 (pp) REVERT: C 4046 ARG cc_start: 0.8848 (mmm160) cc_final: 0.8453 (mmm160) REVERT: D 393 MET cc_start: 0.8677 (mmm) cc_final: 0.7995 (mmm) REVERT: D 890 HIS cc_start: 0.9056 (t-90) cc_final: 0.8490 (t-90) REVERT: D 935 MET cc_start: 0.8851 (ppp) cc_final: 0.8645 (ppp) REVERT: D 995 MET cc_start: 0.8668 (tpp) cc_final: 0.7997 (tpp) REVERT: D 1062 TYR cc_start: 0.7472 (m-80) cc_final: 0.6991 (m-80) REVERT: D 1113 MET cc_start: 0.8769 (mtm) cc_final: 0.8551 (mtt) REVERT: D 1421 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8662 (mmp) REVERT: D 2442 MET cc_start: 0.8204 (mmm) cc_final: 0.7944 (mmm) REVERT: D 2727 HIS cc_start: 0.8948 (t-90) cc_final: 0.8458 (t-90) REVERT: D 2731 LYS cc_start: 0.8934 (ptpp) cc_final: 0.8678 (pttm) REVERT: D 2732 TRP cc_start: 0.9110 (t-100) cc_final: 0.8757 (t-100) REVERT: D 2734 MET cc_start: 0.9089 (mmp) cc_final: 0.8748 (mmm) REVERT: D 2757 MET cc_start: 0.8426 (mmm) cc_final: 0.8214 (mmp) REVERT: D 2772 ARG cc_start: 0.8899 (mtm110) cc_final: 0.8590 (mtm110) REVERT: D 2773 TRP cc_start: 0.8787 (t-100) cc_final: 0.8562 (t-100) REVERT: D 2775 ILE cc_start: 0.9448 (mt) cc_final: 0.9194 (tt) REVERT: D 2779 LEU cc_start: 0.9330 (mt) cc_final: 0.9088 (mt) REVERT: D 2798 MET cc_start: 0.8328 (mmt) cc_final: 0.8088 (mmm) REVERT: D 2840 MET cc_start: 0.8996 (mtp) cc_final: 0.8761 (mmm) REVERT: D 2843 MET cc_start: 0.8671 (mtp) cc_final: 0.8385 (mtp) REVERT: D 2939 TYR cc_start: 0.8727 (m-80) cc_final: 0.8320 (m-80) REVERT: D 3003 MET cc_start: 0.8703 (ptm) cc_final: 0.8376 (ptm) REVERT: D 3131 TYR cc_start: 0.8975 (m-80) cc_final: 0.8470 (m-80) REVERT: D 3235 MET cc_start: 0.7633 (ppp) cc_final: 0.7409 (ppp) REVERT: D 3239 LEU cc_start: 0.9194 (mp) cc_final: 0.8946 (mt) REVERT: D 4046 ARG cc_start: 0.8860 (mmm160) cc_final: 0.8351 (mmp80) REVERT: H 74 LYS cc_start: 0.9185 (ttpp) cc_final: 0.8717 (ttpt) outliers start: 57 outliers final: 29 residues processed: 953 average time/residue: 1.1929 time to fit residues: 2006.0416 Evaluate side-chains 954 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 918 time to evaluate : 12.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 3057 LEU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2777 GLU Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2777 GLU Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 2871 LEU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1421 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 9.9990 chunk 948 optimal weight: 0.0770 chunk 24 optimal weight: 8.9990 chunk 1243 optimal weight: 5.9990 chunk 689 optimal weight: 50.0000 chunk 1425 optimal weight: 7.9990 chunk 1154 optimal weight: 0.0970 chunk 1 optimal weight: 8.9990 chunk 852 optimal weight: 6.9990 chunk 1499 optimal weight: 5.9990 chunk 421 optimal weight: 0.0020 overall best weight: 2.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 ASN ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN ** B 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 ASN ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 HIS ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1939 ASN D1974 ASN ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3178 HIS ** D3252 HIS ** 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: 0.8215 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 141648 Z= 0.213 Angle : 0.543 16.092 191392 Z= 0.275 Chirality : 0.039 0.171 20988 Planarity : 0.004 0.125 24588 Dihedral : 5.101 81.543 19026 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 0.47 % Allowed : 6.38 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.40 (0.07), residues: 17212 helix: 2.06 (0.06), residues: 8972 sheet: 0.15 (0.13), residues: 1708 loop : -0.43 (0.08), residues: 6532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C2773 HIS 0.009 0.001 HIS C3700 PHE 0.030 0.001 PHE C4305 TYR 0.030 0.001 TYR A3138 ARG 0.011 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 935 time to evaluate : 11.763 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 128 MET cc_start: 0.8956 (mtm) cc_final: 0.8750 (mtp) REVERT: A 890 HIS cc_start: 0.9186 (t-90) cc_final: 0.8693 (t-90) REVERT: A 935 MET cc_start: 0.8848 (ppp) cc_final: 0.8627 (ppp) REVERT: A 995 MET cc_start: 0.8698 (tpp) cc_final: 0.8044 (tpp) REVERT: A 999 LEU cc_start: 0.9417 (mm) cc_final: 0.9155 (mm) REVERT: A 1062 TYR cc_start: 0.7653 (m-80) cc_final: 0.7094 (m-80) REVERT: A 1421 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8635 (mmp) REVERT: A 2192 MET cc_start: 0.8599 (tpp) cc_final: 0.8350 (tpt) REVERT: A 2214 MET cc_start: 0.9226 (mmm) cc_final: 0.9019 (mmp) REVERT: A 2234 MET cc_start: 0.8717 (mtp) cc_final: 0.8430 (mtp) REVERT: A 2384 MET cc_start: 0.8923 (mmt) cc_final: 0.8711 (mmt) REVERT: A 2720 PHE cc_start: 0.9005 (t80) cc_final: 0.8780 (t80) REVERT: A 2727 HIS cc_start: 0.8952 (t-90) cc_final: 0.7902 (t-90) REVERT: A 2731 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8449 (pttt) REVERT: A 2734 MET cc_start: 0.9084 (mmp) cc_final: 0.8782 (mmm) REVERT: A 2779 LEU cc_start: 0.9300 (mt) cc_final: 0.9011 (mt) REVERT: A 2782 MET cc_start: 0.8251 (tpp) cc_final: 0.7958 (tpp) REVERT: A 2798 MET cc_start: 0.8048 (mmm) cc_final: 0.7764 (mmm) REVERT: A 2843 MET cc_start: 0.8796 (mtp) cc_final: 0.8337 (ttm) REVERT: A 2844 MET cc_start: 0.8635 (ptm) cc_final: 0.7543 (ttm) REVERT: A 2848 TYR cc_start: 0.8092 (m-80) cc_final: 0.7411 (m-80) REVERT: A 2939 TYR cc_start: 0.8546 (m-80) cc_final: 0.8217 (m-80) REVERT: A 3003 MET cc_start: 0.8788 (ptt) cc_final: 0.8462 (ptm) REVERT: A 3057 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8997 (pp) REVERT: A 3104 MET cc_start: 0.8482 (ptm) cc_final: 0.8111 (ptt) REVERT: A 3235 MET cc_start: 0.7020 (ptt) cc_final: 0.6329 (ppp) REVERT: A 3304 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8168 (tp-100) REVERT: A 4046 ARG cc_start: 0.8815 (mmm160) cc_final: 0.8326 (mmp80) REVERT: A 4052 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: B 128 MET cc_start: 0.8971 (mtm) cc_final: 0.8755 (mtp) REVERT: B 890 HIS cc_start: 0.9169 (t-90) cc_final: 0.8632 (t-90) REVERT: B 995 MET cc_start: 0.8704 (tpp) cc_final: 0.8044 (tpp) REVERT: B 1062 TYR cc_start: 0.7451 (m-80) cc_final: 0.6998 (m-80) REVERT: B 1113 MET cc_start: 0.8869 (mtm) cc_final: 0.8648 (mtt) REVERT: B 1494 MET cc_start: 0.8084 (mmm) cc_final: 0.7756 (tpt) REVERT: B 1948 MET cc_start: 0.8810 (mmp) cc_final: 0.8596 (tpp) REVERT: B 2214 MET cc_start: 0.9229 (mmm) cc_final: 0.9022 (mmp) REVERT: B 2234 MET cc_start: 0.8679 (mtp) cc_final: 0.8383 (mtp) REVERT: B 2442 MET cc_start: 0.8153 (mmm) cc_final: 0.7910 (mmm) REVERT: B 2727 HIS cc_start: 0.8898 (t-90) cc_final: 0.8401 (t-90) REVERT: B 2732 TRP cc_start: 0.9003 (t-100) cc_final: 0.8650 (t-100) REVERT: B 2772 ARG cc_start: 0.8909 (mtm110) cc_final: 0.8615 (mtm110) REVERT: B 2779 LEU cc_start: 0.9340 (mt) cc_final: 0.9124 (mt) REVERT: B 2798 MET cc_start: 0.8256 (mmt) cc_final: 0.7974 (mmm) REVERT: B 2843 MET cc_start: 0.8733 (mtp) cc_final: 0.8198 (ttm) REVERT: B 2844 MET cc_start: 0.8706 (ptm) cc_final: 0.8460 (ptm) REVERT: B 2848 TYR cc_start: 0.8124 (m-80) cc_final: 0.7847 (m-80) REVERT: B 2939 TYR cc_start: 0.8530 (m-80) cc_final: 0.8198 (m-80) REVERT: B 3003 MET cc_start: 0.8662 (ptm) cc_final: 0.8354 (ptm) REVERT: B 3104 MET cc_start: 0.8513 (ptm) cc_final: 0.8252 (ptm) REVERT: B 3131 TYR cc_start: 0.8936 (m-80) cc_final: 0.8585 (m-80) REVERT: B 3228 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6343 (t80) REVERT: B 3235 MET cc_start: 0.7080 (ptt) cc_final: 0.6337 (ppp) REVERT: B 3273 MET cc_start: 0.8620 (mtp) cc_final: 0.8385 (mtp) REVERT: C 128 MET cc_start: 0.8937 (mtm) cc_final: 0.8719 (mtp) REVERT: C 890 HIS cc_start: 0.9158 (t-90) cc_final: 0.8641 (t-90) REVERT: C 935 MET cc_start: 0.8897 (ppp) cc_final: 0.8689 (ppp) REVERT: C 995 MET cc_start: 0.8678 (tpp) cc_final: 0.7992 (tpp) REVERT: C 1062 TYR cc_start: 0.7549 (m-80) cc_final: 0.7059 (m-80) REVERT: C 1494 MET cc_start: 0.7940 (tmm) cc_final: 0.7733 (tpt) REVERT: C 2150 MET cc_start: 0.8445 (mmm) cc_final: 0.8235 (mtt) REVERT: C 2214 MET cc_start: 0.9230 (mmm) cc_final: 0.9007 (mmp) REVERT: C 2442 MET cc_start: 0.8183 (mmm) cc_final: 0.7922 (mmm) REVERT: C 2727 HIS cc_start: 0.8909 (t-90) cc_final: 0.8471 (t-90) REVERT: C 2732 TRP cc_start: 0.9046 (t-100) cc_final: 0.8670 (t-100) REVERT: C 2772 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8640 (mtm110) REVERT: C 2779 LEU cc_start: 0.9388 (mt) cc_final: 0.9145 (mt) REVERT: C 2798 MET cc_start: 0.8270 (mmt) cc_final: 0.7974 (mmm) REVERT: C 2840 MET cc_start: 0.8710 (mmm) cc_final: 0.8415 (mmm) REVERT: C 2843 MET cc_start: 0.8694 (mtp) cc_final: 0.8219 (ttm) REVERT: C 2848 TYR cc_start: 0.8099 (m-80) cc_final: 0.7749 (m-80) REVERT: C 2905 ARG cc_start: 0.8832 (tpp-160) cc_final: 0.8243 (tpp-160) REVERT: C 2939 TYR cc_start: 0.8562 (m-80) cc_final: 0.8218 (m-80) REVERT: C 3003 MET cc_start: 0.8666 (ptm) cc_final: 0.8364 (ptm) REVERT: C 3104 MET cc_start: 0.8521 (ptm) cc_final: 0.8269 (ptm) REVERT: C 3131 TYR cc_start: 0.8994 (m-80) cc_final: 0.8583 (m-80) REVERT: C 3233 HIS cc_start: 0.8038 (m90) cc_final: 0.7670 (m170) REVERT: C 3235 MET cc_start: 0.7025 (ptt) cc_final: 0.6488 (tmm) REVERT: C 3273 MET cc_start: 0.8630 (mtp) cc_final: 0.8383 (mtp) REVERT: C 4052 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7740 (mtp) REVERT: D 393 MET cc_start: 0.8694 (mmm) cc_final: 0.8036 (mmm) REVERT: D 890 HIS cc_start: 0.9148 (t-90) cc_final: 0.8646 (t-90) REVERT: D 935 MET cc_start: 0.8871 (ppp) cc_final: 0.8578 (ppp) REVERT: D 995 MET cc_start: 0.8664 (tpp) cc_final: 0.8014 (tpp) REVERT: D 1062 TYR cc_start: 0.7612 (m-80) cc_final: 0.7066 (m-80) REVERT: D 1113 MET cc_start: 0.8794 (mtm) cc_final: 0.8588 (mtt) REVERT: D 1168 MET cc_start: 0.8463 (mmm) cc_final: 0.8159 (mmm) REVERT: D 1421 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8653 (mmp) REVERT: D 2214 MET cc_start: 0.9252 (mmm) cc_final: 0.9043 (mmp) REVERT: D 2442 MET cc_start: 0.8209 (mmm) cc_final: 0.7942 (mmm) REVERT: D 2727 HIS cc_start: 0.8997 (t-90) cc_final: 0.8440 (t-90) REVERT: D 2732 TRP cc_start: 0.9151 (t-100) cc_final: 0.8741 (t-100) REVERT: D 2772 ARG cc_start: 0.8931 (mtm110) cc_final: 0.8616 (mtm110) REVERT: D 2773 TRP cc_start: 0.8806 (t-100) cc_final: 0.8571 (t-100) REVERT: D 2775 ILE cc_start: 0.9444 (mt) cc_final: 0.9093 (tt) REVERT: D 2779 LEU cc_start: 0.9308 (mt) cc_final: 0.9035 (mt) REVERT: D 2840 MET cc_start: 0.9027 (mtp) cc_final: 0.8819 (mmm) REVERT: D 2843 MET cc_start: 0.8686 (mtp) cc_final: 0.8335 (mtp) REVERT: D 2844 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8429 (tmm) REVERT: D 2905 ARG cc_start: 0.8885 (tpp-160) cc_final: 0.8531 (tpp-160) REVERT: D 2939 TYR cc_start: 0.8753 (m-80) cc_final: 0.8340 (m-80) REVERT: D 3003 MET cc_start: 0.8732 (ptm) cc_final: 0.8419 (ptm) REVERT: D 3072 MET cc_start: 0.8347 (tpp) cc_final: 0.8125 (tpp) REVERT: D 3131 TYR cc_start: 0.9009 (m-80) cc_final: 0.8475 (m-80) REVERT: D 3235 MET cc_start: 0.7660 (ppp) cc_final: 0.7389 (ppp) REVERT: D 3239 LEU cc_start: 0.9206 (mp) cc_final: 0.8949 (mt) REVERT: D 3242 LEU cc_start: 0.8942 (mp) cc_final: 0.8058 (tp) REVERT: D 4046 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8311 (mmp80) REVERT: D 4052 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7599 (mtp) outliers start: 69 outliers final: 44 residues processed: 958 average time/residue: 1.1881 time to fit residues: 2013.5801 Evaluate side-chains 977 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 925 time to evaluate : 11.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3057 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3239 LEU Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2456 MET Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3228 TYR Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2871 LEU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3819 MET Chi-restraints excluded: chain C residue 4052 MET Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1421 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2871 LEU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3819 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4052 MET Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 3.9990 chunk 1504 optimal weight: 0.5980 chunk 330 optimal weight: 0.9990 chunk 980 optimal weight: 8.9990 chunk 412 optimal weight: 7.9990 chunk 1671 optimal weight: 9.9990 chunk 1387 optimal weight: 6.9990 chunk 774 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 553 optimal weight: 7.9990 chunk 877 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 GLN A1939 ASN ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1939 ASN ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 HIS ** C3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 57 ASN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 141648 Z= 0.259 Angle : 0.558 15.873 191392 Z= 0.281 Chirality : 0.039 0.171 20988 Planarity : 0.004 0.124 24588 Dihedral : 5.058 77.089 19026 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 0.67 % Allowed : 6.72 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.40 (0.07), residues: 17212 helix: 2.06 (0.06), residues: 8996 sheet: 0.14 (0.12), residues: 1732 loop : -0.44 (0.08), residues: 6484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A2773 HIS 0.009 0.001 HIS A3700 PHE 0.030 0.001 PHE C4305 TYR 0.017 0.001 TYR A3138 ARG 0.011 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 931 time to evaluate : 11.905 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 317 MET cc_start: 0.7262 (mtp) cc_final: 0.6995 (mtp) REVERT: A 890 HIS cc_start: 0.9235 (t-90) cc_final: 0.8779 (t-90) REVERT: A 935 MET cc_start: 0.8824 (ppp) cc_final: 0.8590 (ppp) REVERT: A 995 MET cc_start: 0.8699 (tpp) cc_final: 0.8133 (tmm) REVERT: A 999 LEU cc_start: 0.9429 (mm) cc_final: 0.8970 (mm) REVERT: A 1062 TYR cc_start: 0.7710 (m-80) cc_final: 0.7077 (m-80) REVERT: A 1168 MET cc_start: 0.8501 (mmm) cc_final: 0.8179 (mmm) REVERT: A 1421 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8664 (mmp) REVERT: A 1494 MET cc_start: 0.7970 (tmm) cc_final: 0.7366 (tmm) REVERT: A 2192 MET cc_start: 0.8634 (tpp) cc_final: 0.8371 (tpt) REVERT: A 2214 MET cc_start: 0.9229 (mmm) cc_final: 0.9016 (mmp) REVERT: A 2234 MET cc_start: 0.8730 (mtp) cc_final: 0.8402 (mtp) REVERT: A 2695 MET cc_start: 0.7927 (ptp) cc_final: 0.7674 (ptp) REVERT: A 2727 HIS cc_start: 0.8962 (t-90) cc_final: 0.7900 (t-90) REVERT: A 2731 LYS cc_start: 0.8966 (ptpp) cc_final: 0.8382 (pttt) REVERT: A 2734 MET cc_start: 0.9074 (mmp) cc_final: 0.8774 (mmt) REVERT: A 2757 MET cc_start: 0.8156 (mmm) cc_final: 0.7860 (mmp) REVERT: A 2772 ARG cc_start: 0.8857 (mtm110) cc_final: 0.8608 (mtm110) REVERT: A 2779 LEU cc_start: 0.9273 (mt) cc_final: 0.8983 (mt) REVERT: A 2782 MET cc_start: 0.8236 (tpp) cc_final: 0.7979 (tpp) REVERT: A 2798 MET cc_start: 0.8073 (mmm) cc_final: 0.7776 (mmm) REVERT: A 2843 MET cc_start: 0.8809 (mtp) cc_final: 0.8344 (ttm) REVERT: A 2844 MET cc_start: 0.8657 (ptm) cc_final: 0.7615 (ttm) REVERT: A 2848 TYR cc_start: 0.8203 (m-80) cc_final: 0.7463 (m-80) REVERT: A 2939 TYR cc_start: 0.8551 (m-80) cc_final: 0.8232 (m-80) REVERT: A 3003 MET cc_start: 0.8795 (ptt) cc_final: 0.8546 (ptm) REVERT: A 3104 MET cc_start: 0.8517 (ptm) cc_final: 0.8166 (ptm) REVERT: A 3131 TYR cc_start: 0.8841 (m-80) cc_final: 0.8524 (m-80) REVERT: A 3235 MET cc_start: 0.7000 (ptt) cc_final: 0.6416 (ppp) REVERT: A 3304 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8168 (tp-100) REVERT: A 4046 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8229 (mmp80) REVERT: A 4052 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7713 (mtp) REVERT: B 890 HIS cc_start: 0.9212 (t-90) cc_final: 0.8705 (t-90) REVERT: B 935 MET cc_start: 0.8832 (ppp) cc_final: 0.8499 (ppp) REVERT: B 995 MET cc_start: 0.8729 (tpp) cc_final: 0.8025 (tpp) REVERT: B 1062 TYR cc_start: 0.7511 (m-80) cc_final: 0.7132 (m-80) REVERT: B 1165 MET cc_start: 0.8483 (mtp) cc_final: 0.8230 (mtp) REVERT: B 1948 MET cc_start: 0.8826 (mmp) cc_final: 0.8608 (tpp) REVERT: B 2214 MET cc_start: 0.9230 (mmm) cc_final: 0.9017 (mmp) REVERT: B 2234 MET cc_start: 0.8697 (mtp) cc_final: 0.8411 (mtp) REVERT: B 2442 MET cc_start: 0.8144 (mmm) cc_final: 0.7893 (mmm) REVERT: B 2727 HIS cc_start: 0.8865 (t-90) cc_final: 0.8501 (t-90) REVERT: B 2732 TRP cc_start: 0.9011 (t-100) cc_final: 0.8620 (t-100) REVERT: B 2772 ARG cc_start: 0.8915 (mtm110) cc_final: 0.8637 (mtm110) REVERT: B 2775 ILE cc_start: 0.9481 (mt) cc_final: 0.9164 (tt) REVERT: B 2779 LEU cc_start: 0.9329 (mt) cc_final: 0.9094 (mt) REVERT: B 2843 MET cc_start: 0.8742 (mtp) cc_final: 0.8244 (ttm) REVERT: B 2844 MET cc_start: 0.8761 (ptm) cc_final: 0.8494 (ptm) REVERT: B 2848 TYR cc_start: 0.8240 (m-80) cc_final: 0.7929 (m-80) REVERT: B 2939 TYR cc_start: 0.8550 (m-80) cc_final: 0.8252 (m-80) REVERT: B 3003 MET cc_start: 0.8661 (ptm) cc_final: 0.8363 (ptm) REVERT: B 3104 MET cc_start: 0.8530 (ptm) cc_final: 0.8269 (ptm) REVERT: B 3131 TYR cc_start: 0.8950 (m-80) cc_final: 0.8574 (m-80) REVERT: B 3228 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6425 (t80) REVERT: B 3235 MET cc_start: 0.7137 (ptt) cc_final: 0.6275 (ppp) REVERT: B 3273 MET cc_start: 0.8643 (mtp) cc_final: 0.8379 (mtp) REVERT: B 4046 ARG cc_start: 0.8867 (mmm160) cc_final: 0.8410 (mmm160) REVERT: B 4052 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7586 (mtp) REVERT: C 128 MET cc_start: 0.8943 (mtm) cc_final: 0.8738 (mtp) REVERT: C 890 HIS cc_start: 0.9208 (t-90) cc_final: 0.8738 (t-90) REVERT: C 935 MET cc_start: 0.8909 (ppp) cc_final: 0.8696 (ppp) REVERT: C 995 MET cc_start: 0.8666 (tpp) cc_final: 0.7990 (tpp) REVERT: C 1062 TYR cc_start: 0.7683 (m-80) cc_final: 0.7201 (m-80) REVERT: C 1505 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7828 (tt) REVERT: C 2214 MET cc_start: 0.9231 (mmm) cc_final: 0.9000 (mmp) REVERT: C 2234 MET cc_start: 0.8715 (mtp) cc_final: 0.8414 (mtp) REVERT: C 2442 MET cc_start: 0.8193 (mmm) cc_final: 0.7932 (mmm) REVERT: C 2727 HIS cc_start: 0.8971 (t-90) cc_final: 0.8468 (t-90) REVERT: C 2732 TRP cc_start: 0.9072 (t-100) cc_final: 0.8677 (t-100) REVERT: C 2772 ARG cc_start: 0.8940 (mtm110) cc_final: 0.8661 (mtm110) REVERT: C 2775 ILE cc_start: 0.9494 (mt) cc_final: 0.9150 (tt) REVERT: C 2779 LEU cc_start: 0.9384 (mt) cc_final: 0.9121 (mt) REVERT: C 2798 MET cc_start: 0.8278 (mmt) cc_final: 0.7955 (mmm) REVERT: C 2840 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8395 (mmm) REVERT: C 2843 MET cc_start: 0.8718 (mtp) cc_final: 0.8280 (ttm) REVERT: C 2848 TYR cc_start: 0.8149 (m-80) cc_final: 0.7858 (m-80) REVERT: C 2895 PHE cc_start: 0.9062 (t80) cc_final: 0.8817 (t80) REVERT: C 2905 ARG cc_start: 0.8828 (tpp-160) cc_final: 0.8243 (tpp-160) REVERT: C 2939 TYR cc_start: 0.8586 (m-80) cc_final: 0.8278 (m-80) REVERT: C 3003 MET cc_start: 0.8666 (ptm) cc_final: 0.8373 (ptm) REVERT: C 3104 MET cc_start: 0.8532 (ptm) cc_final: 0.8276 (ptm) REVERT: C 3131 TYR cc_start: 0.8992 (m-80) cc_final: 0.8567 (m-80) REVERT: C 3228 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.7128 (t80) REVERT: C 3233 HIS cc_start: 0.7998 (m90) cc_final: 0.7676 (m170) REVERT: C 3273 MET cc_start: 0.8631 (mtp) cc_final: 0.8381 (mtp) REVERT: C 4046 ARG cc_start: 0.8842 (mmm160) cc_final: 0.8421 (mmm160) REVERT: C 4048 PHE cc_start: 0.8759 (t80) cc_final: 0.8507 (t80) REVERT: C 4052 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7725 (mtp) REVERT: D 890 HIS cc_start: 0.9180 (t-90) cc_final: 0.8715 (t-90) REVERT: D 935 MET cc_start: 0.8890 (ppp) cc_final: 0.8635 (ppp) REVERT: D 1062 TYR cc_start: 0.7744 (m-80) cc_final: 0.7249 (m-80) REVERT: D 1113 MET cc_start: 0.8809 (mtm) cc_final: 0.8489 (mtt) REVERT: D 1168 MET cc_start: 0.8481 (mmm) cc_final: 0.8200 (mmm) REVERT: D 1421 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8637 (mmp) REVERT: D 2214 MET cc_start: 0.9242 (mmm) cc_final: 0.9024 (mmp) REVERT: D 2442 MET cc_start: 0.8207 (mmm) cc_final: 0.7939 (mmm) REVERT: D 2727 HIS cc_start: 0.9020 (t-90) cc_final: 0.8802 (t-90) REVERT: D 2732 TRP cc_start: 0.9124 (t-100) cc_final: 0.8741 (t-100) REVERT: D 2772 ARG cc_start: 0.8947 (mtm110) cc_final: 0.8632 (mtm110) REVERT: D 2775 ILE cc_start: 0.9444 (mt) cc_final: 0.9105 (tt) REVERT: D 2779 LEU cc_start: 0.9303 (mt) cc_final: 0.9029 (mt) REVERT: D 2840 MET cc_start: 0.9056 (mtp) cc_final: 0.8783 (mmm) REVERT: D 2843 MET cc_start: 0.8724 (mtp) cc_final: 0.8359 (mtp) REVERT: D 2844 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8451 (tmm) REVERT: D 2905 ARG cc_start: 0.8909 (tpp-160) cc_final: 0.8520 (tpp-160) REVERT: D 2939 TYR cc_start: 0.8745 (m-80) cc_final: 0.8337 (m-80) REVERT: D 3003 MET cc_start: 0.8736 (ptm) cc_final: 0.8435 (ptm) REVERT: D 3072 MET cc_start: 0.8427 (tpp) cc_final: 0.8182 (tpp) REVERT: D 3131 TYR cc_start: 0.9020 (m-80) cc_final: 0.8506 (m-80) REVERT: D 3235 MET cc_start: 0.7685 (ppp) cc_final: 0.7412 (ppp) REVERT: D 3239 LEU cc_start: 0.9206 (mp) cc_final: 0.8989 (mt) REVERT: D 4046 ARG cc_start: 0.8854 (mmm160) cc_final: 0.8443 (mmm160) outliers start: 96 outliers final: 57 residues processed: 983 average time/residue: 1.2415 time to fit residues: 2173.6383 Evaluate side-chains 994 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 927 time to evaluate : 11.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3066 GLU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3819 MET Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1510 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3228 TYR Chi-restraints excluded: chain B residue 3239 LEU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 3819 MET Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4052 MET Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1510 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 2871 LEU Chi-restraints excluded: chain C residue 3066 GLU Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3228 TYR Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4052 MET Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1421 MET Chi-restraints excluded: chain D residue 1510 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2871 LEU Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 952 optimal weight: 20.0000 chunk 1220 optimal weight: 10.0000 chunk 945 optimal weight: 50.0000 chunk 1407 optimal weight: 0.0870 chunk 933 optimal weight: 9.9990 chunk 1665 optimal weight: 4.9990 chunk 1042 optimal weight: 2.9990 chunk 1015 optimal weight: 8.9990 chunk 768 optimal weight: 4.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3179 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 GLN ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 HIS ** C3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 971 GLN ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 141648 Z= 0.231 Angle : 0.560 17.730 191392 Z= 0.280 Chirality : 0.039 0.183 20988 Planarity : 0.004 0.123 24588 Dihedral : 5.008 74.248 19024 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 0.57 % Allowed : 7.01 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.44 (0.07), residues: 17212 helix: 2.11 (0.06), residues: 8968 sheet: 0.15 (0.12), residues: 1708 loop : -0.42 (0.08), residues: 6536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C2773 HIS 0.009 0.001 HIS C3700 PHE 0.034 0.001 PHE C3162 TYR 0.020 0.001 TYR A3138 ARG 0.012 0.000 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 932 time to evaluate : 11.835 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: A 393 MET cc_start: 0.8608 (mmm) cc_final: 0.8107 (mmm) REVERT: A 890 HIS cc_start: 0.9254 (t-90) cc_final: 0.8833 (t-90) REVERT: A 935 MET cc_start: 0.8804 (ppp) cc_final: 0.8584 (ppp) REVERT: A 995 MET cc_start: 0.8710 (tpp) cc_final: 0.8128 (tmm) REVERT: A 999 LEU cc_start: 0.9437 (mm) cc_final: 0.8971 (mm) REVERT: A 1062 TYR cc_start: 0.7744 (m-80) cc_final: 0.7324 (m-80) REVERT: A 1168 MET cc_start: 0.8471 (mmm) cc_final: 0.8150 (mmm) REVERT: A 1421 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8656 (mmp) REVERT: A 1494 MET cc_start: 0.7967 (tmm) cc_final: 0.7354 (tmm) REVERT: A 2192 MET cc_start: 0.8665 (tpp) cc_final: 0.8405 (tpt) REVERT: A 2214 MET cc_start: 0.9229 (mmm) cc_final: 0.9016 (mmp) REVERT: A 2695 MET cc_start: 0.7983 (ptp) cc_final: 0.7618 (pmm) REVERT: A 2727 HIS cc_start: 0.9010 (t-90) cc_final: 0.8640 (t-90) REVERT: A 2734 MET cc_start: 0.9069 (mmp) cc_final: 0.8863 (mmt) REVERT: A 2772 ARG cc_start: 0.8852 (mtm110) cc_final: 0.8576 (mtm110) REVERT: A 2779 LEU cc_start: 0.9261 (mt) cc_final: 0.8983 (mt) REVERT: A 2782 MET cc_start: 0.8245 (tpp) cc_final: 0.7900 (tpp) REVERT: A 2798 MET cc_start: 0.8098 (mmm) cc_final: 0.7796 (mmm) REVERT: A 2843 MET cc_start: 0.8808 (mtp) cc_final: 0.8329 (ttm) REVERT: A 2844 MET cc_start: 0.8679 (ptm) cc_final: 0.7533 (ttm) REVERT: A 2848 TYR cc_start: 0.8295 (m-80) cc_final: 0.7527 (m-80) REVERT: A 2939 TYR cc_start: 0.8564 (m-80) cc_final: 0.8226 (m-80) REVERT: A 3003 MET cc_start: 0.8796 (ptt) cc_final: 0.8550 (ptm) REVERT: A 3104 MET cc_start: 0.8515 (ptm) cc_final: 0.8217 (ptm) REVERT: A 3131 TYR cc_start: 0.8843 (m-80) cc_final: 0.8535 (m-80) REVERT: A 3137 LEU cc_start: 0.9302 (mt) cc_final: 0.9009 (mt) REVERT: A 3235 MET cc_start: 0.7024 (ptt) cc_final: 0.6312 (ppp) REVERT: A 3304 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8135 (tp-100) REVERT: A 4046 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8441 (mmm160) REVERT: A 4052 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7747 (mtp) REVERT: B 128 MET cc_start: 0.8948 (mtm) cc_final: 0.8745 (mtp) REVERT: B 890 HIS cc_start: 0.9221 (t-90) cc_final: 0.8774 (t-90) REVERT: B 1165 MET cc_start: 0.8475 (mtp) cc_final: 0.8230 (mtp) REVERT: B 1494 MET cc_start: 0.8026 (mmm) cc_final: 0.7816 (tpt) REVERT: B 1505 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7761 (tt) REVERT: B 1948 MET cc_start: 0.8831 (mmp) cc_final: 0.8612 (tpp) REVERT: B 2214 MET cc_start: 0.9229 (mmm) cc_final: 0.9014 (mmp) REVERT: B 2234 MET cc_start: 0.8695 (mtp) cc_final: 0.8406 (mtp) REVERT: B 2442 MET cc_start: 0.8141 (mmm) cc_final: 0.7855 (mmm) REVERT: B 2731 LYS cc_start: 0.8872 (pttm) cc_final: 0.8580 (mttp) REVERT: B 2732 TRP cc_start: 0.9000 (t-100) cc_final: 0.8605 (t-100) REVERT: B 2734 MET cc_start: 0.9076 (mmp) cc_final: 0.8791 (mmt) REVERT: B 2772 ARG cc_start: 0.8907 (mtm110) cc_final: 0.8627 (mtm110) REVERT: B 2775 ILE cc_start: 0.9479 (mt) cc_final: 0.9157 (tt) REVERT: B 2779 LEU cc_start: 0.9293 (mt) cc_final: 0.9055 (mt) REVERT: B 2843 MET cc_start: 0.8754 (mtp) cc_final: 0.8255 (ttm) REVERT: B 2844 MET cc_start: 0.8783 (ptm) cc_final: 0.8568 (ptm) REVERT: B 2848 TYR cc_start: 0.8285 (m-80) cc_final: 0.7964 (m-80) REVERT: B 2858 MET cc_start: 0.8823 (mmp) cc_final: 0.8621 (mmt) REVERT: B 2895 PHE cc_start: 0.9044 (t80) cc_final: 0.8841 (t80) REVERT: B 2939 TYR cc_start: 0.8550 (m-80) cc_final: 0.8248 (m-80) REVERT: B 3003 MET cc_start: 0.8667 (ptm) cc_final: 0.8371 (ptm) REVERT: B 3104 MET cc_start: 0.8533 (ptm) cc_final: 0.8266 (ptm) REVERT: B 3131 TYR cc_start: 0.8935 (m-80) cc_final: 0.8592 (m-80) REVERT: B 3137 LEU cc_start: 0.9289 (mt) cc_final: 0.8960 (mt) REVERT: B 3228 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7163 (t80) REVERT: B 3273 MET cc_start: 0.8661 (mtp) cc_final: 0.8404 (mtp) REVERT: B 3281 LEU cc_start: 0.8629 (mp) cc_final: 0.8025 (mt) REVERT: B 4052 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7582 (mtp) REVERT: B 4814 MET cc_start: 0.7964 (mmm) cc_final: 0.7721 (mmm) REVERT: C 128 MET cc_start: 0.8923 (mtm) cc_final: 0.8648 (mtp) REVERT: C 890 HIS cc_start: 0.9293 (t-90) cc_final: 0.8848 (t-90) REVERT: C 935 MET cc_start: 0.8914 (ppp) cc_final: 0.8585 (ppp) REVERT: C 1113 MET cc_start: 0.8774 (mtm) cc_final: 0.8491 (mtt) REVERT: C 2214 MET cc_start: 0.9226 (mmm) cc_final: 0.9004 (mmp) REVERT: C 2234 MET cc_start: 0.8703 (mtp) cc_final: 0.8404 (mtp) REVERT: C 2442 MET cc_start: 0.8161 (mmm) cc_final: 0.7900 (mmm) REVERT: C 2732 TRP cc_start: 0.9052 (t-100) cc_final: 0.8696 (t-100) REVERT: C 2734 MET cc_start: 0.9073 (mmp) cc_final: 0.8760 (mmt) REVERT: C 2772 ARG cc_start: 0.8916 (mtm110) cc_final: 0.8625 (mtm110) REVERT: C 2779 LEU cc_start: 0.9346 (mt) cc_final: 0.9108 (mt) REVERT: C 2798 MET cc_start: 0.8277 (mmt) cc_final: 0.7941 (mmm) REVERT: C 2840 MET cc_start: 0.8735 (mmm) cc_final: 0.8413 (mmm) REVERT: C 2843 MET cc_start: 0.8730 (mtp) cc_final: 0.8223 (ttm) REVERT: C 2848 TYR cc_start: 0.8196 (m-80) cc_final: 0.7864 (m-80) REVERT: C 2895 PHE cc_start: 0.9052 (t80) cc_final: 0.8799 (t80) REVERT: C 2905 ARG cc_start: 0.8803 (tpp-160) cc_final: 0.8226 (tpp-160) REVERT: C 2939 TYR cc_start: 0.8574 (m-80) cc_final: 0.8263 (m-80) REVERT: C 3003 MET cc_start: 0.8666 (ptm) cc_final: 0.8384 (ptm) REVERT: C 3104 MET cc_start: 0.8531 (ptm) cc_final: 0.8276 (ptm) REVERT: C 3131 TYR cc_start: 0.8988 (m-80) cc_final: 0.8561 (m-80) REVERT: C 3233 HIS cc_start: 0.7951 (m90) cc_final: 0.7614 (m170) REVERT: C 3273 MET cc_start: 0.8621 (mtp) cc_final: 0.8368 (mtp) REVERT: C 4052 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7729 (mtp) REVERT: D 890 HIS cc_start: 0.9212 (t-90) cc_final: 0.8759 (t-90) REVERT: D 935 MET cc_start: 0.8879 (ppp) cc_final: 0.8632 (ppp) REVERT: D 1062 TYR cc_start: 0.7825 (m-80) cc_final: 0.7309 (m-80) REVERT: D 1113 MET cc_start: 0.8804 (mtm) cc_final: 0.8507 (mtt) REVERT: D 1168 MET cc_start: 0.8478 (mmm) cc_final: 0.8201 (mmm) REVERT: D 1421 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8658 (mmp) REVERT: D 2214 MET cc_start: 0.9245 (mmm) cc_final: 0.9022 (mmp) REVERT: D 2442 MET cc_start: 0.8188 (mmm) cc_final: 0.7958 (mmm) REVERT: D 2727 HIS cc_start: 0.8933 (t-90) cc_final: 0.8661 (t-90) REVERT: D 2731 LYS cc_start: 0.8867 (pttm) cc_final: 0.8591 (pttm) REVERT: D 2732 TRP cc_start: 0.9116 (t-100) cc_final: 0.8720 (t-100) REVERT: D 2772 ARG cc_start: 0.8943 (mtm110) cc_final: 0.8631 (mtm110) REVERT: D 2773 TRP cc_start: 0.8775 (t-100) cc_final: 0.8370 (t-100) REVERT: D 2775 ILE cc_start: 0.9437 (mt) cc_final: 0.9105 (tt) REVERT: D 2777 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: D 2779 LEU cc_start: 0.9269 (mt) cc_final: 0.8998 (mt) REVERT: D 2840 MET cc_start: 0.9040 (mtp) cc_final: 0.8776 (mmm) REVERT: D 2843 MET cc_start: 0.8725 (mtp) cc_final: 0.8352 (mtp) REVERT: D 2844 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: D 2905 ARG cc_start: 0.8891 (tpp-160) cc_final: 0.8566 (tpp-160) REVERT: D 2939 TYR cc_start: 0.8757 (m-80) cc_final: 0.8350 (m-80) REVERT: D 3003 MET cc_start: 0.8729 (ptm) cc_final: 0.8438 (ptm) REVERT: D 3072 MET cc_start: 0.8423 (tpp) cc_final: 0.8171 (tpp) REVERT: D 3131 TYR cc_start: 0.9004 (m-80) cc_final: 0.8492 (m-80) REVERT: D 3235 MET cc_start: 0.7690 (ppp) cc_final: 0.7422 (ppp) REVERT: D 3239 LEU cc_start: 0.9225 (mp) cc_final: 0.8991 (mt) REVERT: D 4046 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8419 (mmm160) REVERT: D 4052 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7630 (mtp) outliers start: 81 outliers final: 58 residues processed: 971 average time/residue: 1.2007 time to fit residues: 2062.1537 Evaluate side-chains 984 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 916 time to evaluate : 11.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3239 LEU Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain B residue 1510 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2456 MET Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3228 TYR Chi-restraints excluded: chain B residue 3239 LEU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4052 MET Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1510 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 2871 LEU Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4052 MET Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1421 MET Chi-restraints excluded: chain D residue 1510 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 2871 LEU Chi-restraints excluded: chain D residue 3066 GLU Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4052 MET Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 6.9990 chunk 665 optimal weight: 0.7980 chunk 994 optimal weight: 5.9990 chunk 501 optimal weight: 0.0870 chunk 327 optimal weight: 2.9990 chunk 322 optimal weight: 0.0870 chunk 1058 optimal weight: 1.9990 chunk 1134 optimal weight: 9.9990 chunk 823 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 1309 optimal weight: 10.0000 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2704 GLN A3115 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3179 ASN ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2729 HIS ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3179 ASN ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 141648 Z= 0.141 Angle : 0.558 20.917 191392 Z= 0.275 Chirality : 0.038 0.180 20988 Planarity : 0.004 0.122 24588 Dihedral : 4.919 71.743 19024 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 0.47 % Allowed : 7.31 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.52 (0.07), residues: 17212 helix: 2.16 (0.06), residues: 8956 sheet: 0.24 (0.12), residues: 1684 loop : -0.39 (0.08), residues: 6572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A2773 HIS 0.009 0.001 HIS C3700 PHE 0.030 0.001 PHE A4305 TYR 0.027 0.001 TYR A3138 ARG 0.013 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 919 time to evaluate : 10.977 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: A 890 HIS cc_start: 0.9265 (t-90) cc_final: 0.8879 (t-90) REVERT: A 935 MET cc_start: 0.8769 (ppp) cc_final: 0.8556 (ppp) REVERT: A 995 MET cc_start: 0.8678 (tpp) cc_final: 0.8078 (tmm) REVERT: A 999 LEU cc_start: 0.9429 (mm) cc_final: 0.8956 (mm) REVERT: A 1062 TYR cc_start: 0.7775 (m-80) cc_final: 0.7263 (m-80) REVERT: A 1168 MET cc_start: 0.8462 (mmm) cc_final: 0.8209 (mmm) REVERT: A 1494 MET cc_start: 0.7873 (tmm) cc_final: 0.7349 (tmm) REVERT: A 1960 ARG cc_start: 0.8567 (ptt-90) cc_final: 0.8367 (ptp90) REVERT: A 2192 MET cc_start: 0.8630 (tpp) cc_final: 0.8400 (tpt) REVERT: A 2727 HIS cc_start: 0.8912 (t-90) cc_final: 0.8508 (t-90) REVERT: A 2731 LYS cc_start: 0.8932 (ptpp) cc_final: 0.8659 (pttm) REVERT: A 2772 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8563 (mtm110) REVERT: A 2779 LEU cc_start: 0.9237 (mt) cc_final: 0.8947 (mt) REVERT: A 2782 MET cc_start: 0.8168 (tpp) cc_final: 0.7834 (tpp) REVERT: A 2840 MET cc_start: 0.8954 (mmm) cc_final: 0.8446 (mmm) REVERT: A 2843 MET cc_start: 0.8799 (mtp) cc_final: 0.8264 (ttm) REVERT: A 2844 MET cc_start: 0.8687 (ptm) cc_final: 0.7583 (ttm) REVERT: A 2848 TYR cc_start: 0.8284 (m-80) cc_final: 0.7491 (m-80) REVERT: A 2939 TYR cc_start: 0.8565 (m-80) cc_final: 0.8230 (m-80) REVERT: A 3003 MET cc_start: 0.8783 (ptt) cc_final: 0.8541 (ptm) REVERT: A 3104 MET cc_start: 0.8498 (ptm) cc_final: 0.8195 (ptt) REVERT: A 3131 TYR cc_start: 0.8803 (m-80) cc_final: 0.8426 (m-80) REVERT: A 3137 LEU cc_start: 0.9302 (mt) cc_final: 0.8977 (mt) REVERT: A 3140 LEU cc_start: 0.9174 (mt) cc_final: 0.8778 (mt) REVERT: A 3235 MET cc_start: 0.6961 (ptt) cc_final: 0.6457 (ppp) REVERT: A 3304 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8112 (tp-100) REVERT: A 4046 ARG cc_start: 0.8799 (mmm160) cc_final: 0.8396 (mmp80) REVERT: A 4052 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: B 890 HIS cc_start: 0.9246 (t-90) cc_final: 0.8841 (t-90) REVERT: B 1062 TYR cc_start: 0.8442 (m-80) cc_final: 0.8211 (m-80) REVERT: B 1113 MET cc_start: 0.8436 (mtt) cc_final: 0.8214 (mtm) REVERT: B 1165 MET cc_start: 0.8425 (mtp) cc_final: 0.8186 (mtp) REVERT: B 1505 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7539 (tt) REVERT: B 1948 MET cc_start: 0.8822 (mmp) cc_final: 0.8595 (tpp) REVERT: B 2214 MET cc_start: 0.9227 (mmm) cc_final: 0.8790 (tpt) REVERT: B 2234 MET cc_start: 0.8670 (mtp) cc_final: 0.8397 (mtp) REVERT: B 2442 MET cc_start: 0.8080 (mmm) cc_final: 0.7747 (mmm) REVERT: B 2731 LYS cc_start: 0.8855 (pttm) cc_final: 0.8572 (mttp) REVERT: B 2732 TRP cc_start: 0.8981 (t-100) cc_final: 0.8584 (t-100) REVERT: B 2772 ARG cc_start: 0.8901 (mtm110) cc_final: 0.8451 (mtm110) REVERT: B 2779 LEU cc_start: 0.9261 (mt) cc_final: 0.9052 (mt) REVERT: B 2843 MET cc_start: 0.8732 (mtp) cc_final: 0.8317 (ttm) REVERT: B 2848 TYR cc_start: 0.8266 (m-80) cc_final: 0.7962 (m-80) REVERT: B 2939 TYR cc_start: 0.8532 (m-80) cc_final: 0.8209 (m-80) REVERT: B 3003 MET cc_start: 0.8644 (ptm) cc_final: 0.8351 (ptm) REVERT: B 3072 MET cc_start: 0.7914 (mmm) cc_final: 0.7311 (mmm) REVERT: B 3104 MET cc_start: 0.8503 (ptm) cc_final: 0.8249 (ptt) REVERT: B 3131 TYR cc_start: 0.8919 (m-80) cc_final: 0.8483 (m-80) REVERT: B 3273 MET cc_start: 0.8628 (mtp) cc_final: 0.8381 (mtp) REVERT: B 3956 MET cc_start: 0.7837 (mmt) cc_final: 0.7568 (mmt) REVERT: B 4046 ARG cc_start: 0.8818 (mmm160) cc_final: 0.8353 (mmm160) REVERT: B 4052 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7562 (mtp) REVERT: C 128 MET cc_start: 0.8872 (mtm) cc_final: 0.8643 (mtp) REVERT: C 890 HIS cc_start: 0.9282 (t-90) cc_final: 0.8888 (t-90) REVERT: C 935 MET cc_start: 0.8915 (ppp) cc_final: 0.8640 (ppp) REVERT: C 995 MET cc_start: 0.8802 (mmm) cc_final: 0.8574 (mtm) REVERT: C 1062 TYR cc_start: 0.8575 (m-80) cc_final: 0.8216 (m-80) REVERT: C 2214 MET cc_start: 0.9225 (mmm) cc_final: 0.9010 (mmp) REVERT: C 2234 MET cc_start: 0.8671 (mtp) cc_final: 0.8357 (mtp) REVERT: C 2442 MET cc_start: 0.8117 (mmm) cc_final: 0.7882 (mmm) REVERT: C 2731 LYS cc_start: 0.8864 (pttm) cc_final: 0.8576 (mtmm) REVERT: C 2732 TRP cc_start: 0.9042 (t-100) cc_final: 0.8658 (t-100) REVERT: C 2734 MET cc_start: 0.9073 (mmp) cc_final: 0.8814 (mmt) REVERT: C 2772 ARG cc_start: 0.8891 (mtm110) cc_final: 0.8431 (mtm110) REVERT: C 2779 LEU cc_start: 0.9336 (mt) cc_final: 0.9093 (mt) REVERT: C 2840 MET cc_start: 0.8759 (mmm) cc_final: 0.8307 (mmm) REVERT: C 2843 MET cc_start: 0.8718 (mtp) cc_final: 0.8227 (ttm) REVERT: C 2848 TYR cc_start: 0.8168 (m-80) cc_final: 0.7861 (m-80) REVERT: C 2871 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9329 (mm) REVERT: C 2905 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8512 (tpp-160) REVERT: C 2939 TYR cc_start: 0.8559 (m-80) cc_final: 0.8226 (m-80) REVERT: C 3003 MET cc_start: 0.8667 (ptm) cc_final: 0.8379 (ptm) REVERT: C 3104 MET cc_start: 0.8503 (ptm) cc_final: 0.8266 (ptt) REVERT: C 3131 TYR cc_start: 0.8976 (m-80) cc_final: 0.8479 (m-80) REVERT: C 3233 HIS cc_start: 0.7892 (m90) cc_final: 0.7569 (m170) REVERT: C 4046 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8352 (mmm160) REVERT: C 4052 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7750 (mtp) REVERT: D 890 HIS cc_start: 0.9241 (t-90) cc_final: 0.8811 (t-90) REVERT: D 935 MET cc_start: 0.8863 (ppp) cc_final: 0.8609 (ppp) REVERT: D 1113 MET cc_start: 0.8737 (mtm) cc_final: 0.8434 (mtt) REVERT: D 1168 MET cc_start: 0.8436 (mmm) cc_final: 0.8180 (mmm) REVERT: D 1421 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8643 (mmp) REVERT: D 2214 MET cc_start: 0.9234 (mmm) cc_final: 0.8805 (tpt) REVERT: D 2234 MET cc_start: 0.8668 (mtp) cc_final: 0.8337 (mtp) REVERT: D 2384 MET cc_start: 0.8865 (mmt) cc_final: 0.8648 (mmt) REVERT: D 2442 MET cc_start: 0.8121 (mmm) cc_final: 0.7879 (mmm) REVERT: D 2727 HIS cc_start: 0.8928 (t-90) cc_final: 0.8613 (t-90) REVERT: D 2731 LYS cc_start: 0.8864 (pttm) cc_final: 0.8519 (pttm) REVERT: D 2732 TRP cc_start: 0.9112 (t-100) cc_final: 0.8740 (t-100) REVERT: D 2734 MET cc_start: 0.9059 (mmp) cc_final: 0.8738 (mmt) REVERT: D 2772 ARG cc_start: 0.8924 (mtm110) cc_final: 0.8594 (mtm110) REVERT: D 2773 TRP cc_start: 0.8777 (t-100) cc_final: 0.8324 (t-100) REVERT: D 2775 ILE cc_start: 0.9443 (mt) cc_final: 0.9096 (tt) REVERT: D 2777 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: D 2779 LEU cc_start: 0.9271 (mt) cc_final: 0.9007 (mt) REVERT: D 2840 MET cc_start: 0.8985 (mtp) cc_final: 0.8778 (mmm) REVERT: D 2843 MET cc_start: 0.8693 (mtp) cc_final: 0.8323 (mtp) REVERT: D 2844 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8435 (tmm) REVERT: D 2895 PHE cc_start: 0.9041 (t80) cc_final: 0.8828 (t80) REVERT: D 2905 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8541 (tpp-160) REVERT: D 2939 TYR cc_start: 0.8732 (m-80) cc_final: 0.8329 (m-80) REVERT: D 3003 MET cc_start: 0.8716 (ptm) cc_final: 0.8418 (ptm) REVERT: D 3072 MET cc_start: 0.8409 (tpp) cc_final: 0.8159 (tpp) REVERT: D 3131 TYR cc_start: 0.8979 (m-80) cc_final: 0.8441 (m-80) REVERT: D 3235 MET cc_start: 0.7573 (ppp) cc_final: 0.7340 (ppp) REVERT: D 3239 LEU cc_start: 0.9190 (mp) cc_final: 0.8953 (mt) REVERT: D 4046 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8444 (mmm160) REVERT: D 4052 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: F 62 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8013 (mt-10) outliers start: 67 outliers final: 41 residues processed: 959 average time/residue: 1.1873 time to fit residues: 2015.5241 Evaluate side-chains 959 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 909 time to evaluate : 11.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4306 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain B residue 1510 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3025 ASP Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4052 MET Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1510 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2871 LEU Chi-restraints excluded: chain C residue 3025 ASP Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 4052 MET Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1421 MET Chi-restraints excluded: chain D residue 1510 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2871 LEU Chi-restraints excluded: chain D residue 3025 ASP Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 4052 MET Chi-restraints excluded: chain D residue 4118 PHE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 10.0000 chunk 1595 optimal weight: 20.0000 chunk 1455 optimal weight: 3.9990 chunk 1552 optimal weight: 30.0000 chunk 934 optimal weight: 10.0000 chunk 676 optimal weight: 5.9990 chunk 1218 optimal weight: 5.9990 chunk 476 optimal weight: 2.9990 chunk 1402 optimal weight: 10.0000 chunk 1467 optimal weight: 9.9990 chunk 1546 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1995 GLN ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4201 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4075 ASN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 GLN ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4201 GLN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 141648 Z= 0.418 Angle : 0.623 19.061 191392 Z= 0.314 Chirality : 0.042 0.260 20988 Planarity : 0.005 0.152 24588 Dihedral : 5.019 71.651 19024 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 0.55 % Allowed : 7.41 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.42 (0.07), residues: 17212 helix: 2.07 (0.06), residues: 8996 sheet: 0.15 (0.12), residues: 1724 loop : -0.42 (0.08), residues: 6492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A2773 HIS 0.010 0.001 HIS D3732 PHE 0.036 0.002 PHE C3854 TYR 0.026 0.002 TYR A3138 ARG 0.014 0.001 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 932 time to evaluate : 11.824 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: A 890 HIS cc_start: 0.9294 (t-90) cc_final: 0.8911 (t-90) REVERT: A 935 MET cc_start: 0.8796 (ppp) cc_final: 0.8575 (ppp) REVERT: A 995 MET cc_start: 0.8704 (tpp) cc_final: 0.8141 (tmm) REVERT: A 999 LEU cc_start: 0.9428 (mm) cc_final: 0.8966 (mm) REVERT: A 1062 TYR cc_start: 0.7861 (m-80) cc_final: 0.7292 (m-80) REVERT: A 1168 MET cc_start: 0.8502 (mmm) cc_final: 0.8193 (mmm) REVERT: A 1487 MET cc_start: 0.8928 (ttm) cc_final: 0.8621 (mtp) REVERT: A 1494 MET cc_start: 0.7892 (tmm) cc_final: 0.7320 (tmm) REVERT: A 2192 MET cc_start: 0.8703 (tpp) cc_final: 0.8436 (tpt) REVERT: A 2695 MET cc_start: 0.8346 (ptp) cc_final: 0.7729 (pmm) REVERT: A 2727 HIS cc_start: 0.9017 (t-90) cc_final: 0.8703 (t-90) REVERT: A 2779 LEU cc_start: 0.9266 (mt) cc_final: 0.8993 (mt) REVERT: A 2843 MET cc_start: 0.8840 (mtp) cc_final: 0.8366 (ttm) REVERT: A 2844 MET cc_start: 0.8738 (ptm) cc_final: 0.8365 (ptm) REVERT: A 2848 TYR cc_start: 0.8448 (m-80) cc_final: 0.8051 (m-80) REVERT: A 2939 TYR cc_start: 0.8594 (m-80) cc_final: 0.8259 (m-80) REVERT: A 3003 MET cc_start: 0.8801 (ptt) cc_final: 0.8557 (ptm) REVERT: A 3104 MET cc_start: 0.8546 (ptm) cc_final: 0.8251 (ptm) REVERT: A 3131 TYR cc_start: 0.8923 (m-80) cc_final: 0.8570 (m-80) REVERT: A 3137 LEU cc_start: 0.9333 (mt) cc_final: 0.9074 (mt) REVERT: A 3235 MET cc_start: 0.6937 (ptt) cc_final: 0.6188 (ppp) REVERT: A 3302 PHE cc_start: 0.9091 (m-80) cc_final: 0.8843 (m-80) REVERT: A 3304 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8163 (tp-100) REVERT: A 3854 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8504 (t80) REVERT: A 4046 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8453 (mmm160) REVERT: A 4052 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7753 (mtp) REVERT: A 4274 MET cc_start: 0.6315 (tpt) cc_final: 0.5392 (ptt) REVERT: B 890 HIS cc_start: 0.9271 (t-90) cc_final: 0.8875 (t-90) REVERT: B 995 MET cc_start: 0.8713 (mtm) cc_final: 0.8304 (mpp) REVERT: B 1062 TYR cc_start: 0.8489 (m-80) cc_final: 0.8260 (m-80) REVERT: B 1165 MET cc_start: 0.8486 (mtp) cc_final: 0.8257 (mtp) REVERT: B 1494 MET cc_start: 0.8252 (tpt) cc_final: 0.8007 (tmm) REVERT: B 1948 MET cc_start: 0.8861 (mmp) cc_final: 0.8636 (tpp) REVERT: B 2214 MET cc_start: 0.9222 (mmm) cc_final: 0.8989 (mmp) REVERT: B 2234 MET cc_start: 0.8766 (mtp) cc_final: 0.8423 (mtp) REVERT: B 2442 MET cc_start: 0.8175 (mmm) cc_final: 0.7863 (mmm) REVERT: B 2732 TRP cc_start: 0.9070 (t-100) cc_final: 0.8644 (t-100) REVERT: B 2779 LEU cc_start: 0.9336 (mt) cc_final: 0.9104 (mt) REVERT: B 2787 TRP cc_start: 0.7575 (m-10) cc_final: 0.6884 (m-10) REVERT: B 2843 MET cc_start: 0.8766 (mtp) cc_final: 0.8256 (ttm) REVERT: B 2848 TYR cc_start: 0.8454 (m-80) cc_final: 0.8114 (m-80) REVERT: B 2939 TYR cc_start: 0.8565 (m-80) cc_final: 0.8270 (m-80) REVERT: B 3003 MET cc_start: 0.8702 (ptm) cc_final: 0.8407 (ptm) REVERT: B 3104 MET cc_start: 0.8561 (ptm) cc_final: 0.8295 (ptm) REVERT: B 3131 TYR cc_start: 0.8980 (m-80) cc_final: 0.8590 (m-80) REVERT: B 3273 MET cc_start: 0.8655 (mtp) cc_final: 0.8416 (mtp) REVERT: B 3854 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8507 (t80) REVERT: B 4046 ARG cc_start: 0.8864 (mmm160) cc_final: 0.8409 (mmm160) REVERT: B 4052 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: B 4057 HIS cc_start: 0.8167 (m90) cc_final: 0.7762 (m90) REVERT: C 890 HIS cc_start: 0.9308 (t-90) cc_final: 0.8923 (t-90) REVERT: C 935 MET cc_start: 0.8933 (ppp) cc_final: 0.8680 (ppp) REVERT: C 1062 TYR cc_start: 0.8591 (m-80) cc_final: 0.8216 (m-80) REVERT: C 1165 MET cc_start: 0.8573 (mtm) cc_final: 0.8186 (mtm) REVERT: C 2214 MET cc_start: 0.9214 (mmm) cc_final: 0.8975 (mmp) REVERT: C 2234 MET cc_start: 0.8769 (mtp) cc_final: 0.8434 (mtp) REVERT: C 2442 MET cc_start: 0.8218 (mmm) cc_final: 0.7934 (mmm) REVERT: C 2731 LYS cc_start: 0.8848 (pttm) cc_final: 0.8557 (mtmm) REVERT: C 2732 TRP cc_start: 0.9077 (t-100) cc_final: 0.8696 (t-100) REVERT: C 2734 MET cc_start: 0.9096 (mmp) cc_final: 0.8819 (mmt) REVERT: C 2779 LEU cc_start: 0.9357 (mt) cc_final: 0.9122 (mt) REVERT: C 2798 MET cc_start: 0.8275 (mmt) cc_final: 0.7929 (mmm) REVERT: C 2843 MET cc_start: 0.8799 (mtp) cc_final: 0.8186 (ttm) REVERT: C 2848 TYR cc_start: 0.8339 (m-80) cc_final: 0.8018 (m-80) REVERT: C 2939 TYR cc_start: 0.8588 (m-80) cc_final: 0.8292 (m-80) REVERT: C 3003 MET cc_start: 0.8718 (ptm) cc_final: 0.8428 (ptm) REVERT: C 3104 MET cc_start: 0.8556 (ptm) cc_final: 0.8298 (ptm) REVERT: C 3131 TYR cc_start: 0.9034 (m-80) cc_final: 0.8570 (m-80) REVERT: C 3233 HIS cc_start: 0.7967 (m90) cc_final: 0.7648 (m170) REVERT: C 3302 PHE cc_start: 0.8995 (m-80) cc_final: 0.8756 (m-80) REVERT: C 3854 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8520 (t80) REVERT: C 4046 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8391 (mmm160) REVERT: C 4052 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7756 (mtp) REVERT: C 4567 TYR cc_start: 0.5536 (t80) cc_final: 0.5172 (t80) REVERT: D 890 HIS cc_start: 0.9287 (t-90) cc_final: 0.8935 (t-90) REVERT: D 935 MET cc_start: 0.8905 (ppp) cc_final: 0.8660 (ppp) REVERT: D 995 MET cc_start: 0.8780 (mtm) cc_final: 0.8292 (mpp) REVERT: D 1062 TYR cc_start: 0.8616 (m-80) cc_final: 0.8216 (m-80) REVERT: D 1113 MET cc_start: 0.8877 (mtm) cc_final: 0.8617 (mtt) REVERT: D 1165 MET cc_start: 0.8563 (mtm) cc_final: 0.8196 (mtm) REVERT: D 1168 MET cc_start: 0.8486 (mmm) cc_final: 0.8208 (mmm) REVERT: D 2214 MET cc_start: 0.9227 (mmm) cc_final: 0.8989 (mmp) REVERT: D 2442 MET cc_start: 0.8222 (mmm) cc_final: 0.7856 (mmp) REVERT: D 2727 HIS cc_start: 0.8947 (t-90) cc_final: 0.8615 (t-90) REVERT: D 2731 LYS cc_start: 0.8863 (pttm) cc_final: 0.8505 (pttm) REVERT: D 2732 TRP cc_start: 0.9140 (t-100) cc_final: 0.8755 (t-100) REVERT: D 2734 MET cc_start: 0.9036 (mmp) cc_final: 0.8742 (mmt) REVERT: D 2773 TRP cc_start: 0.8830 (t-100) cc_final: 0.8361 (t-100) REVERT: D 2777 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: D 2779 LEU cc_start: 0.9325 (mt) cc_final: 0.9087 (mt) REVERT: D 2840 MET cc_start: 0.9033 (mtp) cc_final: 0.8780 (mmm) REVERT: D 2843 MET cc_start: 0.8731 (mtp) cc_final: 0.8388 (mtp) REVERT: D 2844 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8462 (tmm) REVERT: D 2895 PHE cc_start: 0.9112 (t80) cc_final: 0.8871 (t80) REVERT: D 2905 ARG cc_start: 0.8901 (tpp-160) cc_final: 0.8543 (tpp80) REVERT: D 2939 TYR cc_start: 0.8768 (m-80) cc_final: 0.8394 (m-80) REVERT: D 3003 MET cc_start: 0.8752 (ptm) cc_final: 0.8535 (ptm) REVERT: D 3072 MET cc_start: 0.8453 (tpp) cc_final: 0.8253 (tpp) REVERT: D 3131 TYR cc_start: 0.9046 (m-80) cc_final: 0.8533 (m-80) REVERT: D 3235 MET cc_start: 0.7593 (ppp) cc_final: 0.7293 (ppp) REVERT: D 3239 LEU cc_start: 0.9268 (mp) cc_final: 0.9020 (mt) REVERT: D 3854 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8504 (t80) REVERT: D 4046 ARG cc_start: 0.8860 (mmm160) cc_final: 0.8488 (mmm160) REVERT: D 4052 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7695 (mtp) REVERT: F 53 LYS cc_start: 0.9377 (mmtp) cc_final: 0.9135 (mttm) REVERT: F 62 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8019 (mt-10) outliers start: 78 outliers final: 51 residues processed: 970 average time/residue: 1.2035 time to fit residues: 2060.4165 Evaluate side-chains 982 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 921 time to evaluate : 11.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1168 MET Chi-restraints excluded: chain B residue 1510 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3025 ASP Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4052 MET Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1510 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2871 LEU Chi-restraints excluded: chain C residue 3025 ASP Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4052 MET Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1510 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2871 LEU Chi-restraints excluded: chain D residue 3025 ASP Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4052 MET Chi-restraints excluded: chain D residue 4118 PHE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 1.9990 chunk 1641 optimal weight: 7.9990 chunk 1001 optimal weight: 5.9990 chunk 778 optimal weight: 0.7980 chunk 1140 optimal weight: 2.9990 chunk 1721 optimal weight: 6.9990 chunk 1584 optimal weight: 50.0000 chunk 1370 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 1058 optimal weight: 5.9990 chunk 840 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4075 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1498 GLN ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 141648 Z= 0.253 Angle : 0.589 19.946 191392 Z= 0.294 Chirality : 0.040 0.368 20988 Planarity : 0.004 0.122 24588 Dihedral : 5.034 70.875 19024 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 0.40 % Allowed : 7.58 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.47 (0.07), residues: 17212 helix: 2.11 (0.06), residues: 8972 sheet: 0.19 (0.13), residues: 1688 loop : -0.39 (0.08), residues: 6552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A2773 HIS 0.009 0.001 HIS C3700 PHE 0.040 0.001 PHE A2895 TYR 0.028 0.001 TYR A3138 ARG 0.015 0.000 ARG A2144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 924 time to evaluate : 11.842 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: A 890 HIS cc_start: 0.9286 (t-90) cc_final: 0.8921 (t-90) REVERT: A 935 MET cc_start: 0.8779 (ppp) cc_final: 0.8559 (ppp) REVERT: A 995 MET cc_start: 0.8692 (tpp) cc_final: 0.8127 (tmm) REVERT: A 999 LEU cc_start: 0.9419 (mm) cc_final: 0.8946 (mm) REVERT: A 1062 TYR cc_start: 0.7896 (m-80) cc_final: 0.7337 (m-80) REVERT: A 1168 MET cc_start: 0.8472 (mmm) cc_final: 0.8186 (mmm) REVERT: A 1487 MET cc_start: 0.8893 (ttm) cc_final: 0.8674 (mtp) REVERT: A 1494 MET cc_start: 0.7893 (tmm) cc_final: 0.7343 (tmm) REVERT: A 1960 ARG cc_start: 0.8566 (ptt-90) cc_final: 0.8355 (ptp90) REVERT: A 2192 MET cc_start: 0.8698 (tpp) cc_final: 0.8431 (tpt) REVERT: A 2695 MET cc_start: 0.8454 (ptp) cc_final: 0.7846 (pmm) REVERT: A 2731 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8714 (pttm) REVERT: A 2779 LEU cc_start: 0.9250 (mt) cc_final: 0.8966 (mt) REVERT: A 2840 MET cc_start: 0.8944 (mmm) cc_final: 0.8423 (mmm) REVERT: A 2843 MET cc_start: 0.8830 (mtp) cc_final: 0.8339 (ttm) REVERT: A 2844 MET cc_start: 0.8722 (ptm) cc_final: 0.8334 (ptm) REVERT: A 2848 TYR cc_start: 0.8424 (m-80) cc_final: 0.8046 (m-80) REVERT: A 2939 TYR cc_start: 0.8594 (m-80) cc_final: 0.8248 (m-80) REVERT: A 3003 MET cc_start: 0.8790 (ptt) cc_final: 0.8552 (ptm) REVERT: A 3072 MET cc_start: 0.8505 (tpp) cc_final: 0.8181 (mmm) REVERT: A 3104 MET cc_start: 0.8526 (ptm) cc_final: 0.8242 (ptt) REVERT: A 3131 TYR cc_start: 0.8869 (m-80) cc_final: 0.8490 (m-80) REVERT: A 3137 LEU cc_start: 0.9299 (mt) cc_final: 0.8962 (mt) REVERT: A 3235 MET cc_start: 0.7061 (ptt) cc_final: 0.6794 (tmm) REVERT: A 3302 PHE cc_start: 0.9070 (m-80) cc_final: 0.8804 (m-80) REVERT: A 3304 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8137 (tp-100) REVERT: A 4046 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8448 (mmm160) REVERT: A 4052 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7728 (mtp) REVERT: A 4274 MET cc_start: 0.6245 (tpt) cc_final: 0.5389 (ptt) REVERT: B 890 HIS cc_start: 0.9277 (t-90) cc_final: 0.8892 (t-90) REVERT: B 995 MET cc_start: 0.8734 (mtm) cc_final: 0.8374 (mpp) REVERT: B 1062 TYR cc_start: 0.8466 (m-80) cc_final: 0.8214 (m-80) REVERT: B 1165 MET cc_start: 0.8465 (mtp) cc_final: 0.8232 (mtp) REVERT: B 1948 MET cc_start: 0.8839 (mmp) cc_final: 0.8608 (tpp) REVERT: B 2214 MET cc_start: 0.9217 (mmm) cc_final: 0.8982 (mmp) REVERT: B 2234 MET cc_start: 0.8727 (mtp) cc_final: 0.8399 (mtp) REVERT: B 2442 MET cc_start: 0.8151 (mmm) cc_final: 0.7861 (mmm) REVERT: B 2732 TRP cc_start: 0.9029 (t-100) cc_final: 0.8649 (t-100) REVERT: B 2772 ARG cc_start: 0.8949 (mtm110) cc_final: 0.8683 (ptt90) REVERT: B 2779 LEU cc_start: 0.9322 (mt) cc_final: 0.9104 (mt) REVERT: B 2848 TYR cc_start: 0.8427 (m-80) cc_final: 0.8112 (m-80) REVERT: B 2939 TYR cc_start: 0.8559 (m-80) cc_final: 0.8253 (m-80) REVERT: B 3003 MET cc_start: 0.8679 (ptm) cc_final: 0.8386 (ptm) REVERT: B 3104 MET cc_start: 0.8534 (ptm) cc_final: 0.8268 (ptm) REVERT: B 3131 TYR cc_start: 0.8935 (m-80) cc_final: 0.8490 (m-80) REVERT: B 3302 PHE cc_start: 0.8968 (m-80) cc_final: 0.8734 (m-80) REVERT: B 4046 ARG cc_start: 0.8837 (mmm160) cc_final: 0.8393 (mmm160) REVERT: B 4052 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7584 (mtp) REVERT: B 4567 TYR cc_start: 0.5602 (t80) cc_final: 0.5173 (t80) REVERT: C 128 MET cc_start: 0.8940 (mtm) cc_final: 0.8711 (mtp) REVERT: C 890 HIS cc_start: 0.9284 (t-90) cc_final: 0.8914 (t-90) REVERT: C 935 MET cc_start: 0.8921 (ppp) cc_final: 0.8661 (ppp) REVERT: C 1062 TYR cc_start: 0.8620 (m-80) cc_final: 0.8221 (m-80) REVERT: C 1165 MET cc_start: 0.8561 (mtm) cc_final: 0.8143 (mtm) REVERT: C 2214 MET cc_start: 0.9214 (mmm) cc_final: 0.8978 (mmp) REVERT: C 2442 MET cc_start: 0.8156 (mmm) cc_final: 0.7877 (mmm) REVERT: C 2731 LYS cc_start: 0.8866 (pttm) cc_final: 0.8587 (mtmm) REVERT: C 2732 TRP cc_start: 0.9036 (t-100) cc_final: 0.8651 (t-100) REVERT: C 2779 LEU cc_start: 0.9343 (mt) cc_final: 0.9101 (mt) REVERT: C 2840 MET cc_start: 0.8754 (mmm) cc_final: 0.8300 (mmm) REVERT: C 2843 MET cc_start: 0.8789 (mtp) cc_final: 0.8545 (mtp) REVERT: C 2848 TYR cc_start: 0.8330 (m-80) cc_final: 0.8022 (m-80) REVERT: C 2905 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8207 (tpp-160) REVERT: C 2939 TYR cc_start: 0.8588 (m-80) cc_final: 0.8281 (m-80) REVERT: C 3003 MET cc_start: 0.8682 (ptm) cc_final: 0.8407 (ptm) REVERT: C 3104 MET cc_start: 0.8531 (ptm) cc_final: 0.8276 (ptm) REVERT: C 3131 TYR cc_start: 0.9004 (m-80) cc_final: 0.8512 (m-80) REVERT: C 3233 HIS cc_start: 0.7909 (m90) cc_final: 0.7570 (m170) REVERT: C 3854 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8375 (t80) REVERT: C 4046 ARG cc_start: 0.8797 (mmm160) cc_final: 0.8407 (mmm160) REVERT: C 4052 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7746 (mtp) REVERT: C 4567 TYR cc_start: 0.5534 (t80) cc_final: 0.5126 (t80) REVERT: D 890 HIS cc_start: 0.9288 (t-90) cc_final: 0.8929 (t-90) REVERT: D 935 MET cc_start: 0.8885 (ppp) cc_final: 0.8632 (ppp) REVERT: D 995 MET cc_start: 0.8722 (mtm) cc_final: 0.8244 (mpp) REVERT: D 1062 TYR cc_start: 0.8605 (m-80) cc_final: 0.8160 (m-80) REVERT: D 1113 MET cc_start: 0.8824 (mtm) cc_final: 0.8549 (mtt) REVERT: D 1165 MET cc_start: 0.8558 (mtm) cc_final: 0.8169 (mtm) REVERT: D 1168 MET cc_start: 0.8455 (mmm) cc_final: 0.8163 (mmm) REVERT: D 2214 MET cc_start: 0.9226 (mmm) cc_final: 0.8988 (mmp) REVERT: D 2234 MET cc_start: 0.8720 (mtp) cc_final: 0.8386 (mtp) REVERT: D 2442 MET cc_start: 0.8158 (mmm) cc_final: 0.7855 (mmm) REVERT: D 2727 HIS cc_start: 0.8917 (t-90) cc_final: 0.8591 (t-90) REVERT: D 2731 LYS cc_start: 0.8852 (pttm) cc_final: 0.8480 (pttm) REVERT: D 2732 TRP cc_start: 0.9127 (t-100) cc_final: 0.8743 (t-100) REVERT: D 2734 MET cc_start: 0.9044 (mmp) cc_final: 0.8814 (mmt) REVERT: D 2772 ARG cc_start: 0.8897 (mtm110) cc_final: 0.8676 (mtm110) REVERT: D 2773 TRP cc_start: 0.8807 (t-100) cc_final: 0.8322 (t-100) REVERT: D 2775 ILE cc_start: 0.9458 (mt) cc_final: 0.9078 (tt) REVERT: D 2777 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: D 2779 LEU cc_start: 0.9316 (mt) cc_final: 0.9062 (mt) REVERT: D 2840 MET cc_start: 0.8995 (mtp) cc_final: 0.8734 (mmm) REVERT: D 2843 MET cc_start: 0.8716 (mtp) cc_final: 0.8381 (mtp) REVERT: D 2844 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8440 (tmm) REVERT: D 2895 PHE cc_start: 0.9087 (t80) cc_final: 0.8859 (t80) REVERT: D 2939 TYR cc_start: 0.8755 (m-80) cc_final: 0.8370 (m-80) REVERT: D 3003 MET cc_start: 0.8575 (ptm) cc_final: 0.8329 (ptm) REVERT: D 3072 MET cc_start: 0.8425 (tpp) cc_final: 0.8212 (tpp) REVERT: D 3131 TYR cc_start: 0.9012 (m-80) cc_final: 0.8500 (m-80) REVERT: D 3235 MET cc_start: 0.7507 (ppp) cc_final: 0.7264 (ppp) REVERT: D 3239 LEU cc_start: 0.9268 (mp) cc_final: 0.9041 (mt) REVERT: D 3302 PHE cc_start: 0.9008 (m-80) cc_final: 0.8785 (m-80) REVERT: D 4046 ARG cc_start: 0.8854 (mmm160) cc_final: 0.8478 (mmm160) REVERT: D 4052 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7672 (mtp) REVERT: F 53 LYS cc_start: 0.9369 (mmtp) cc_final: 0.9124 (mttm) outliers start: 56 outliers final: 45 residues processed: 951 average time/residue: 1.1949 time to fit residues: 2005.9250 Evaluate side-chains 968 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 916 time to evaluate : 11.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4558 HIS Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1510 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2871 LEU Chi-restraints excluded: chain B residue 3025 ASP Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4052 MET Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1510 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2871 LEU Chi-restraints excluded: chain C residue 3025 ASP Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4052 MET Chi-restraints excluded: chain C residue 4558 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1510 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2871 LEU Chi-restraints excluded: chain D residue 3025 ASP Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 4052 MET Chi-restraints excluded: chain D residue 4118 PHE Chi-restraints excluded: chain D residue 4558 HIS Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 5.9990 chunk 1460 optimal weight: 4.9990 chunk 419 optimal weight: 6.9990 chunk 1264 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 1373 optimal weight: 2.9990 chunk 574 optimal weight: 8.9990 chunk 1409 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 252 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2704 GLN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.045164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.032264 restraints weight = 1232882.908| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.79 r_work: 0.2738 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 141648 Z= 0.213 Angle : 0.585 20.105 191392 Z= 0.290 Chirality : 0.040 0.479 20988 Planarity : 0.004 0.121 24588 Dihedral : 4.971 70.022 19024 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 0.43 % Allowed : 7.65 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.51 (0.07), residues: 17212 helix: 2.15 (0.06), residues: 8960 sheet: 0.24 (0.13), residues: 1632 loop : -0.38 (0.08), residues: 6620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A2773 HIS 0.009 0.001 HIS D3700 PHE 0.035 0.001 PHE C2895 TYR 0.027 0.001 TYR D3138 ARG 0.015 0.000 ARG F 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39509.72 seconds wall clock time: 690 minutes 10.62 seconds (41410.62 seconds total)