Starting phenix.real_space_refine on Mon Mar 18 16:50:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9r_26407/03_2024/7u9r_26407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9r_26407/03_2024/7u9r_26407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9r_26407/03_2024/7u9r_26407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9r_26407/03_2024/7u9r_26407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9r_26407/03_2024/7u9r_26407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9r_26407/03_2024/7u9r_26407_updated.pdb" } resolution = 3.69 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= 0.016 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 936 5.16 5 C 88228 2.51 5 N 23612 2.21 5 O 25848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 954": "OD1" <-> "OD2" Residue "A GLU 993": "OE1" <-> "OE2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1076": "OE1" <-> "OE2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1718": "NH1" <-> "NH2" Residue "A GLU 1724": "OE1" <-> "OE2" Residue "A ASP 1808": "OD1" <-> "OD2" Residue "A GLU 1853": "OE1" <-> "OE2" Residue "A ASP 1982": "OD1" <-> "OD2" Residue "A GLU 2001": "OE1" <-> "OE2" Residue "A GLU 2010": "OE1" <-> "OE2" Residue "A GLU 2072": "OE1" <-> "OE2" Residue "A TYR 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2223": "OE1" <-> "OE2" Residue "A ARG 2258": "NH1" <-> "NH2" Residue "A GLU 2377": "OE1" <-> "OE2" Residue "A PHE 2440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2463": "OD1" <-> "OD2" Residue "A GLU 2489": "OE1" <-> "OE2" Residue "A GLU 2715": "OE1" <-> "OE2" Residue "A ASP 2730": "OD1" <-> "OD2" Residue "A TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3025": "OD1" <-> "OD2" Residue "A PHE 3060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3212": "OE1" <-> "OE2" Residue "A TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3324": "OE1" <-> "OE2" Residue "A GLU 3718": "OE1" <-> "OE2" Residue "A ASP 3832": "OD1" <-> "OD2" Residue "A PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4194": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4563": "OE1" <-> "OE2" Residue "A TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4678": "OD1" <-> "OD2" Residue "A TYR 4793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4930": "OE1" <-> "OE2" Residue "A GLU 4950": "OE1" <-> "OE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D GLU 835": "OE1" <-> "OE2" Residue "D PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 954": "OD1" <-> "OD2" Residue "D GLU 993": "OE1" <-> "OE2" Residue "D TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1076": "OE1" <-> "OE2" Residue "D TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1718": "NH1" <-> "NH2" Residue "D GLU 1724": "OE1" <-> "OE2" Residue "D ASP 1808": "OD1" <-> "OD2" Residue "D GLU 1853": "OE1" <-> "OE2" Residue "D ASP 1982": "OD1" <-> "OD2" Residue "D GLU 2001": "OE1" <-> "OE2" Residue "D GLU 2010": "OE1" <-> "OE2" Residue "D GLU 2072": "OE1" <-> "OE2" Residue "D TYR 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2223": "OE1" <-> "OE2" Residue "D ARG 2258": "NH1" <-> "NH2" Residue "D GLU 2377": "OE1" <-> "OE2" Residue "D PHE 2440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2463": "OD1" <-> "OD2" Residue "D GLU 2489": "OE1" <-> "OE2" Residue "D GLU 2715": "OE1" <-> "OE2" Residue "D ASP 2730": "OD1" <-> "OD2" Residue "D TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3025": "OD1" <-> "OD2" Residue "D PHE 3060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3212": "OE1" <-> "OE2" Residue "D TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3324": "OE1" <-> "OE2" Residue "D GLU 3718": "OE1" <-> "OE2" Residue "D ASP 3832": "OD1" <-> "OD2" Residue "D PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4194": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4563": "OE1" <-> "OE2" Residue "D TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4678": "OD1" <-> "OD2" Residue "D TYR 4793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4930": "OE1" <-> "OE2" Residue "D GLU 4950": "OE1" <-> "OE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B GLU 835": "OE1" <-> "OE2" Residue "B PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 954": "OD1" <-> "OD2" Residue "B GLU 993": "OE1" <-> "OE2" Residue "B TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1076": "OE1" <-> "OE2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1312": "OE1" <-> "OE2" Residue "B PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1718": "NH1" <-> "NH2" Residue "B GLU 1724": "OE1" <-> "OE2" Residue "B ASP 1808": "OD1" <-> "OD2" Residue "B GLU 1853": "OE1" <-> "OE2" Residue "B ASP 1982": "OD1" <-> "OD2" Residue "B GLU 2001": "OE1" <-> "OE2" Residue "B GLU 2010": "OE1" <-> "OE2" Residue "B GLU 2072": "OE1" <-> "OE2" Residue "B TYR 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2223": "OE1" <-> "OE2" Residue "B ARG 2258": "NH1" <-> "NH2" Residue "B GLU 2377": "OE1" <-> "OE2" Residue "B PHE 2440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2463": "OD1" <-> "OD2" Residue "B GLU 2489": "OE1" <-> "OE2" Residue "B GLU 2715": "OE1" <-> "OE2" Residue "B ASP 2730": "OD1" <-> "OD2" Residue "B TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3025": "OD1" <-> "OD2" Residue "B PHE 3060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3212": "OE1" <-> "OE2" Residue "B TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3324": "OE1" <-> "OE2" Residue "B GLU 3718": "OE1" <-> "OE2" Residue "B ASP 3832": "OD1" <-> "OD2" Residue "B PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4194": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4563": "OE1" <-> "OE2" Residue "B TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4678": "OD1" <-> "OD2" Residue "B TYR 4793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4930": "OE1" <-> "OE2" Residue "B GLU 4950": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "C PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 954": "OD1" <-> "OD2" Residue "C GLU 993": "OE1" <-> "OE2" Residue "C TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1076": "OE1" <-> "OE2" Residue "C TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1718": "NH1" <-> "NH2" Residue "C GLU 1724": "OE1" <-> "OE2" Residue "C ASP 1808": "OD1" <-> "OD2" Residue "C GLU 1853": "OE1" <-> "OE2" Residue "C ASP 1982": "OD1" <-> "OD2" Residue "C GLU 2001": "OE1" <-> "OE2" Residue "C GLU 2010": "OE1" <-> "OE2" Residue "C GLU 2072": "OE1" <-> "OE2" Residue "C TYR 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2223": "OE1" <-> "OE2" Residue "C ARG 2258": "NH1" <-> "NH2" Residue "C GLU 2377": "OE1" <-> "OE2" Residue "C PHE 2440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2463": "OD1" <-> "OD2" Residue "C GLU 2489": "OE1" <-> "OE2" Residue "C GLU 2715": "OE1" <-> "OE2" Residue "C ASP 2730": "OD1" <-> "OD2" Residue "C TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3025": "OD1" <-> "OD2" Residue "C PHE 3060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3212": "OE1" <-> "OE2" Residue "C TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3324": "OE1" <-> "OE2" Residue "C GLU 3718": "OE1" <-> "OE2" Residue "C ASP 3832": "OD1" <-> "OD2" Residue "C PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4194": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4563": "OE1" <-> "OE2" Residue "C TYR 4591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4678": "OD1" <-> "OD2" Residue "C TYR 4793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4930": "OE1" <-> "OE2" Residue "C GLU 4950": "OE1" <-> "OE2" Time to flip residues: 0.38s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138656 Number of models: 1 Model: "" Number of chains: 12 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: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 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, 33763 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: 34485 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 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, 33763 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: 34485 Chain: "B" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 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, 33763 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: 34485 Chain: "C" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 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, 33763 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: 34485 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33910 SG CYS A4888 182.235 208.123 123.584 1.00113.34 S ATOM 33935 SG CYS A4891 181.045 206.481 120.357 1.00111.83 S ATOM 70135 SG CYS D4888 172.315 182.207 123.510 1.00113.34 S ATOM 70160 SG CYS D4891 173.954 181.014 120.282 1.00111.83 S ATOM A030I SG CYS B4888 208.523 197.628 123.791 1.00113.34 S ATOM A0317 SG CYS B4891 206.864 198.798 120.565 1.00111.83 S ATOM A0T2L SG CYS C4888 197.673 171.511 123.998 1.00113.34 S ATOM A0T3A SG CYS C4891 198.851 173.158 120.769 1.00111.83 S Time building chain proxies: 93.22, per 1000 atoms: 0.67 Number of scatterers: 138656 At special positions: 0 Unit cell: (380.304, 380.304, 209.334, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 936 16.00 P 24 15.00 O 25848 8.00 N 23612 7.00 C 88228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 65 " distance=2.04 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 65 " distance=2.04 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 65 " distance=2.04 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 65 " distance=2.04 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " 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: 39.03 Conformation dependent library (CDL) restraints added in 33.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " Number of angles added : 4 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 72 sheets defined 59.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 37.97 Creating SS restraints... Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.745A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.012A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.957A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.745A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.012A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.957A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.745A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.012A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.957A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.745A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.011A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.957A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.033A 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: 4.377A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.599A 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: 4.153A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.381A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.674A pdb=" N ALA A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.054A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.752A pdb=" N HIS A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 509 removed outlier: 4.964A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.702A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 4.300A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.630A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 5.570A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.764A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.486A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.305A 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: 4.401A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.078A 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: 3.517A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 4.232A pdb=" N GLU A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 Processing helix chain 'A' and resid 954 through 961 removed outlier: 5.143A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 5.242A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.757A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.079A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.657A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.009A 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 1499 through 1504 removed outlier: 5.334A pdb=" N ASN A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A1504 " --> pdb=" O ARG A1500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1499 through 1504' Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.781A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.150A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1666 Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.882A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.547A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 5.727A pdb=" N THR A1737 " --> pdb=" O THR A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 4.121A pdb=" N GLN A1777 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR A1778 " --> pdb=" O GLU A1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1773 through 1778' Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 3.584A pdb=" N SER A1803 " --> pdb=" O VAL A1799 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1901 through 1948 removed outlier: 3.991A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1966 removed outlier: 3.888A pdb=" N ALA A1959 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 4.502A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.828A 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: 3.970A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.563A 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: 4.832A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.661A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.008A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.028A 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: 4.188A 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 2292 through 2307 removed outlier: 4.055A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 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: 9.014A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A2409 " --> pdb=" O GLU A2405 " (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: 5.642A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.854A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 4.914A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 4.372A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2532 removed outlier: 5.387A 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: 4.146A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 3.822A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A2589 " --> pdb=" O MET A2585 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2622 Proline residue: A2606 - end of helix removed outlier: 5.726A pdb=" N LYS A2619 " --> pdb=" O GLU A2615 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR A2620 " --> pdb=" O ARG A2616 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.178A 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: 4.221A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) removed outlier: 4.078A 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: 4.163A pdb=" N GLU A2718 " --> pdb=" O PRO A2714 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.320A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 3.914A 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: 5.286A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2881 through 2900 removed outlier: 4.531A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2921 removed outlier: 4.697A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.700A 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 2950 removed outlier: 4.630A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A2949 " --> pdb=" O GLY A2945 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A2950 " --> pdb=" O GLY A2946 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.641A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 5.176A 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: 4.141A 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: 5.312A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3117 through 3123 removed outlier: 4.817A pdb=" N LEU A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.211A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3172 through 3177 removed outlier: 3.995A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3177' Processing helix chain 'A' and resid 3182 through 3188 Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.159A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3231 through 3254 removed outlier: 4.612A pdb=" N MET A3235 " --> pdb=" O MET A3231 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 4.511A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS A3252 " --> pdb=" O ARG A3248 " (cutoff:3.500A) Proline residue: A3254 - end of helix Processing helix chain 'A' and resid 3269 through 3291 removed outlier: 4.229A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE A3290 " --> pdb=" O ASN A3286 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A3291 " --> pdb=" O ASN A3287 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.643A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.165A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3317 removed outlier: 4.407A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3318 through 3330 removed outlier: 3.872A pdb=" N LYS A3329 " --> pdb=" O LYS A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3606 removed outlier: 5.438A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.592A 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 3628 Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 5.135A 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 Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.877A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.962A 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: 4.474A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 Processing helix chain 'A' and resid 3851 through 3860 Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.740A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 3.761A pdb=" N SER A3938 " --> pdb=" O SER A3934 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3958 Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 4.584A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 3.881A 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: 5.164A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.759A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 4.021A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A4098 " --> pdb=" O ILE A4094 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 3.638A pdb=" N GLN A4116 " --> pdb=" O ASP A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4131 Proline residue: A4131 - end of helix Processing helix chain 'A' and resid 4153 through 4163 Proline residue: A4163 - end of helix Processing helix chain 'A' and resid 4164 through 4179 removed outlier: 3.774A pdb=" N SER A4168 " --> pdb=" O GLN A4164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A4178 " --> pdb=" O PHE A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4182 through 4207 removed outlier: 4.444A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4259 removed outlier: 3.993A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4272 removed outlier: 3.982A pdb=" N GLN A4267 " --> pdb=" O SER A4263 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4521 removed outlier: 4.164A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS A4521 " --> pdb=" O LEU A4517 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 3.927A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.446A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4662 removed outlier: 5.189A pdb=" N GLU A4659 " --> pdb=" O ASP A4655 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE A4660 " --> pdb=" O LYS A4656 " (cutoff:3.500A) Processing helix chain 'A' and resid 4663 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 3.755A pdb=" N ASP A4681 " --> pdb=" O LEU A4677 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 3.711A pdb=" N VAL A4697 " --> pdb=" O SER A4693 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP A4702 " --> pdb=" O LEU A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4717 removed outlier: 5.543A pdb=" N ASN A4717 " --> pdb=" O VAL A4713 " (cutoff:3.500A) Processing helix chain 'A' and resid 4718 through 4736 removed outlier: 3.682A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4737 through 4751 removed outlier: 4.583A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 4.039A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A4761 " --> pdb=" O LEU A4757 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.317A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.725A 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: 4.328A pdb=" N VAL A4819 " --> pdb=" O PHE A4815 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4832 removed outlier: 4.778A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU A4832 " --> pdb=" O GLY A4828 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4857 through 4887 removed outlier: 5.606A pdb=" N ILE A4861 " --> pdb=" O ILE A4857 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.246A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A4900 " --> pdb=" O ASP A4896 " (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 2377 through 2382 removed outlier: 4.313A pdb=" N ILE A2382 " --> pdb=" O GLU A2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2377 through 2382' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.033A 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: 4.377A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.600A 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: 4.153A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.382A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 3.674A pdb=" N ALA D 328 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.054A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 removed outlier: 3.752A pdb=" N HIS D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 509 removed outlier: 4.964A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.702A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 555 removed outlier: 4.301A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 563 removed outlier: 3.630A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 556 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 5.570A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.765A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.486A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.306A 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: 4.401A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.078A 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: 3.517A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 4.232A pdb=" N GLU D 920 " --> pdb=" O PRO D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 Processing helix chain 'D' and resid 954 through 961 removed outlier: 5.143A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 5.242A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.757A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.079A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.656A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.009A 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 1499 through 1504 removed outlier: 5.334A pdb=" N ASN D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY D1504 " --> pdb=" O ARG D1500 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1499 through 1504' Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.781A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.150A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1666 Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.882A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.547A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1737 removed outlier: 5.727A pdb=" N THR D1737 " --> pdb=" O THR D1733 " (cutoff:3.500A) Processing helix chain 'D' and resid 1773 through 1778 removed outlier: 4.122A pdb=" N GLN D1777 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR D1778 " --> pdb=" O GLU D1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1773 through 1778' Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 3.584A pdb=" N SER D1803 " --> pdb=" O VAL D1799 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1901 through 1948 removed outlier: 3.990A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1955 through 1966 removed outlier: 3.888A pdb=" N ALA D1959 " --> pdb=" O ALA D1955 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 4.503A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 Processing helix chain 'D' and resid 2057 through 2073 Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.828A 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: 3.970A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.563A 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: 4.832A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.661A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.008A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.028A 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: 4.188A 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 2292 through 2307 removed outlier: 4.055A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D2298 " --> pdb=" O GLU D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 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: 9.014A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D2409 " --> pdb=" O GLU D2405 " (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: 5.642A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.854A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 4.914A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 4.372A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2510 through 2532 removed outlier: 5.387A 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: 4.146A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 3.822A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU D2589 " --> pdb=" O MET D2585 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2622 Proline residue: D2606 - end of helix removed outlier: 5.726A pdb=" N LYS D2619 " --> pdb=" O GLU D2615 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR D2620 " --> pdb=" O ARG D2616 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.178A 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: 4.220A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) removed outlier: 4.078A 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: 4.163A pdb=" N GLU D2718 " --> pdb=" O PRO D2714 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR D2719 " --> pdb=" O GLU D2715 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.320A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 3.915A 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: 5.285A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2881 through 2900 removed outlier: 4.531A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2921 removed outlier: 4.697A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.699A 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 2950 removed outlier: 4.631A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY D2949 " --> pdb=" O GLY D2945 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS D2950 " --> pdb=" O GLY D2946 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.641A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 5.176A 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: 4.141A 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: 5.311A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3117 through 3123 removed outlier: 4.817A pdb=" N LEU D3123 " --> pdb=" O GLU D3119 " (cutoff:3.500A) Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.211A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3172 through 3177 removed outlier: 3.994A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3177' Processing helix chain 'D' and resid 3182 through 3188 Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.158A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3231 through 3254 removed outlier: 4.612A pdb=" N MET D3235 " --> pdb=" O MET D3231 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 4.512A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS D3252 " --> pdb=" O ARG D3248 " (cutoff:3.500A) Proline residue: D3254 - end of helix Processing helix chain 'D' and resid 3269 through 3291 removed outlier: 4.229A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE D3290 " --> pdb=" O ASN D3286 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP D3291 " --> pdb=" O ASN D3287 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.643A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.165A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3317 removed outlier: 4.408A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) Processing helix chain 'D' and resid 3318 through 3330 removed outlier: 3.873A pdb=" N LYS D3329 " --> pdb=" O LYS D3325 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3606 removed outlier: 5.439A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.592A 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 3628 Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 5.135A 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 Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.876A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.962A 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: 4.475A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 Processing helix chain 'D' and resid 3851 through 3860 Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.740A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 3.760A pdb=" N SER D3938 " --> pdb=" O SER D3934 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3958 Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 4.583A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 3.881A 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: 5.164A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.758A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 4.021A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D4098 " --> pdb=" O ILE D4094 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 3.637A pdb=" N GLN D4116 " --> pdb=" O ASP D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4131 Proline residue: D4131 - end of helix Processing helix chain 'D' and resid 4153 through 4163 Proline residue: D4163 - end of helix Processing helix chain 'D' and resid 4164 through 4179 removed outlier: 3.774A pdb=" N SER D4168 " --> pdb=" O GLN D4164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D4178 " --> pdb=" O PHE D4174 " (cutoff:3.500A) Processing helix chain 'D' and resid 4182 through 4207 removed outlier: 4.444A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4259 removed outlier: 3.993A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4272 removed outlier: 3.982A pdb=" N GLN D4267 " --> pdb=" O SER D4263 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4521 removed outlier: 4.164A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS D4521 " --> pdb=" O LEU D4517 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 3.927A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.446A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4662 removed outlier: 5.189A pdb=" N GLU D4659 " --> pdb=" O ASP D4655 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE D4660 " --> pdb=" O LYS D4656 " (cutoff:3.500A) Processing helix chain 'D' and resid 4663 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 3.754A pdb=" N ASP D4681 " --> pdb=" O LEU D4677 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 3.712A pdb=" N VAL D4697 " --> pdb=" O SER D4693 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP D4702 " --> pdb=" O LEU D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4717 removed outlier: 5.544A pdb=" N ASN D4717 " --> pdb=" O VAL D4713 " (cutoff:3.500A) Processing helix chain 'D' and resid 4718 through 4736 removed outlier: 3.683A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4737 through 4751 removed outlier: 4.583A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 4.040A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR D4761 " --> pdb=" O LEU D4757 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.317A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.725A 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: 4.329A pdb=" N VAL D4819 " --> pdb=" O PHE D4815 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4832 removed outlier: 4.779A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU D4832 " --> pdb=" O GLY D4828 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4857 through 4887 removed outlier: 5.606A pdb=" N ILE D4861 " --> pdb=" O ILE D4857 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.246A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR D4900 " --> pdb=" O ASP D4896 " (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 2377 through 2382 removed outlier: 4.312A pdb=" N ILE D2382 " --> pdb=" O GLU D2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2377 through 2382' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.033A 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: 4.377A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.599A 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: 4.153A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.381A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.674A pdb=" N ALA B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.054A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 removed outlier: 3.752A pdb=" N HIS B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 509 removed outlier: 4.964A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.701A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 4.300A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 563 removed outlier: 3.631A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 5.570A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.764A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.486A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.306A 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: 4.401A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.078A 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: 3.516A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 4.233A pdb=" N GLU B 920 " --> pdb=" O PRO B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 Processing helix chain 'B' and resid 954 through 961 removed outlier: 5.142A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 5.242A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.757A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.079A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.657A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.009A 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 1499 through 1504 removed outlier: 5.334A pdb=" N ASN B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY B1504 " --> pdb=" O ARG B1500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1499 through 1504' Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.781A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.150A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1666 Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.882A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.546A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1737 removed outlier: 5.726A pdb=" N THR B1737 " --> pdb=" O THR B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1773 through 1778 removed outlier: 4.122A pdb=" N GLN B1777 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR B1778 " --> pdb=" O GLU B1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1773 through 1778' Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 3.584A pdb=" N SER B1803 " --> pdb=" O VAL B1799 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1901 through 1948 removed outlier: 3.991A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1955 through 1966 removed outlier: 3.888A pdb=" N ALA B1959 " --> pdb=" O ALA B1955 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 4.503A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.828A 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: 3.970A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.562A 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: 4.832A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.660A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.008A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.028A 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: 4.188A 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 2292 through 2307 removed outlier: 4.055A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B2298 " --> pdb=" O GLU B2294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 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: 9.014A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B2409 " --> pdb=" O GLU B2405 " (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: 5.642A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.855A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 4.914A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 4.372A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2510 through 2532 removed outlier: 5.387A 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: 4.146A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 3.822A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B2589 " --> pdb=" O MET B2585 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2622 Proline residue: B2606 - end of helix removed outlier: 5.726A pdb=" N LYS B2619 " --> pdb=" O GLU B2615 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR B2620 " --> pdb=" O ARG B2616 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.178A 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: 4.220A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) removed outlier: 4.078A 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: 4.163A pdb=" N GLU B2718 " --> pdb=" O PRO B2714 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR B2719 " --> pdb=" O GLU B2715 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.320A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 3.915A 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: 5.285A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2881 through 2900 removed outlier: 4.531A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2921 removed outlier: 4.697A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.700A 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 2950 removed outlier: 4.630A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B2949 " --> pdb=" O GLY B2945 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS B2950 " --> pdb=" O GLY B2946 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.641A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 5.175A 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: 4.141A 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: 5.312A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3117 through 3123 removed outlier: 4.817A pdb=" N LEU B3123 " --> pdb=" O GLU B3119 " (cutoff:3.500A) Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.211A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3172 through 3177 removed outlier: 3.995A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3177' Processing helix chain 'B' and resid 3182 through 3188 Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.159A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3231 through 3254 removed outlier: 4.612A pdb=" N MET B3235 " --> pdb=" O MET B3231 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 4.511A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS B3252 " --> pdb=" O ARG B3248 " (cutoff:3.500A) Proline residue: B3254 - end of helix Processing helix chain 'B' and resid 3269 through 3291 removed outlier: 4.230A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B3290 " --> pdb=" O ASN B3286 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B3291 " --> pdb=" O ASN B3287 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.642A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.164A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3317 removed outlier: 4.407A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) Processing helix chain 'B' and resid 3318 through 3330 removed outlier: 3.873A pdb=" N LYS B3329 " --> pdb=" O LYS B3325 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3606 removed outlier: 5.438A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.591A 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 3628 Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 5.135A 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 Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.877A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.962A 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: 4.474A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 Processing helix chain 'B' and resid 3851 through 3860 Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.740A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 3.761A pdb=" N SER B3938 " --> pdb=" O SER B3934 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3958 Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 4.584A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 3.881A 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: 5.164A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.759A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 4.022A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B4098 " --> pdb=" O ILE B4094 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 3.638A pdb=" N GLN B4116 " --> pdb=" O ASP B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4131 Proline residue: B4131 - end of helix Processing helix chain 'B' and resid 4153 through 4163 Proline residue: B4163 - end of helix Processing helix chain 'B' and resid 4164 through 4179 removed outlier: 3.774A pdb=" N SER B4168 " --> pdb=" O GLN B4164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B4178 " --> pdb=" O PHE B4174 " (cutoff:3.500A) Processing helix chain 'B' and resid 4182 through 4207 removed outlier: 4.444A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4259 removed outlier: 3.992A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4272 removed outlier: 3.982A pdb=" N GLN B4267 " --> pdb=" O SER B4263 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4521 removed outlier: 4.164A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS B4521 " --> pdb=" O LEU B4517 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 3.928A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.446A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4662 removed outlier: 5.190A pdb=" N GLU B4659 " --> pdb=" O ASP B4655 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE B4660 " --> pdb=" O LYS B4656 " (cutoff:3.500A) Processing helix chain 'B' and resid 4663 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 3.755A pdb=" N ASP B4681 " --> pdb=" O LEU B4677 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 3.711A pdb=" N VAL B4697 " --> pdb=" O SER B4693 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP B4702 " --> pdb=" O LEU B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4717 removed outlier: 5.544A pdb=" N ASN B4717 " --> pdb=" O VAL B4713 " (cutoff:3.500A) Processing helix chain 'B' and resid 4718 through 4736 removed outlier: 3.682A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4737 through 4751 removed outlier: 4.582A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 4.040A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR B4761 " --> pdb=" O LEU B4757 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.317A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.725A 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: 4.328A pdb=" N VAL B4819 " --> pdb=" O PHE B4815 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4832 removed outlier: 4.779A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU B4832 " --> pdb=" O GLY B4828 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4857 through 4887 removed outlier: 5.606A pdb=" N ILE B4861 " --> pdb=" O ILE B4857 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.246A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR B4900 " --> pdb=" O ASP B4896 " (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 2377 through 2382 removed outlier: 4.312A pdb=" N ILE B2382 " --> pdb=" O GLU B2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2377 through 2382' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.033A 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: 4.377A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.600A 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: 4.153A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.382A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 3.673A pdb=" N ALA C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.054A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 removed outlier: 3.753A pdb=" N HIS C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.964A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.702A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 555 removed outlier: 4.301A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 removed outlier: 3.630A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 556 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 5.570A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.764A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.486A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.305A 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: 4.401A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.078A 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: 3.517A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 4.232A pdb=" N GLU C 920 " --> pdb=" O PRO C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 Processing helix chain 'C' and resid 954 through 961 removed outlier: 5.142A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 5.242A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.757A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.079A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.657A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.009A 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 1499 through 1504 removed outlier: 5.334A pdb=" N ASN C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY C1504 " --> pdb=" O ARG C1500 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1499 through 1504' Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.780A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.150A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1666 Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.882A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.546A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1737 removed outlier: 5.726A pdb=" N THR C1737 " --> pdb=" O THR C1733 " (cutoff:3.500A) Processing helix chain 'C' and resid 1773 through 1778 removed outlier: 4.121A pdb=" N GLN C1777 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR C1778 " --> pdb=" O GLU C1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1773 through 1778' Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 3.584A pdb=" N SER C1803 " --> pdb=" O VAL C1799 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1901 through 1948 removed outlier: 3.991A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1955 through 1966 removed outlier: 3.888A pdb=" N ALA C1959 " --> pdb=" O ALA C1955 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 4.502A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 Processing helix chain 'C' and resid 2057 through 2073 Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.828A 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: 3.970A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.563A 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: 4.832A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.661A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.007A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.027A 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: 4.187A 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 2292 through 2307 removed outlier: 4.055A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C2298 " --> pdb=" O GLU C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 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: 9.013A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C2409 " --> pdb=" O GLU C2405 " (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: 5.642A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.855A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 4.914A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 4.372A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2510 through 2532 removed outlier: 5.387A 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: 4.146A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 3.822A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU C2589 " --> pdb=" O MET C2585 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2622 Proline residue: C2606 - end of helix removed outlier: 5.726A pdb=" N LYS C2619 " --> pdb=" O GLU C2615 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR C2620 " --> pdb=" O ARG C2616 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.178A 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: 4.221A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) removed outlier: 4.078A 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: 4.162A pdb=" N GLU C2718 " --> pdb=" O PRO C2714 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR C2719 " --> pdb=" O GLU C2715 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.319A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 3.915A 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: 5.286A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2881 through 2900 removed outlier: 4.531A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2921 removed outlier: 4.697A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.699A 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 2950 removed outlier: 4.631A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY C2949 " --> pdb=" O GLY C2945 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C2950 " --> pdb=" O GLY C2946 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.641A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 5.176A 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: 4.141A 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: 5.312A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3117 through 3123 removed outlier: 4.817A pdb=" N LEU C3123 " --> pdb=" O GLU C3119 " (cutoff:3.500A) Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.210A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3172 through 3177 removed outlier: 3.994A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3177' Processing helix chain 'C' and resid 3182 through 3188 Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.158A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3231 through 3254 removed outlier: 4.611A pdb=" N MET C3235 " --> pdb=" O MET C3231 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 4.511A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS C3252 " --> pdb=" O ARG C3248 " (cutoff:3.500A) Proline residue: C3254 - end of helix Processing helix chain 'C' and resid 3269 through 3291 removed outlier: 4.228A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE C3290 " --> pdb=" O ASN C3286 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C3291 " --> pdb=" O ASN C3287 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.642A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.165A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3317 removed outlier: 4.407A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) Processing helix chain 'C' and resid 3318 through 3330 removed outlier: 3.872A pdb=" N LYS C3329 " --> pdb=" O LYS C3325 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3606 removed outlier: 5.438A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.592A 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 3628 Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 5.135A 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 Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.877A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.962A 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: 4.474A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 Processing helix chain 'C' and resid 3851 through 3860 Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.740A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 3.761A pdb=" N SER C3938 " --> pdb=" O SER C3934 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3958 Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 4.583A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 3.881A 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: 5.164A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.758A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 4.022A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C4098 " --> pdb=" O ILE C4094 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 3.638A pdb=" N GLN C4116 " --> pdb=" O ASP C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4131 Proline residue: C4131 - end of helix Processing helix chain 'C' and resid 4153 through 4163 Proline residue: C4163 - end of helix Processing helix chain 'C' and resid 4164 through 4179 removed outlier: 3.773A pdb=" N SER C4168 " --> pdb=" O GLN C4164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C4178 " --> pdb=" O PHE C4174 " (cutoff:3.500A) Processing helix chain 'C' and resid 4182 through 4207 removed outlier: 4.444A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4259 removed outlier: 3.993A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4272 removed outlier: 3.981A pdb=" N GLN C4267 " --> pdb=" O SER C4263 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4521 removed outlier: 4.165A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS C4521 " --> pdb=" O LEU C4517 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 3.927A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.446A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4662 removed outlier: 5.190A pdb=" N GLU C4659 " --> pdb=" O ASP C4655 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE C4660 " --> pdb=" O LYS C4656 " (cutoff:3.500A) Processing helix chain 'C' and resid 4663 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 3.756A pdb=" N ASP C4681 " --> pdb=" O LEU C4677 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 3.711A pdb=" N VAL C4697 " --> pdb=" O SER C4693 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP C4702 " --> pdb=" O LEU C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4717 removed outlier: 5.543A pdb=" N ASN C4717 " --> pdb=" O VAL C4713 " (cutoff:3.500A) Processing helix chain 'C' and resid 4718 through 4736 removed outlier: 3.682A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4737 through 4751 removed outlier: 4.583A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 4.040A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR C4761 " --> pdb=" O LEU C4757 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.317A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.725A 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: 4.329A pdb=" N VAL C4819 " --> pdb=" O PHE C4815 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4832 removed outlier: 4.778A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU C4832 " --> pdb=" O GLY C4828 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4857 through 4887 removed outlier: 5.606A pdb=" N ILE C4861 " --> pdb=" O ILE C4857 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.247A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR C4900 " --> pdb=" O ASP C4896 " (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 2377 through 2382 removed outlier: 4.312A pdb=" N ILE C2382 " --> pdb=" O GLU C2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2377 through 2382' Processing helix chain 'C' and resid 4614 through 4619 Processing sheet with id= 1, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.541A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.541A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.542A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.540A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.582A pdb=" N GLU A 50 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A 36 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 215 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 121 through 124 removed outlier: 5.391A pdb=" N LEU A 121 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 128 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= 8, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.649A pdb=" N HIS A 202 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 10, first strand: chain 'A' and resid 314 through 318 removed outlier: 3.516A pdb=" N SER A 307 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 14.588A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 300 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 12, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 13, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.767A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.893A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A1617 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.590A pdb=" N GLU A1478 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.304A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 3.849A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 1280 through 1284 removed outlier: 6.633A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A1433 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A1432 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU A1505 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 5.151A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 2741 through 2744 Processing sheet with id= 21, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.718A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 47 through 52 removed outlier: 3.582A pdb=" N GLU D 50 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS D 36 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 215 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 121 through 124 removed outlier: 5.391A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= 25, first strand: chain 'D' and resid 193 through 196 removed outlier: 3.649A pdb=" N HIS D 202 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 27, first strand: chain 'D' and resid 314 through 318 removed outlier: 3.517A pdb=" N SER D 307 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 14.587A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 300 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 29, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 30, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.767A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.893A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D1617 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 777 through 780 removed outlier: 3.591A pdb=" N GLU D1478 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.304A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 3.849A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 1280 through 1284 removed outlier: 6.632A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE D1433 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D1432 " --> pdb=" O LEU D1505 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU D1505 " --> pdb=" O ILE D1432 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 5.151A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 2741 through 2744 Processing sheet with id= 38, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.718A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.583A pdb=" N GLU B 50 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 36 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 215 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 121 through 124 removed outlier: 5.391A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= 42, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.649A pdb=" N HIS B 202 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 44, first strand: chain 'B' and resid 314 through 318 removed outlier: 3.516A pdb=" N SER B 307 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 14.588A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 300 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 46, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 47, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.767A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.893A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP B1617 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 777 through 780 removed outlier: 3.590A pdb=" N GLU B1478 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.304A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 3.848A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'B' and resid 1280 through 1284 removed outlier: 6.632A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B1433 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B1432 " --> pdb=" O LEU B1505 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU B1505 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 5.151A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'B' and resid 2741 through 2744 Processing sheet with id= 55, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.718A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.583A pdb=" N GLU C 50 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 36 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 215 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 121 through 124 removed outlier: 5.391A pdb=" N LEU C 121 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET C 128 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= 59, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.648A pdb=" N HIS C 202 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 61, first strand: chain 'C' and resid 314 through 318 removed outlier: 3.516A pdb=" N SER C 307 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 14.587A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 300 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 63, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 64, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.767A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.893A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C1617 " --> pdb=" O PHE C 802 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'C' and resid 777 through 780 removed outlier: 3.590A pdb=" N GLU C1478 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.304A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 3.848A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'C' and resid 1280 through 1284 removed outlier: 6.633A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE C1433 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C1432 " --> pdb=" O LEU C1505 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU C1505 " --> pdb=" O ILE C1432 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 5.150A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'C' and resid 2741 through 2744 Processing sheet with id= 72, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.719A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) 7400 hydrogen bonds defined for protein. 22096 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: 88.64 Time building geometry restraints manager: 43.45 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: 45384 1.34 - 1.47: 32802 1.47 - 1.59: 61938 1.59 - 1.71: 40 1.71 - 1.84: 1512 Bond restraints: 141676 Sorted by residual: bond pdb=" N ASP D4646 " pdb=" CA ASP D4646 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.25e-02 6.40e+03 9.07e+00 bond pdb=" N ASP B4646 " pdb=" CA ASP B4646 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.25e-02 6.40e+03 8.99e+00 bond pdb=" N ASP A4646 " pdb=" CA ASP A4646 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.25e-02 6.40e+03 8.68e+00 bond pdb=" N ASP C4646 " pdb=" CA ASP C4646 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.25e-02 6.40e+03 8.48e+00 bond pdb=" N ILE B4926 " pdb=" CA ILE B4926 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.23e+00 ... (remaining 141671 not shown) Histogram of bond angle deviations from ideal: 95.71 - 105.71: 3043 105.71 - 115.71: 87136 115.71 - 125.71: 98991 125.71 - 135.71: 2234 135.71 - 145.71: 20 Bond angle restraints: 191424 Sorted by residual: angle pdb=" CA ARG A4242 " pdb=" CB ARG A4242 " pdb=" CG ARG A4242 " ideal model delta sigma weight residual 114.10 133.86 -19.76 2.00e+00 2.50e-01 9.76e+01 angle pdb=" CA ARG C4242 " pdb=" CB ARG C4242 " pdb=" CG ARG C4242 " ideal model delta sigma weight residual 114.10 133.86 -19.76 2.00e+00 2.50e-01 9.76e+01 angle pdb=" CA ARG D4242 " pdb=" CB ARG D4242 " pdb=" CG ARG D4242 " ideal model delta sigma weight residual 114.10 133.85 -19.75 2.00e+00 2.50e-01 9.75e+01 angle pdb=" CA ARG B4242 " pdb=" CB ARG B4242 " pdb=" CG ARG B4242 " ideal model delta sigma weight residual 114.10 133.81 -19.71 2.00e+00 2.50e-01 9.72e+01 angle pdb=" CA LEU C2800 " pdb=" CB LEU C2800 " pdb=" CG LEU C2800 " ideal model delta sigma weight residual 116.30 145.71 -29.41 3.50e+00 8.16e-02 7.06e+01 ... (remaining 191419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 76357 18.00 - 36.01: 7051 36.01 - 54.01: 1397 54.01 - 72.02: 452 72.02 - 90.02: 167 Dihedral angle restraints: 85424 sinusoidal: 35064 harmonic: 50360 Sorted by residual: dihedral pdb=" CD ARG B1614 " pdb=" NE ARG B1614 " pdb=" CZ ARG B1614 " pdb=" NH1 ARG B1614 " ideal model delta sinusoidal sigma weight residual 0.00 -82.94 82.94 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CD ARG A1614 " pdb=" NE ARG A1614 " pdb=" CZ ARG A1614 " pdb=" NH1 ARG A1614 " ideal model delta sinusoidal sigma weight residual 0.00 -82.88 82.88 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CD ARG C1614 " pdb=" NE ARG C1614 " pdb=" CZ ARG C1614 " pdb=" NH1 ARG C1614 " ideal model delta sinusoidal sigma weight residual 0.00 -82.86 82.86 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 85421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 20657 0.112 - 0.223: 299 0.223 - 0.335: 28 0.335 - 0.447: 0 0.447 - 0.559: 4 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CA TRP D4645 " pdb=" N TRP D4645 " pdb=" C TRP D4645 " pdb=" CB TRP D4645 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" CA TRP B4645 " pdb=" N TRP B4645 " pdb=" C TRP B4645 " pdb=" CB TRP B4645 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" CA TRP A4645 " pdb=" N TRP A4645 " pdb=" C TRP A4645 " pdb=" CB TRP A4645 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 20985 not shown) Planarity restraints: 24592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1614 " 1.005 9.50e-02 1.11e+02 4.50e-01 1.23e+02 pdb=" NE ARG B1614 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B1614 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B1614 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B1614 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1614 " 1.005 9.50e-02 1.11e+02 4.50e-01 1.23e+02 pdb=" NE ARG D1614 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D1614 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D1614 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D1614 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1614 " 1.004 9.50e-02 1.11e+02 4.50e-01 1.23e+02 pdb=" NE ARG A1614 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A1614 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A1614 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A1614 " 0.017 2.00e-02 2.50e+03 ... (remaining 24589 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 266 2.35 - 2.98: 69739 2.98 - 3.62: 223615 3.62 - 4.26: 332242 4.26 - 4.90: 544221 Nonbonded interactions: 1170083 Sorted by model distance: nonbonded pdb=" OE1 GLU D3922 " pdb="CA CA D5003 " model vdw 1.708 2.510 nonbonded pdb=" OE1 GLU A3922 " pdb="CA CA A5003 " model vdw 1.709 2.510 nonbonded pdb=" OE1 GLU C3922 " pdb="CA CA C5003 " model vdw 1.709 2.510 nonbonded pdb=" OE1 GLU B3922 " pdb="CA CA B5003 " model vdw 1.709 2.510 nonbonded pdb=" O ARG D2793 " pdb=" OG SER D2797 " model vdw 2.012 2.440 ... (remaining 1170078 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 5005)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.750 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: 0.120 Extract box with map and model: 30.440 Check model and map are aligned: 1.460 Set scattering table: 0.920 Process input model: 417.480 Find NCS groups from input model: 7.430 Set up NCS constraints: 0.920 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:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 468.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.003 0.084 141676 Z= 0.222 Angle : 0.847 29.413 191424 Z= 0.436 Chirality : 0.042 0.559 20988 Planarity : 0.010 0.450 24592 Dihedral : 15.246 90.023 52936 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 2.45 % Allowed : 0.88 % Favored : 96.67 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.06 (0.06), residues: 17212 helix: 1.55 (0.05), residues: 9048 sheet: 0.45 (0.12), residues: 1640 loop : -0.36 (0.07), residues: 6524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP D4288 HIS 0.013 0.001 HIS C3732 PHE 0.060 0.002 PHE C4640 TYR 0.086 0.002 TYR B2848 ARG 0.023 0.001 ARG D 111 *********************** 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 1025 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 653 time to evaluate : 11.884 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: A 272 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7813 (ptm160) REVERT: A 393 MET cc_start: 0.7403 (mmm) cc_final: 0.7074 (mmm) REVERT: A 1165 MET cc_start: 0.7113 (mtt) cc_final: 0.6768 (mtt) REVERT: A 1300 MET cc_start: 0.8464 (mmt) cc_final: 0.8165 (tpp) REVERT: A 1487 MET cc_start: 0.7954 (mtp) cc_final: 0.7678 (mtp) REVERT: A 1761 MET cc_start: 0.8378 (ttp) cc_final: 0.8150 (ttm) REVERT: A 1906 MET cc_start: 0.8523 (mmm) cc_final: 0.8246 (mmm) REVERT: A 2681 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7074 (mmp) REVERT: A 2715 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: A 3072 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7362 (tmm) REVERT: A 3079 GLN cc_start: 0.2446 (OUTLIER) cc_final: 0.1256 (mm110) REVERT: A 3784 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8562 (mmmt) REVERT: A 4256 MET cc_start: 0.3305 (ppp) cc_final: 0.2740 (tpt) REVERT: A 4258 MET cc_start: 0.1343 (OUTLIER) cc_final: -0.0789 (mmm) REVERT: A 4268 MET cc_start: 0.3744 (OUTLIER) cc_final: 0.3533 (tpp) REVERT: A 4274 MET cc_start: 0.2821 (mmm) cc_final: 0.1837 (mmm) REVERT: A 4292 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5196 (mmm) REVERT: A 4726 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6819 (mmp) REVERT: A 4743 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9040 (mt) REVERT: A 4943 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8362 (mtp) REVERT: D 393 MET cc_start: 0.7483 (mmm) cc_final: 0.7188 (mmm) REVERT: D 1421 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8058 (mmm) REVERT: D 1487 MET cc_start: 0.7881 (mtp) cc_final: 0.7649 (mtp) REVERT: D 1724 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: D 1761 MET cc_start: 0.8676 (ttp) cc_final: 0.8397 (ttp) REVERT: D 2681 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5587 (mmt) REVERT: D 2688 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.5029 (mmm) REVERT: D 2783 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7695 (tp) REVERT: D 3072 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6737 (tmm) REVERT: D 3079 GLN cc_start: 0.2616 (OUTLIER) cc_final: 0.2386 (mm110) REVERT: D 3104 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6113 (tpt) REVERT: D 3246 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6392 (ttm) REVERT: D 3323 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6938 (mmp) REVERT: D 3784 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8645 (mmmt) REVERT: D 3866 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9153 (p) REVERT: D 4258 MET cc_start: 0.1779 (OUTLIER) cc_final: -0.0045 (mmm) REVERT: D 4274 MET cc_start: 0.2758 (mmm) cc_final: 0.2083 (mmm) REVERT: D 4292 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.5069 (mmm) REVERT: D 4726 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7502 (tpp) REVERT: D 4748 MET cc_start: 0.6554 (tpt) cc_final: 0.6214 (tpt) REVERT: D 4804 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: D 4943 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8386 (mtp) REVERT: B 655 MET cc_start: 0.7661 (tpt) cc_final: 0.7237 (tpt) REVERT: B 1165 MET cc_start: 0.7081 (mtt) cc_final: 0.6531 (mtm) REVERT: B 1721 MET cc_start: 0.7989 (mmm) cc_final: 0.7751 (mmm) REVERT: B 1724 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: B 2442 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7287 (mmm) REVERT: B 2584 MET cc_start: 0.8461 (mmt) cc_final: 0.8246 (mmt) REVERT: B 2585 MET cc_start: 0.7571 (pmm) cc_final: 0.7326 (pmm) REVERT: B 2681 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7199 (mmp) REVERT: B 2688 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5403 (mmm) REVERT: B 2689 MET cc_start: 0.5761 (mmp) cc_final: 0.5551 (mmp) REVERT: B 2858 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8832 (mmm) REVERT: B 3104 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6922 (ptp) REVERT: B 3231 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5573 (tpt) REVERT: B 3719 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7274 (tpp) REVERT: B 4256 MET cc_start: 0.2756 (ppp) cc_final: 0.2290 (tpt) REVERT: B 4258 MET cc_start: -0.0845 (OUTLIER) cc_final: -0.1270 (mtp) REVERT: B 4504 MET cc_start: 0.7082 (tmm) cc_final: 0.6597 (tmm) REVERT: B 4672 MET cc_start: 0.5114 (pmm) cc_final: 0.4747 (ptt) REVERT: B 4726 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7471 (mmp) REVERT: B 4814 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7843 (mmm) REVERT: C 317 MET cc_start: 0.7172 (mtm) cc_final: 0.6861 (mtm) REVERT: C 833 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8647 (mtmm) REVERT: C 895 MET cc_start: 0.6082 (ppp) cc_final: 0.5858 (tmm) REVERT: C 1036 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8847 (p) REVERT: C 1421 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: C 1975 MET cc_start: 0.8158 (ptt) cc_final: 0.7893 (ptm) REVERT: C 2084 MET cc_start: 0.7873 (mtm) cc_final: 0.7533 (mtp) REVERT: C 2142 MET cc_start: 0.8102 (mmp) cc_final: 0.7853 (mmm) REVERT: C 2214 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8757 (mmm) REVERT: C 2347 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7885 (mmm) REVERT: C 2384 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8260 (mmm) REVERT: C 2585 MET cc_start: 0.6316 (pmm) cc_final: 0.6091 (pmm) REVERT: C 2681 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6409 (mmp) REVERT: C 2695 MET cc_start: 0.5283 (OUTLIER) cc_final: 0.4886 (tpp) REVERT: C 2840 MET cc_start: 0.8413 (mmp) cc_final: 0.7970 (mmt) REVERT: C 3046 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7666 (mmp) REVERT: C 3072 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7165 (tmm) REVERT: C 3241 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8460 (ppp) REVERT: C 3246 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7408 (ttm) REVERT: C 3273 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6236 (mtp) REVERT: C 3323 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.5148 (mmm) REVERT: C 3954 MET cc_start: 0.8587 (mmm) cc_final: 0.8366 (mmm) REVERT: C 3999 MET cc_start: 0.8218 (mtp) cc_final: 0.7895 (mtt) REVERT: C 4256 MET cc_start: 0.1999 (ppp) cc_final: 0.1082 (tmm) REVERT: C 4258 MET cc_start: -0.1098 (OUTLIER) cc_final: -0.1693 (ttp) REVERT: C 4568 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7547 (tpp) REVERT: C 4743 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8261 (tp) REVERT: C 4814 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7610 (mmm) outliers start: 372 outliers final: 62 residues processed: 804 average time/residue: 1.2187 time to fit residues: 1710.7061 Evaluate side-chains 733 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 613 time to evaluate : 11.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 1614 ARG Chi-restraints excluded: chain A residue 2214 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2831 VAL Chi-restraints excluded: chain A residue 3019 ILE Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 3079 GLN Chi-restraints excluded: chain A residue 3231 MET Chi-restraints excluded: chain A residue 3272 HIS Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3328 LYS Chi-restraints excluded: chain A residue 3784 LYS Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4242 ARG Chi-restraints excluded: chain A residue 4258 MET Chi-restraints excluded: chain A residue 4268 MET Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4726 MET Chi-restraints excluded: chain A residue 4743 LEU Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain D residue 1133 ARG Chi-restraints excluded: chain D residue 1421 MET Chi-restraints excluded: chain D residue 1564 MET Chi-restraints excluded: chain D residue 1614 ARG Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 1729 MET Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2688 MET Chi-restraints excluded: chain D residue 2752 LYS Chi-restraints excluded: chain D residue 2783 LEU Chi-restraints excluded: chain D residue 2835 ARG Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 3046 MET Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3079 GLN Chi-restraints excluded: chain D residue 3104 MET Chi-restraints excluded: chain D residue 3152 ARG Chi-restraints excluded: chain D residue 3231 MET Chi-restraints excluded: chain D residue 3246 MET Chi-restraints excluded: chain D residue 3272 HIS Chi-restraints excluded: chain D residue 3323 MET Chi-restraints excluded: chain D residue 3784 LYS Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 4242 ARG Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain D residue 4268 MET Chi-restraints excluded: chain D residue 4292 MET Chi-restraints excluded: chain D residue 4726 MET Chi-restraints excluded: chain D residue 4804 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4943 MET Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 1564 MET Chi-restraints excluded: chain B residue 1614 ARG Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2442 MET Chi-restraints excluded: chain B residue 2681 MET Chi-restraints excluded: chain B residue 2688 MET Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2858 MET Chi-restraints excluded: chain B residue 3019 ILE Chi-restraints excluded: chain B residue 3079 GLN Chi-restraints excluded: chain B residue 3104 MET Chi-restraints excluded: chain B residue 3152 ARG Chi-restraints excluded: chain B residue 3231 MET Chi-restraints excluded: chain B residue 3246 MET Chi-restraints excluded: chain B residue 3272 HIS Chi-restraints excluded: chain B residue 3328 LYS Chi-restraints excluded: chain B residue 3719 MET Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4647 LYS Chi-restraints excluded: chain B residue 4726 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 833 LYS Chi-restraints excluded: chain C residue 1036 THR Chi-restraints excluded: chain C residue 1421 MET Chi-restraints excluded: chain C residue 1564 MET Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1729 MET Chi-restraints excluded: chain C residue 1946 GLU Chi-restraints excluded: chain C residue 2214 MET Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2384 MET Chi-restraints excluded: chain C residue 2512 MET Chi-restraints excluded: chain C residue 2681 MET Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2715 GLU Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 3019 ILE Chi-restraints excluded: chain C residue 3046 MET Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3079 GLN Chi-restraints excluded: chain C residue 3231 MET Chi-restraints excluded: chain C residue 3241 MET Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 3273 MET Chi-restraints excluded: chain C residue 3323 MET Chi-restraints excluded: chain C residue 3328 LYS Chi-restraints excluded: chain C residue 3719 MET Chi-restraints excluded: chain C residue 3784 LYS Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 4052 MET Chi-restraints excluded: chain C residue 4258 MET Chi-restraints excluded: chain C residue 4568 MET Chi-restraints excluded: chain C residue 4647 LYS Chi-restraints excluded: chain C residue 4726 MET Chi-restraints excluded: chain C residue 4743 LEU Chi-restraints excluded: chain C residue 4814 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: 5.9990 chunk 726 optimal weight: 10.0000 chunk 447 optimal weight: 0.7980 chunk 883 optimal weight: 9.9990 chunk 699 optimal weight: 0.2980 chunk 1354 optimal weight: 10.0000 chunk 524 optimal weight: 2.9990 chunk 823 optimal weight: 9.9990 chunk 1008 optimal weight: 9.9990 chunk 1569 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN A 150 GLN A 487 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN A2739 ASN A2867 ASN ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS A4863 GLN A4945 GLN ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN ** G 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN D 150 GLN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2217 HIS D2692 GLN D2867 ASN ** D2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2978 HIS ** D3953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4863 GLN B 150 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 HIS B1147 GLN ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2217 HIS B2464 HIS B2692 GLN B2867 ASN ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS B4863 GLN B4945 GLN C 150 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1844 GLN ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2464 HIS C2978 HIS C4863 GLN C4945 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 141676 Z= 0.254 Angle : 0.624 12.583 191424 Z= 0.324 Chirality : 0.041 0.223 20988 Planarity : 0.005 0.195 24592 Dihedral : 7.092 140.930 19389 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.31 % Favored : 97.60 % Rotamer: Outliers : 0.49 % Allowed : 3.53 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.25 (0.06), residues: 17212 helix: 1.78 (0.05), residues: 9096 sheet: 0.50 (0.13), residues: 1556 loop : -0.39 (0.07), residues: 6560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D2732 HIS 0.011 0.001 HIS D2729 PHE 0.042 0.002 PHE B4640 TYR 0.037 0.002 TYR D2848 ARG 0.029 0.001 ARG B1614 *********************** 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 712 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 638 time to evaluate : 11.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6464 (mpp) cc_final: 0.5826 (ptp) REVERT: A 1113 MET cc_start: 0.7430 (mtm) cc_final: 0.7115 (mtt) REVERT: A 1165 MET cc_start: 0.7985 (mtt) cc_final: 0.7741 (mtt) REVERT: A 1487 MET cc_start: 0.8205 (mtp) cc_final: 0.7987 (mtp) REVERT: A 1906 MET cc_start: 0.8562 (mmm) cc_final: 0.8215 (mmm) REVERT: A 2214 MET cc_start: 0.8598 (mmm) cc_final: 0.8116 (mmp) REVERT: A 2384 MET cc_start: 0.8572 (mmm) cc_final: 0.8360 (tpp) REVERT: A 2828 MET cc_start: 0.7284 (mmt) cc_final: 0.7072 (mmm) REVERT: A 2840 MET cc_start: 0.8303 (mmp) cc_final: 0.8033 (mmp) REVERT: A 3273 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6480 (mtm) REVERT: A 4258 MET cc_start: 0.1745 (ptp) cc_final: -0.0615 (mmm) REVERT: A 4274 MET cc_start: 0.2728 (mmm) cc_final: 0.1569 (mmm) REVERT: A 4292 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.5064 (mmm) REVERT: A 4672 MET cc_start: 0.5261 (pmm) cc_final: 0.4176 (ptt) REVERT: A 4814 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7863 (mtm) REVERT: A 4943 MET cc_start: 0.8814 (mtt) cc_final: 0.8534 (mtp) REVERT: D 241 MET cc_start: 0.6538 (mpp) cc_final: 0.5657 (ptp) REVERT: D 393 MET cc_start: 0.7608 (mmm) cc_final: 0.7157 (mmm) REVERT: D 1113 MET cc_start: 0.7861 (mtm) cc_final: 0.7390 (mtm) REVERT: D 1724 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: D 1906 MET cc_start: 0.8549 (mmm) cc_final: 0.8246 (mmm) REVERT: D 1953 MET cc_start: 0.6145 (mpp) cc_final: 0.5518 (mpp) REVERT: D 2798 MET cc_start: 0.7045 (tpp) cc_final: 0.6289 (tpp) REVERT: D 2840 MET cc_start: 0.8172 (mmm) cc_final: 0.7956 (mmm) REVERT: D 3003 MET cc_start: 0.8411 (mtp) cc_final: 0.8196 (ptp) REVERT: D 3072 MET cc_start: 0.7165 (ttp) cc_final: 0.6933 (ptt) REVERT: D 4052 MET cc_start: 0.8064 (mmp) cc_final: 0.7788 (mmm) REVERT: D 4258 MET cc_start: 0.2057 (ptp) cc_final: 0.0031 (mmm) REVERT: D 4274 MET cc_start: 0.2547 (mmm) cc_final: 0.2108 (mmm) REVERT: D 4672 MET cc_start: 0.5629 (pmm) cc_final: 0.3941 (ptp) REVERT: D 4748 MET cc_start: 0.6558 (tpt) cc_final: 0.6276 (tpt) REVERT: D 4814 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7822 (mtm) REVERT: D 4943 MET cc_start: 0.8826 (mtt) cc_final: 0.8587 (mtp) REVERT: B 494 MET cc_start: 0.8497 (mmm) cc_final: 0.8117 (mmm) REVERT: B 935 MET cc_start: 0.5834 (ttp) cc_final: 0.5196 (tmm) REVERT: B 1165 MET cc_start: 0.8040 (mtt) cc_final: 0.7485 (mtm) REVERT: B 1168 MET cc_start: 0.7320 (mmm) cc_final: 0.6783 (mmm) REVERT: B 1721 MET cc_start: 0.8038 (mmm) cc_final: 0.7827 (mmp) REVERT: B 1724 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: B 2840 MET cc_start: 0.8401 (mmp) cc_final: 0.8134 (mmp) REVERT: B 3104 MET cc_start: 0.7408 (ptp) cc_final: 0.7079 (ptp) REVERT: B 3263 MET cc_start: 0.7615 (mpp) cc_final: 0.7105 (mpp) REVERT: B 3605 MET cc_start: 0.2391 (ppp) cc_final: 0.1972 (ppp) REVERT: B 3954 MET cc_start: 0.8892 (mmm) cc_final: 0.8492 (mmm) REVERT: B 4256 MET cc_start: 0.2944 (ppp) cc_final: 0.2228 (tmm) REVERT: B 4258 MET cc_start: -0.0934 (ptp) cc_final: -0.1464 (mtp) REVERT: B 4279 MET cc_start: 0.3085 (mmm) cc_final: 0.2074 (mtt) REVERT: B 4504 MET cc_start: 0.7220 (tmm) cc_final: 0.6716 (tmm) REVERT: B 4568 MET cc_start: 0.7708 (mmp) cc_final: 0.7505 (mmm) REVERT: B 4672 MET cc_start: 0.4887 (pmm) cc_final: 0.4333 (ptt) REVERT: B 4814 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7831 (mtm) REVERT: B 4943 MET cc_start: 0.8727 (mmt) cc_final: 0.8233 (mmm) REVERT: C 935 MET cc_start: 0.4506 (tmm) cc_final: 0.3668 (tpt) REVERT: C 1487 MET cc_start: 0.7762 (mtm) cc_final: 0.7494 (mtp) REVERT: C 2084 MET cc_start: 0.8307 (mtm) cc_final: 0.8079 (mtp) REVERT: C 2167 MET cc_start: 0.8174 (mtp) cc_final: 0.7962 (mtm) REVERT: C 2279 MET cc_start: 0.8447 (tpp) cc_final: 0.7783 (tmm) REVERT: C 3072 MET cc_start: 0.7589 (ttp) cc_final: 0.7300 (tmm) REVERT: C 3235 MET cc_start: 0.7361 (mmm) cc_final: 0.6933 (tpp) REVERT: C 3999 MET cc_start: 0.8548 (mtp) cc_final: 0.8180 (mtt) REVERT: C 4256 MET cc_start: 0.2009 (ppp) cc_final: 0.1129 (tmm) REVERT: C 4258 MET cc_start: -0.1175 (ptp) cc_final: -0.1883 (ttp) REVERT: C 4268 MET cc_start: 0.2929 (tpt) cc_final: 0.2413 (tpp) REVERT: C 4504 MET cc_start: 0.6636 (tmm) cc_final: 0.6372 (tmm) REVERT: C 4568 MET cc_start: 0.8084 (mmp) cc_final: 0.7484 (tpp) REVERT: C 4672 MET cc_start: 0.5234 (pmm) cc_final: 0.4602 (pmm) REVERT: C 4804 MET cc_start: 0.8982 (tpp) cc_final: 0.8673 (tpt) REVERT: C 4814 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7728 (mtm) outliers start: 74 outliers final: 13 residues processed: 667 average time/residue: 1.1323 time to fit residues: 1354.4999 Evaluate side-chains 635 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 614 time to evaluate : 10.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1946 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3772 THR Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3231 MET Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain C residue 1724 GLU Chi-restraints excluded: chain C residue 2384 MET Chi-restraints excluded: chain C residue 3272 HIS Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain C residue 4925 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 6.9990 chunk 487 optimal weight: 10.0000 chunk 1306 optimal weight: 20.0000 chunk 1068 optimal weight: 6.9990 chunk 432 optimal weight: 20.0000 chunk 1572 optimal weight: 0.4980 chunk 1698 optimal weight: 20.0000 chunk 1400 optimal weight: 9.9990 chunk 1558 optimal weight: 1.9990 chunk 535 optimal weight: 10.0000 chunk 1261 optimal weight: 9.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3964 GLN E 26 HIS F 26 HIS ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2464 HIS ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2739 ASN D2867 ASN D2978 HIS D3031 ASN ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4766 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 HIS ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2464 HIS ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2978 HIS ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 141676 Z= 0.292 Angle : 0.595 13.166 191424 Z= 0.309 Chirality : 0.040 0.253 20988 Planarity : 0.005 0.128 24592 Dihedral : 5.786 83.856 19059 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.33 % Rotamer: Outliers : 0.44 % Allowed : 5.07 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.34 (0.06), residues: 17212 helix: 1.91 (0.05), residues: 9144 sheet: 0.36 (0.13), residues: 1576 loop : -0.43 (0.08), residues: 6492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C2732 HIS 0.013 0.001 HIS B3233 PHE 0.031 0.002 PHE B4640 TYR 0.027 0.002 TYR D 462 ARG 0.010 0.001 ARG E 14 *********************** 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 698 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 631 time to evaluate : 11.818 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: H 58 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8385 (mtmm) REVERT: H 62 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: A 241 MET cc_start: 0.6492 (mpp) cc_final: 0.5754 (ptp) REVERT: A 1306 MET cc_start: 0.8584 (mtp) cc_final: 0.8289 (mtp) REVERT: A 2172 MET cc_start: 0.8526 (mtp) cc_final: 0.8068 (mtp) REVERT: A 2681 MET cc_start: 0.7576 (mmm) cc_final: 0.7021 (mtt) REVERT: A 3954 MET cc_start: 0.8944 (mmm) cc_final: 0.8262 (mpp) REVERT: A 4094 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8745 (mm) REVERT: A 4274 MET cc_start: 0.2383 (mmm) cc_final: 0.1581 (mmm) REVERT: A 4292 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.5049 (mmm) REVERT: A 4504 MET cc_start: 0.7681 (tmm) cc_final: 0.7093 (tmm) REVERT: A 4748 MET cc_start: 0.6621 (tpt) cc_final: 0.6238 (tpt) REVERT: A 4814 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7886 (mtm) REVERT: E 62 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: F 62 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: G 62 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: G 108 GLU cc_start: 0.7837 (pm20) cc_final: 0.7339 (pm20) REVERT: D 393 MET cc_start: 0.7599 (mmm) cc_final: 0.7166 (mmm) REVERT: D 981 MET cc_start: 0.0278 (ptp) cc_final: 0.0025 (ptp) REVERT: D 1165 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (mtt) REVERT: D 1564 MET cc_start: 0.8131 (mmm) cc_final: 0.7552 (tpp) REVERT: D 1724 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: D 1953 MET cc_start: 0.6265 (mpp) cc_final: 0.5810 (mpp) REVERT: D 2142 MET cc_start: 0.8308 (mmm) cc_final: 0.7801 (mmt) REVERT: D 2214 MET cc_start: 0.8803 (mmm) cc_final: 0.8375 (mmm) REVERT: D 2605 MET cc_start: 0.7977 (tmm) cc_final: 0.7746 (tmm) REVERT: D 2681 MET cc_start: 0.6958 (mmm) cc_final: 0.6306 (mmt) REVERT: D 3003 MET cc_start: 0.8450 (mtp) cc_final: 0.8226 (ptp) REVERT: D 3072 MET cc_start: 0.7263 (ttp) cc_final: 0.6829 (tmm) REVERT: D 3104 MET cc_start: 0.7167 (ptm) cc_final: 0.6961 (ptp) REVERT: D 3954 MET cc_start: 0.8881 (mmm) cc_final: 0.8576 (tpp) REVERT: D 4258 MET cc_start: 0.2137 (ptp) cc_final: 0.0265 (mmm) REVERT: D 4274 MET cc_start: 0.2692 (mmm) cc_final: 0.1553 (mmm) REVERT: D 4292 MET cc_start: 0.5017 (mmm) cc_final: 0.4375 (mmm) REVERT: D 4504 MET cc_start: 0.7659 (tmm) cc_final: 0.7049 (tmm) REVERT: D 4672 MET cc_start: 0.5710 (pmm) cc_final: 0.4244 (ptp) REVERT: D 4707 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7851 (mmm) REVERT: D 4814 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7938 (ttm) REVERT: B 494 MET cc_start: 0.8573 (mmm) cc_final: 0.8310 (mmm) REVERT: B 935 MET cc_start: 0.5693 (ttp) cc_final: 0.5091 (tmm) REVERT: B 1165 MET cc_start: 0.8127 (mtt) cc_final: 0.7710 (mtm) REVERT: B 1168 MET cc_start: 0.7407 (mmm) cc_final: 0.6979 (mmm) REVERT: B 1724 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: B 1953 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.5436 (mtm) REVERT: B 2214 MET cc_start: 0.8710 (mmm) cc_final: 0.8353 (mmm) REVERT: B 2384 MET cc_start: 0.8794 (mmp) cc_final: 0.8519 (mmm) REVERT: B 2584 MET cc_start: 0.8501 (mmt) cc_final: 0.8262 (mmt) REVERT: B 2828 MET cc_start: 0.7273 (mmt) cc_final: 0.6935 (mmt) REVERT: B 2844 MET cc_start: 0.8378 (mmm) cc_final: 0.8145 (mmm) REVERT: B 3246 MET cc_start: 0.8319 (tpp) cc_final: 0.7810 (tpp) REVERT: B 4186 MET cc_start: 0.8157 (mmm) cc_final: 0.7890 (mmm) REVERT: B 4256 MET cc_start: 0.2816 (ppp) cc_final: 0.2178 (tmm) REVERT: B 4258 MET cc_start: -0.0871 (ptp) cc_final: -0.1403 (mtp) REVERT: B 4268 MET cc_start: 0.2790 (OUTLIER) cc_final: 0.2572 (tpt) REVERT: B 4279 MET cc_start: 0.2932 (mmm) cc_final: 0.1982 (mtt) REVERT: B 4504 MET cc_start: 0.7364 (tmm) cc_final: 0.6854 (tmm) REVERT: B 4672 MET cc_start: 0.4697 (pmm) cc_final: 0.4399 (ptt) REVERT: B 4814 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7908 (mtm) REVERT: C 935 MET cc_start: 0.4676 (tmm) cc_final: 0.3915 (tpt) REVERT: C 1306 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: C 1487 MET cc_start: 0.8129 (mtm) cc_final: 0.7825 (mtp) REVERT: C 1721 MET cc_start: 0.8182 (mmm) cc_final: 0.7906 (mmp) REVERT: C 1975 MET cc_start: 0.8202 (ptm) cc_final: 0.7899 (ptt) REVERT: C 2142 MET cc_start: 0.8400 (mmm) cc_final: 0.7943 (mmt) REVERT: C 2279 MET cc_start: 0.8433 (tpp) cc_final: 0.7777 (tmm) REVERT: C 2406 MET cc_start: 0.8172 (mmp) cc_final: 0.7926 (mmm) REVERT: C 2605 MET cc_start: 0.8769 (tmm) cc_final: 0.8487 (tmm) REVERT: C 2840 MET cc_start: 0.8245 (mmp) cc_final: 0.7956 (mmp) REVERT: C 2843 MET cc_start: 0.8517 (ptp) cc_final: 0.8238 (ptp) REVERT: C 3072 MET cc_start: 0.7584 (ttp) cc_final: 0.7289 (tmm) REVERT: C 3235 MET cc_start: 0.7478 (mmm) cc_final: 0.6984 (tpp) REVERT: C 3246 MET cc_start: 0.8329 (tpp) cc_final: 0.7950 (tpp) REVERT: C 3605 MET cc_start: 0.2262 (ppp) cc_final: 0.1953 (ppp) REVERT: C 3978 MET cc_start: 0.8663 (ttp) cc_final: 0.8407 (ttp) REVERT: C 4052 MET cc_start: 0.7486 (mpp) cc_final: 0.7245 (mpp) REVERT: C 4109 MET cc_start: 0.7039 (mtm) cc_final: 0.6691 (mtt) REVERT: C 4139 MET cc_start: 0.9078 (tpt) cc_final: 0.8784 (tpt) REVERT: C 4256 MET cc_start: 0.1884 (ppp) cc_final: 0.1059 (tmm) REVERT: C 4258 MET cc_start: -0.1326 (ptp) cc_final: -0.1994 (ttp) REVERT: C 4504 MET cc_start: 0.6867 (tmm) cc_final: 0.6402 (tmm) REVERT: C 4568 MET cc_start: 0.8062 (mmp) cc_final: 0.7627 (tpp) REVERT: C 4707 MET cc_start: 0.8100 (mmm) cc_final: 0.7802 (tpp) REVERT: C 4814 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: C 4943 MET cc_start: 0.8690 (tpp) cc_final: 0.8406 (mtt) outliers start: 67 outliers final: 25 residues processed: 665 average time/residue: 1.1234 time to fit residues: 1352.2355 Evaluate side-chains 660 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 618 time to evaluate : 11.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1946 GLU Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 3772 THR Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 4009 ASN Chi-restraints excluded: chain A residue 4094 ILE Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 2717 LEU Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 3978 MET Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 1953 MET Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 3147 TYR Chi-restraints excluded: chain B residue 4009 ASN Chi-restraints excluded: chain B residue 4268 MET Chi-restraints excluded: chain B residue 4804 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1306 MET Chi-restraints excluded: chain C residue 3147 TYR Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 7.9990 chunk 1181 optimal weight: 40.0000 chunk 815 optimal weight: 20.0000 chunk 174 optimal weight: 0.6980 chunk 750 optimal weight: 6.9990 chunk 1055 optimal weight: 7.9990 chunk 1577 optimal weight: 7.9990 chunk 1670 optimal weight: 0.6980 chunk 824 optimal weight: 0.2980 chunk 1495 optimal weight: 8.9990 chunk 450 optimal weight: 10.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 HIS ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3614 HIS ** A3953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4766 GLN D 150 GLN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 HIS ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1844 GLN ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2978 HIS ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2464 HIS ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3614 HIS C 150 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 HIS ** C1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2692 GLN C2978 HIS ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 141676 Z= 0.203 Angle : 0.547 14.683 191424 Z= 0.282 Chirality : 0.039 0.192 20988 Planarity : 0.004 0.122 24592 Dihedral : 5.480 82.201 19049 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.45 % Favored : 97.44 % Rotamer: Outliers : 0.47 % Allowed : 6.14 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.45 (0.06), residues: 17212 helix: 2.02 (0.05), residues: 9172 sheet: 0.40 (0.13), residues: 1540 loop : -0.39 (0.08), residues: 6500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B2732 HIS 0.013 0.001 HIS B3272 PHE 0.025 0.001 PHE C4640 TYR 0.024 0.001 TYR C 462 ARG 0.012 0.000 ARG H 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 698 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 626 time to evaluate : 11.515 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: H 58 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8265 (mtmm) REVERT: H 62 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: H 67 MET cc_start: 0.8467 (mtp) cc_final: 0.8218 (mtp) REVERT: A 241 MET cc_start: 0.6441 (mpp) cc_final: 0.5823 (ptp) REVERT: A 349 MET cc_start: 0.7368 (mmp) cc_final: 0.7035 (mmt) REVERT: A 1306 MET cc_start: 0.8581 (mtp) cc_final: 0.8266 (mtp) REVERT: A 2214 MET cc_start: 0.8611 (mmm) cc_final: 0.8219 (mmm) REVERT: A 2234 MET cc_start: 0.8199 (mmm) cc_final: 0.7856 (mtp) REVERT: A 3068 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8719 (tp) REVERT: A 3954 MET cc_start: 0.8881 (mmm) cc_final: 0.8239 (mpp) REVERT: A 3956 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8487 (mmp) REVERT: A 4292 MET cc_start: 0.5365 (OUTLIER) cc_final: 0.4976 (mmm) REVERT: A 4502 MET cc_start: 0.8301 (ttp) cc_final: 0.7768 (ttp) REVERT: A 4672 MET cc_start: 0.5421 (pmm) cc_final: 0.4024 (ptp) REVERT: A 4814 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: E 62 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: G 62 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: D 241 MET cc_start: 0.6839 (mpp) cc_final: 0.5916 (ptp) REVERT: D 393 MET cc_start: 0.7639 (mmm) cc_final: 0.7259 (mmm) REVERT: D 981 MET cc_start: 0.0166 (ptp) cc_final: -0.0154 (ptp) REVERT: D 1724 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: D 1953 MET cc_start: 0.6322 (mpp) cc_final: 0.5981 (mpp) REVERT: D 2142 MET cc_start: 0.8270 (mmm) cc_final: 0.8048 (mmt) REVERT: D 2214 MET cc_start: 0.8753 (mmm) cc_final: 0.8469 (mmp) REVERT: D 2589 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8938 (tp) REVERT: D 2605 MET cc_start: 0.7990 (tmm) cc_final: 0.7726 (tmm) REVERT: D 2734 MET cc_start: 0.7946 (mpp) cc_final: 0.7563 (mpp) REVERT: D 2773 TRP cc_start: 0.7714 (t-100) cc_final: 0.7489 (t-100) REVERT: D 2828 MET cc_start: 0.7524 (mmt) cc_final: 0.7268 (mmt) REVERT: D 2840 MET cc_start: 0.8265 (mmm) cc_final: 0.7994 (mpp) REVERT: D 3003 MET cc_start: 0.8513 (mtp) cc_final: 0.8308 (ptp) REVERT: D 3068 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8373 (tt) REVERT: D 3072 MET cc_start: 0.7233 (ttp) cc_final: 0.6803 (tmm) REVERT: D 3104 MET cc_start: 0.7227 (ptm) cc_final: 0.7016 (ptp) REVERT: D 3231 MET cc_start: 0.8021 (tpp) cc_final: 0.7659 (tpp) REVERT: D 3954 MET cc_start: 0.8849 (mmm) cc_final: 0.8550 (tpp) REVERT: D 4258 MET cc_start: 0.2058 (ptp) cc_final: 0.0350 (mmm) REVERT: D 4274 MET cc_start: 0.2375 (mmm) cc_final: 0.1490 (mmm) REVERT: D 4279 MET cc_start: 0.3933 (mmp) cc_final: 0.3280 (mmt) REVERT: D 4292 MET cc_start: 0.5092 (mmm) cc_final: 0.4447 (mmm) REVERT: D 4504 MET cc_start: 0.7682 (tmm) cc_final: 0.7076 (tmm) REVERT: D 4707 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7820 (mmm) REVERT: D 4814 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7972 (ttm) REVERT: B 778 MET cc_start: 0.8178 (mtp) cc_final: 0.7956 (mtm) REVERT: B 1165 MET cc_start: 0.8120 (mtt) cc_final: 0.7780 (mtm) REVERT: B 1168 MET cc_start: 0.7474 (mmm) cc_final: 0.6987 (mmm) REVERT: B 1421 MET cc_start: 0.8087 (tpp) cc_final: 0.7875 (mmm) REVERT: B 1724 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: B 1948 MET cc_start: 0.8099 (mmp) cc_final: 0.7700 (mmm) REVERT: B 2214 MET cc_start: 0.8647 (mmm) cc_final: 0.8317 (mmm) REVERT: B 2384 MET cc_start: 0.8728 (mmp) cc_final: 0.8452 (mmm) REVERT: B 2456 MET cc_start: 0.8411 (mmt) cc_final: 0.8164 (mmt) REVERT: B 2828 MET cc_start: 0.7202 (mmt) cc_final: 0.6785 (mmt) REVERT: B 2840 MET cc_start: 0.8190 (mmp) cc_final: 0.7662 (mmm) REVERT: B 3104 MET cc_start: 0.7413 (ptp) cc_final: 0.7112 (ptp) REVERT: B 3262 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: B 3263 MET cc_start: 0.7950 (mpp) cc_final: 0.7240 (mpp) REVERT: B 3323 MET cc_start: 0.5944 (mmm) cc_final: 0.5630 (mtp) REVERT: B 3605 MET cc_start: 0.2127 (ppp) cc_final: 0.1639 (ppp) REVERT: B 3954 MET cc_start: 0.8898 (mmm) cc_final: 0.8696 (mmm) REVERT: B 4052 MET cc_start: 0.7757 (mmm) cc_final: 0.7386 (mmm) REVERT: B 4186 MET cc_start: 0.8217 (mmm) cc_final: 0.7919 (mmm) REVERT: B 4256 MET cc_start: 0.2823 (ppp) cc_final: 0.2112 (tmm) REVERT: B 4258 MET cc_start: -0.0887 (ptp) cc_final: -0.1407 (mtp) REVERT: B 4279 MET cc_start: 0.2861 (mmm) cc_final: 0.2026 (mtt) REVERT: B 4504 MET cc_start: 0.7369 (tmm) cc_final: 0.6876 (tmm) REVERT: B 4568 MET cc_start: 0.7842 (mmp) cc_final: 0.7129 (tpp) REVERT: B 4672 MET cc_start: 0.4812 (pmm) cc_final: 0.4430 (ptt) REVERT: B 4804 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: B 4814 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7877 (ttm) REVERT: C 935 MET cc_start: 0.4694 (tmm) cc_final: 0.4107 (tpt) REVERT: C 1306 MET cc_start: 0.8809 (mtm) cc_final: 0.8423 (mtp) REVERT: C 1487 MET cc_start: 0.8205 (mtm) cc_final: 0.7914 (mtp) REVERT: C 1564 MET cc_start: 0.8258 (mmm) cc_final: 0.7869 (mmm) REVERT: C 1721 MET cc_start: 0.8081 (mmm) cc_final: 0.7780 (mmp) REVERT: C 1948 MET cc_start: 0.8106 (mmp) cc_final: 0.7871 (mmm) REVERT: C 2214 MET cc_start: 0.9052 (mmm) cc_final: 0.8657 (mmm) REVERT: C 2279 MET cc_start: 0.8375 (tpp) cc_final: 0.7731 (tmm) REVERT: C 2347 MET cc_start: 0.8762 (tpp) cc_final: 0.8547 (mmm) REVERT: C 2406 MET cc_start: 0.8097 (mmp) cc_final: 0.7808 (mmm) REVERT: C 2605 MET cc_start: 0.8699 (tmm) cc_final: 0.8441 (tmm) REVERT: C 3003 MET cc_start: 0.8599 (ptp) cc_final: 0.8208 (ptt) REVERT: C 3046 MET cc_start: 0.8370 (mmm) cc_final: 0.8013 (mmm) REVERT: C 3068 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8284 (tt) REVERT: C 3072 MET cc_start: 0.7513 (ttp) cc_final: 0.7241 (tmm) REVERT: C 3246 MET cc_start: 0.8342 (tpp) cc_final: 0.7945 (tpp) REVERT: C 3605 MET cc_start: 0.2179 (ppp) cc_final: 0.1921 (ppp) REVERT: C 3978 MET cc_start: 0.8640 (ttp) cc_final: 0.8401 (ttp) REVERT: C 4109 MET cc_start: 0.7089 (mtm) cc_final: 0.6755 (mtt) REVERT: C 4139 MET cc_start: 0.9092 (tpt) cc_final: 0.8786 (tpt) REVERT: C 4256 MET cc_start: 0.2024 (ppp) cc_final: 0.1280 (tmm) REVERT: C 4258 MET cc_start: -0.1322 (ptp) cc_final: -0.2046 (ttp) REVERT: C 4504 MET cc_start: 0.7033 (tmm) cc_final: 0.6587 (tmm) REVERT: C 4672 MET cc_start: 0.5120 (pmm) cc_final: 0.4680 (pmm) REVERT: C 4707 MET cc_start: 0.8007 (mmm) cc_final: 0.7763 (tpp) REVERT: C 4814 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7773 (mtm) outliers start: 72 outliers final: 19 residues processed: 671 average time/residue: 1.1296 time to fit residues: 1374.3478 Evaluate side-chains 659 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 622 time to evaluate : 11.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4557 VAL Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 2589 LEU Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 4009 ASN Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2938 GLN Chi-restraints excluded: chain B residue 3262 GLU Chi-restraints excluded: chain B residue 4804 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 4009 ASN Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 40.0000 chunk 948 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 1243 optimal weight: 10.0000 chunk 689 optimal weight: 8.9990 chunk 1425 optimal weight: 8.9990 chunk 1154 optimal weight: 50.0000 chunk 1 optimal weight: 0.4980 chunk 852 optimal weight: 6.9990 chunk 1499 optimal weight: 8.9990 chunk 421 optimal weight: 9.9990 overall best weight: 6.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1844 GLN ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2224 ASN ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2739 ASN ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 487 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1021 GLN D2224 ASN ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2978 HIS ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3964 GLN ** D4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2224 ASN B2464 HIS ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2739 ASN ** B2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2659 GLN ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2739 ASN C2953 HIS C2978 HIS ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 141676 Z= 0.362 Angle : 0.608 16.417 191424 Z= 0.313 Chirality : 0.041 0.259 20988 Planarity : 0.005 0.169 24592 Dihedral : 5.504 86.763 19049 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.86 % Favored : 97.02 % Rotamer: Outliers : 0.57 % Allowed : 6.61 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.34 (0.06), residues: 17212 helix: 1.95 (0.05), residues: 9172 sheet: 0.16 (0.13), residues: 1512 loop : -0.44 (0.07), residues: 6528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B2732 HIS 0.010 0.001 HIS A3700 PHE 0.036 0.002 PHE A3854 TYR 0.028 0.002 TYR A 462 ARG 0.008 0.001 ARG C3152 *********************** 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 717 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 630 time to evaluate : 13.794 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: H 58 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8360 (mtmm) REVERT: H 62 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: A 494 MET cc_start: 0.8756 (mmm) cc_final: 0.8370 (mmm) REVERT: A 964 MET cc_start: 0.0683 (mpp) cc_final: 0.0283 (mtm) REVERT: A 1306 MET cc_start: 0.8611 (mtp) cc_final: 0.8313 (mtp) REVERT: A 2234 MET cc_start: 0.8302 (mmm) cc_final: 0.7923 (mtp) REVERT: A 3068 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (tp) REVERT: A 3235 MET cc_start: 0.7841 (mmm) cc_final: 0.7431 (mmm) REVERT: A 3954 MET cc_start: 0.8894 (mmm) cc_final: 0.8625 (tpp) REVERT: A 4274 MET cc_start: 0.0538 (mmp) cc_final: -0.0133 (mmm) REVERT: A 4292 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.5095 (mmm) REVERT: A 4504 MET cc_start: 0.7758 (tmm) cc_final: 0.7471 (tmm) REVERT: A 4814 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7962 (ttm) REVERT: E 62 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: G 62 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: D 241 MET cc_start: 0.6818 (mpp) cc_final: 0.5907 (ptp) REVERT: D 393 MET cc_start: 0.7635 (mmm) cc_final: 0.7188 (mmm) REVERT: D 981 MET cc_start: -0.0018 (ptp) cc_final: -0.0374 (ptp) REVERT: D 1564 MET cc_start: 0.8029 (mmm) cc_final: 0.7275 (tpt) REVERT: D 1724 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: D 1953 MET cc_start: 0.6540 (mpp) cc_final: 0.6299 (mpp) REVERT: D 2142 MET cc_start: 0.8209 (mmm) cc_final: 0.7865 (mmt) REVERT: D 2456 MET cc_start: 0.8340 (mmt) cc_final: 0.7598 (mmt) REVERT: D 2512 MET cc_start: 0.8796 (tpp) cc_final: 0.8436 (tpp) REVERT: D 2589 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8957 (tp) REVERT: D 2605 MET cc_start: 0.8190 (tmm) cc_final: 0.7911 (tmm) REVERT: D 2734 MET cc_start: 0.7934 (mpp) cc_final: 0.7615 (mpp) REVERT: D 2773 TRP cc_start: 0.7846 (t-100) cc_final: 0.7548 (t-100) REVERT: D 2828 MET cc_start: 0.7567 (mmt) cc_final: 0.7239 (mmt) REVERT: D 3003 MET cc_start: 0.8564 (mtp) cc_final: 0.8338 (mtm) REVERT: D 3072 MET cc_start: 0.7281 (ttp) cc_final: 0.6925 (tmm) REVERT: D 3104 MET cc_start: 0.7443 (ptm) cc_final: 0.7193 (ptp) REVERT: D 3231 MET cc_start: 0.8141 (tpp) cc_final: 0.7459 (tpp) REVERT: D 3954 MET cc_start: 0.8891 (mmm) cc_final: 0.8595 (tpp) REVERT: D 4258 MET cc_start: 0.2145 (ptp) cc_final: 0.0358 (mmm) REVERT: D 4274 MET cc_start: 0.2453 (mmm) cc_final: 0.1363 (mmm) REVERT: D 4292 MET cc_start: 0.5121 (mmm) cc_final: 0.4518 (mmm) REVERT: D 4672 MET cc_start: 0.5408 (pmm) cc_final: 0.4957 (pmm) REVERT: D 4707 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7790 (mmm) REVERT: D 4814 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (ttm) REVERT: B 393 MET cc_start: 0.7304 (mmm) cc_final: 0.7059 (mmm) REVERT: B 892 LEU cc_start: 0.7715 (mt) cc_final: 0.7463 (tp) REVERT: B 1165 MET cc_start: 0.8292 (mtt) cc_final: 0.7875 (mtm) REVERT: B 1168 MET cc_start: 0.7599 (mmm) cc_final: 0.7309 (mmt) REVERT: B 1564 MET cc_start: 0.8330 (mmm) cc_final: 0.8065 (mmm) REVERT: B 1724 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: B 1948 MET cc_start: 0.8041 (mmp) cc_final: 0.7713 (mmm) REVERT: B 2142 MET cc_start: 0.8167 (mmm) cc_final: 0.7741 (mpp) REVERT: B 2214 MET cc_start: 0.8611 (mmm) cc_final: 0.8235 (mmm) REVERT: B 2442 MET cc_start: 0.8003 (mmm) cc_final: 0.7694 (mmm) REVERT: B 2844 MET cc_start: 0.8310 (mmm) cc_final: 0.8035 (mmm) REVERT: B 3246 MET cc_start: 0.8319 (tpp) cc_final: 0.8043 (tpp) REVERT: B 3605 MET cc_start: 0.2313 (ppp) cc_final: 0.2011 (ppp) REVERT: B 4052 MET cc_start: 0.7802 (mmm) cc_final: 0.7433 (mmm) REVERT: B 4256 MET cc_start: 0.2772 (ppp) cc_final: 0.2056 (tmm) REVERT: B 4258 MET cc_start: -0.0781 (ptp) cc_final: -0.1285 (mtp) REVERT: B 4279 MET cc_start: 0.2988 (mmm) cc_final: 0.2131 (mtt) REVERT: B 4504 MET cc_start: 0.7512 (tmm) cc_final: 0.7050 (tmm) REVERT: B 4672 MET cc_start: 0.5014 (pmm) cc_final: 0.4742 (ptt) REVERT: B 4804 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8523 (mmm) REVERT: B 4814 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: C 935 MET cc_start: 0.4757 (tmm) cc_final: 0.4326 (tpt) REVERT: C 1168 MET cc_start: 0.7625 (mmm) cc_final: 0.7407 (mmt) REVERT: C 1487 MET cc_start: 0.8349 (mtm) cc_final: 0.8082 (mtp) REVERT: C 1721 MET cc_start: 0.8109 (mmm) cc_final: 0.7752 (mmp) REVERT: C 1948 MET cc_start: 0.8213 (mmp) cc_final: 0.7987 (mmm) REVERT: C 1975 MET cc_start: 0.8073 (ptm) cc_final: 0.7715 (ptt) REVERT: C 2084 MET cc_start: 0.8542 (mtm) cc_final: 0.8333 (mtp) REVERT: C 2279 MET cc_start: 0.8357 (tpp) cc_final: 0.7722 (tmm) REVERT: C 2512 MET cc_start: 0.8909 (tpp) cc_final: 0.8612 (tpt) REVERT: C 2605 MET cc_start: 0.8780 (tmm) cc_final: 0.8521 (tmm) REVERT: C 3003 MET cc_start: 0.8633 (ptp) cc_final: 0.8397 (ptt) REVERT: C 3046 MET cc_start: 0.8525 (mmm) cc_final: 0.8206 (mmm) REVERT: C 3068 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8380 (tt) REVERT: C 3072 MET cc_start: 0.7605 (ttp) cc_final: 0.7286 (tmm) REVERT: C 3235 MET cc_start: 0.7337 (tpt) cc_final: 0.6871 (tpp) REVERT: C 3246 MET cc_start: 0.8393 (tpp) cc_final: 0.8019 (tpp) REVERT: C 3323 MET cc_start: 0.6172 (tpp) cc_final: 0.5767 (mmm) REVERT: C 3954 MET cc_start: 0.8933 (mmm) cc_final: 0.8709 (mmm) REVERT: C 3978 MET cc_start: 0.8644 (ttp) cc_final: 0.8439 (ttp) REVERT: C 4052 MET cc_start: 0.7934 (mmm) cc_final: 0.7637 (mpp) REVERT: C 4109 MET cc_start: 0.7267 (mtm) cc_final: 0.6914 (mtt) REVERT: C 4256 MET cc_start: 0.1736 (ppp) cc_final: 0.1041 (tmm) REVERT: C 4258 MET cc_start: -0.1335 (ptp) cc_final: -0.1961 (ttp) REVERT: C 4504 MET cc_start: 0.7240 (tmm) cc_final: 0.7039 (tmm) REVERT: C 4568 MET cc_start: 0.8012 (mmp) cc_final: 0.7469 (mmm) REVERT: C 4672 MET cc_start: 0.5217 (pmm) cc_final: 0.4755 (pmm) REVERT: C 4814 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7912 (ttm) outliers start: 87 outliers final: 35 residues processed: 686 average time/residue: 1.1401 time to fit residues: 1422.7766 Evaluate side-chains 675 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 625 time to evaluate : 11.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 4009 ASN Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 1946 GLU Chi-restraints excluded: chain D residue 2589 LEU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 4009 ASN Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4557 VAL Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2938 GLN Chi-restraints excluded: chain B residue 2953 HIS Chi-restraints excluded: chain B residue 3272 HIS Chi-restraints excluded: chain B residue 4009 ASN Chi-restraints excluded: chain B residue 4557 VAL Chi-restraints excluded: chain B residue 4804 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3122 ILE Chi-restraints excluded: chain C residue 4009 ASN Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 40.0000 chunk 1504 optimal weight: 0.8980 chunk 330 optimal weight: 3.9990 chunk 980 optimal weight: 40.0000 chunk 412 optimal weight: 10.0000 chunk 1671 optimal weight: 6.9990 chunk 1387 optimal weight: 20.0000 chunk 774 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 553 optimal weight: 10.0000 chunk 877 optimal weight: 10.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 106 ASN A 150 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS F 106 ASN D 150 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 GLN ** D2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4762 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1562 ASN B1844 GLN ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2464 HIS ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1021 GLN ** C2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2978 HIS ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 141676 Z= 0.301 Angle : 0.572 16.875 191424 Z= 0.294 Chirality : 0.040 0.199 20988 Planarity : 0.004 0.153 24592 Dihedral : 5.438 88.097 19049 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.62 % Favored : 97.25 % Rotamer: Outliers : 0.56 % Allowed : 7.34 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.39 (0.06), residues: 17212 helix: 2.00 (0.05), residues: 9168 sheet: 0.14 (0.14), residues: 1432 loop : -0.42 (0.07), residues: 6612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B2732 HIS 0.011 0.001 HIS C3700 PHE 0.028 0.001 PHE A3854 TYR 0.024 0.001 TYR A 462 ARG 0.011 0.000 ARG A2793 *********************** 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 712 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 627 time to evaluate : 11.591 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: H 58 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8328 (mtmm) REVERT: H 62 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: A 241 MET cc_start: 0.6686 (mpp) cc_final: 0.6013 (ptp) REVERT: A 964 MET cc_start: 0.0625 (mpp) cc_final: 0.0237 (mtm) REVERT: A 1306 MET cc_start: 0.8580 (mtp) cc_final: 0.8270 (mtp) REVERT: A 2234 MET cc_start: 0.8307 (mmm) cc_final: 0.7915 (mtp) REVERT: A 3068 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8764 (tp) REVERT: A 3954 MET cc_start: 0.8859 (mmm) cc_final: 0.8606 (tpp) REVERT: A 4274 MET cc_start: 0.0726 (mmp) cc_final: -0.0039 (mmm) REVERT: A 4292 MET cc_start: 0.5578 (OUTLIER) cc_final: 0.5134 (mmm) REVERT: A 4814 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7957 (ttm) REVERT: E 62 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: G 53 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8730 (mtmm) REVERT: G 62 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: D 241 MET cc_start: 0.6794 (mpp) cc_final: 0.6015 (ptp) REVERT: D 393 MET cc_start: 0.7608 (mmm) cc_final: 0.7270 (mmm) REVERT: D 981 MET cc_start: 0.0136 (ptp) cc_final: -0.0234 (ptp) REVERT: D 1168 MET cc_start: 0.7388 (mmt) cc_final: 0.7154 (mmm) REVERT: D 1564 MET cc_start: 0.7984 (mmm) cc_final: 0.7421 (tpt) REVERT: D 1724 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: D 1975 MET cc_start: 0.8232 (ptm) cc_final: 0.8018 (ptt) REVERT: D 2142 MET cc_start: 0.8185 (mmm) cc_final: 0.7765 (mpp) REVERT: D 2214 MET cc_start: 0.8612 (mmm) cc_final: 0.8128 (mmm) REVERT: D 2234 MET cc_start: 0.8487 (mmm) cc_final: 0.8248 (mtp) REVERT: D 2456 MET cc_start: 0.8413 (mmt) cc_final: 0.8163 (mmt) REVERT: D 2605 MET cc_start: 0.8267 (tmm) cc_final: 0.7932 (tmm) REVERT: D 2773 TRP cc_start: 0.7856 (t-100) cc_final: 0.7525 (t-100) REVERT: D 2828 MET cc_start: 0.7543 (mmt) cc_final: 0.7189 (mmt) REVERT: D 2840 MET cc_start: 0.8256 (mmm) cc_final: 0.8009 (mpp) REVERT: D 3003 MET cc_start: 0.8560 (mtp) cc_final: 0.8326 (mtm) REVERT: D 3072 MET cc_start: 0.7348 (ttp) cc_final: 0.6978 (tmm) REVERT: D 3231 MET cc_start: 0.8125 (tpp) cc_final: 0.7461 (tpp) REVERT: D 4258 MET cc_start: 0.2070 (ptp) cc_final: 0.0328 (mmm) REVERT: D 4279 MET cc_start: 0.3973 (mmp) cc_final: 0.3426 (mmt) REVERT: D 4292 MET cc_start: 0.5149 (mmm) cc_final: 0.4544 (mmm) REVERT: D 4504 MET cc_start: 0.7690 (tmm) cc_final: 0.7425 (tmm) REVERT: D 4707 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7725 (mmm) REVERT: D 4814 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7925 (ttm) REVERT: B 393 MET cc_start: 0.7366 (mmm) cc_final: 0.7086 (mmm) REVERT: B 892 LEU cc_start: 0.7761 (mt) cc_final: 0.7520 (tp) REVERT: B 981 MET cc_start: 0.0213 (pmm) cc_final: 0.0010 (pmm) REVERT: B 1165 MET cc_start: 0.8254 (mtt) cc_final: 0.7914 (mtm) REVERT: B 1168 MET cc_start: 0.7588 (mmm) cc_final: 0.7316 (mmt) REVERT: B 1724 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: B 1948 MET cc_start: 0.8003 (mmp) cc_final: 0.7705 (mmm) REVERT: B 2142 MET cc_start: 0.8161 (mmm) cc_final: 0.7709 (mpp) REVERT: B 2214 MET cc_start: 0.8608 (mmm) cc_final: 0.8193 (mmm) REVERT: B 2512 MET cc_start: 0.9057 (tpt) cc_final: 0.8848 (tpp) REVERT: B 2773 TRP cc_start: 0.8121 (t-100) cc_final: 0.7833 (t-100) REVERT: B 2828 MET cc_start: 0.7254 (mmt) cc_final: 0.6925 (mmt) REVERT: B 3235 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7476 (mmm) REVERT: B 3246 MET cc_start: 0.8273 (tpp) cc_final: 0.7940 (tpp) REVERT: B 3605 MET cc_start: 0.2501 (ppp) cc_final: 0.2236 (ppp) REVERT: B 3954 MET cc_start: 0.8913 (mmm) cc_final: 0.8673 (mmt) REVERT: B 4052 MET cc_start: 0.7765 (mmm) cc_final: 0.7393 (mmm) REVERT: B 4256 MET cc_start: 0.2789 (ppp) cc_final: 0.2046 (tmm) REVERT: B 4258 MET cc_start: -0.0801 (ptp) cc_final: -0.1255 (mtp) REVERT: B 4279 MET cc_start: 0.3039 (mmm) cc_final: 0.2175 (mtt) REVERT: B 4502 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7422 (ttp) REVERT: B 4504 MET cc_start: 0.7534 (tmm) cc_final: 0.7070 (tmm) REVERT: B 4672 MET cc_start: 0.5068 (pmm) cc_final: 0.4851 (ptt) REVERT: B 4814 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7937 (ttm) REVERT: C 935 MET cc_start: 0.4826 (tmm) cc_final: 0.4237 (tpt) REVERT: C 1107 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8094 (p) REVERT: C 1487 MET cc_start: 0.8321 (mtm) cc_final: 0.8041 (mtp) REVERT: C 1721 MET cc_start: 0.8029 (mmm) cc_final: 0.7643 (mmp) REVERT: C 1948 MET cc_start: 0.8189 (mmp) cc_final: 0.7973 (mmm) REVERT: C 2084 MET cc_start: 0.8526 (mtm) cc_final: 0.8299 (mtp) REVERT: C 2214 MET cc_start: 0.8880 (mmm) cc_final: 0.8375 (mmm) REVERT: C 2279 MET cc_start: 0.8336 (tpp) cc_final: 0.7797 (tmm) REVERT: C 2605 MET cc_start: 0.8716 (tmm) cc_final: 0.8457 (tmm) REVERT: C 2840 MET cc_start: 0.8480 (mmp) cc_final: 0.8088 (mmp) REVERT: C 3003 MET cc_start: 0.8623 (ptp) cc_final: 0.8397 (ptt) REVERT: C 3046 MET cc_start: 0.8443 (mmm) cc_final: 0.8128 (mmm) REVERT: C 3068 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8387 (tt) REVERT: C 3072 MET cc_start: 0.7565 (ttp) cc_final: 0.7254 (tmm) REVERT: C 3235 MET cc_start: 0.7318 (tpt) cc_final: 0.6785 (tpp) REVERT: C 3246 MET cc_start: 0.8378 (tpp) cc_final: 0.8008 (tpp) REVERT: C 3954 MET cc_start: 0.8960 (mmm) cc_final: 0.8677 (mmm) REVERT: C 4052 MET cc_start: 0.7920 (mmm) cc_final: 0.7537 (mmm) REVERT: C 4109 MET cc_start: 0.7379 (mtm) cc_final: 0.7029 (mtt) REVERT: C 4256 MET cc_start: 0.1723 (ppp) cc_final: 0.1068 (tmm) REVERT: C 4258 MET cc_start: -0.1316 (ptp) cc_final: -0.1933 (ttp) REVERT: C 4568 MET cc_start: 0.7945 (mmp) cc_final: 0.7390 (mmm) REVERT: C 4672 MET cc_start: 0.5326 (pmm) cc_final: 0.4590 (pmm) REVERT: C 4814 MET cc_start: 0.8272 (ttm) cc_final: 0.7943 (ttm) outliers start: 85 outliers final: 39 residues processed: 681 average time/residue: 1.1380 time to fit residues: 1407.4999 Evaluate side-chains 679 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 625 time to evaluate : 11.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3978 MET Chi-restraints excluded: chain A residue 4009 ASN Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4557 VAL Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1552 VAL Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 2589 LEU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 4009 ASN Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4557 VAL Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2938 GLN Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3272 HIS Chi-restraints excluded: chain B residue 4009 ASN Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4557 VAL Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 1021 GLN Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 2618 TRP Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3122 ILE Chi-restraints excluded: chain C residue 4009 ASN Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 6.9990 chunk 188 optimal weight: 50.0000 chunk 952 optimal weight: 9.9990 chunk 1220 optimal weight: 9.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 50.0000 chunk 933 optimal weight: 3.9990 chunk 1665 optimal weight: 9.9990 chunk 1042 optimal weight: 4.9990 chunk 1015 optimal weight: 1.9990 chunk 768 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 26 HIS F 106 ASN D 23 GLN D 150 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2702 ASN D2704 GLN ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2978 HIS ** C3272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 141676 Z= 0.293 Angle : 0.571 16.340 191424 Z= 0.293 Chirality : 0.039 0.209 20988 Planarity : 0.004 0.143 24592 Dihedral : 5.383 89.365 19046 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.02 % Rotamer: Outliers : 0.56 % Allowed : 7.69 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.41 (0.06), residues: 17212 helix: 2.02 (0.05), residues: 9172 sheet: 0.20 (0.13), residues: 1508 loop : -0.42 (0.07), residues: 6532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B2732 HIS 0.046 0.001 HIS F 26 PHE 0.028 0.001 PHE A3854 TYR 0.022 0.001 TYR D 462 ARG 0.008 0.000 ARG C3152 *********************** 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 714 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 629 time to evaluate : 11.720 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: H 58 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8338 (mtmm) REVERT: H 62 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: A 241 MET cc_start: 0.6681 (mpp) cc_final: 0.6015 (ptp) REVERT: A 655 MET cc_start: 0.8569 (mmm) cc_final: 0.8325 (mmm) REVERT: A 964 MET cc_start: 0.0723 (mpp) cc_final: 0.0331 (mtm) REVERT: A 1306 MET cc_start: 0.8608 (mtp) cc_final: 0.8288 (mtp) REVERT: A 1842 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 1953 MET cc_start: 0.6731 (mpp) cc_final: 0.5894 (mpp) REVERT: A 2234 MET cc_start: 0.8335 (mmm) cc_final: 0.7938 (mtp) REVERT: A 3068 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8687 (tp) REVERT: A 3235 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7469 (mmm) REVERT: A 4274 MET cc_start: 0.0761 (mmp) cc_final: -0.0160 (mmm) REVERT: A 4292 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.5141 (mmm) REVERT: A 4504 MET cc_start: 0.7558 (tmm) cc_final: 0.7086 (tmm) REVERT: A 4672 MET cc_start: 0.5657 (pmm) cc_final: 0.5312 (pmm) REVERT: A 4814 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7936 (ttm) REVERT: E 62 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: G 62 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: D 241 MET cc_start: 0.6731 (mpp) cc_final: 0.6012 (ptp) REVERT: D 393 MET cc_start: 0.7684 (mmm) cc_final: 0.7325 (mmm) REVERT: D 981 MET cc_start: 0.0022 (ptp) cc_final: -0.0327 (ptp) REVERT: D 1724 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: D 1842 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8490 (mt) REVERT: D 2142 MET cc_start: 0.8187 (mmm) cc_final: 0.7731 (mpp) REVERT: D 2214 MET cc_start: 0.8598 (mmm) cc_final: 0.8111 (mmm) REVERT: D 2234 MET cc_start: 0.8488 (mmm) cc_final: 0.8263 (mtp) REVERT: D 2442 MET cc_start: 0.7868 (mmm) cc_final: 0.7578 (tpp) REVERT: D 2456 MET cc_start: 0.8488 (mmt) cc_final: 0.8180 (mmt) REVERT: D 2605 MET cc_start: 0.8312 (tmm) cc_final: 0.7992 (tmm) REVERT: D 2773 TRP cc_start: 0.7893 (t-100) cc_final: 0.7537 (t-100) REVERT: D 2828 MET cc_start: 0.7545 (mmt) cc_final: 0.7169 (mmt) REVERT: D 2844 MET cc_start: 0.8734 (tpp) cc_final: 0.8528 (mmm) REVERT: D 3003 MET cc_start: 0.8549 (mtp) cc_final: 0.8309 (mtm) REVERT: D 3072 MET cc_start: 0.7353 (ttp) cc_final: 0.6978 (tmm) REVERT: D 3231 MET cc_start: 0.8154 (tpp) cc_final: 0.7590 (tpp) REVERT: D 4258 MET cc_start: 0.2085 (ptp) cc_final: 0.0319 (mmm) REVERT: D 4274 MET cc_start: 0.1866 (mmp) cc_final: 0.1480 (mmm) REVERT: D 4279 MET cc_start: 0.3945 (mmp) cc_final: 0.3380 (mmt) REVERT: D 4292 MET cc_start: 0.5102 (mmm) cc_final: 0.4512 (mmm) REVERT: D 4504 MET cc_start: 0.7648 (tmm) cc_final: 0.7173 (tmm) REVERT: D 4707 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: D 4814 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7914 (ttm) REVERT: B 393 MET cc_start: 0.7364 (mmm) cc_final: 0.7062 (mmm) REVERT: B 892 LEU cc_start: 0.7780 (mt) cc_final: 0.7541 (tp) REVERT: B 981 MET cc_start: 0.0208 (pmm) cc_final: -0.0006 (pmm) REVERT: B 1165 MET cc_start: 0.8278 (mtt) cc_final: 0.7911 (mtm) REVERT: B 1168 MET cc_start: 0.7622 (mmm) cc_final: 0.7260 (mmm) REVERT: B 1564 MET cc_start: 0.8317 (mmm) cc_final: 0.8069 (mmm) REVERT: B 1724 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: B 1842 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8512 (mt) REVERT: B 1948 MET cc_start: 0.8019 (mmp) cc_final: 0.7693 (mmm) REVERT: B 1953 MET cc_start: 0.6738 (mpp) cc_final: 0.5704 (mpp) REVERT: B 2142 MET cc_start: 0.8148 (mmm) cc_final: 0.7639 (mpp) REVERT: B 2214 MET cc_start: 0.8610 (mmm) cc_final: 0.8206 (mmm) REVERT: B 2234 MET cc_start: 0.8433 (mmm) cc_final: 0.8194 (mtp) REVERT: B 2828 MET cc_start: 0.7247 (mmt) cc_final: 0.6803 (mmt) REVERT: B 3246 MET cc_start: 0.8260 (tpp) cc_final: 0.7911 (tpp) REVERT: B 3605 MET cc_start: 0.2442 (ppp) cc_final: 0.2190 (ppp) REVERT: B 3954 MET cc_start: 0.8929 (mmm) cc_final: 0.8602 (mmm) REVERT: B 4052 MET cc_start: 0.7752 (mmm) cc_final: 0.7411 (mmm) REVERT: B 4256 MET cc_start: 0.2776 (ppp) cc_final: 0.2047 (tmm) REVERT: B 4258 MET cc_start: -0.0785 (ptp) cc_final: -0.1274 (mtp) REVERT: B 4279 MET cc_start: 0.2909 (mmm) cc_final: 0.2034 (mtt) REVERT: B 4502 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7430 (ttp) REVERT: B 4504 MET cc_start: 0.7530 (tmm) cc_final: 0.7040 (tmm) REVERT: B 4672 MET cc_start: 0.5213 (pmm) cc_final: 0.4856 (ptt) REVERT: B 4814 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7947 (ttm) REVERT: C 935 MET cc_start: 0.4821 (tmm) cc_final: 0.4264 (tpt) REVERT: C 1487 MET cc_start: 0.8337 (mtm) cc_final: 0.8063 (mtp) REVERT: C 1721 MET cc_start: 0.8024 (mmm) cc_final: 0.7627 (mmp) REVERT: C 1842 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8516 (mt) REVERT: C 2214 MET cc_start: 0.8857 (mmm) cc_final: 0.8326 (mmm) REVERT: C 2279 MET cc_start: 0.8331 (tpp) cc_final: 0.7795 (tmm) REVERT: C 2347 MET cc_start: 0.8804 (tpp) cc_final: 0.8592 (mmm) REVERT: C 2456 MET cc_start: 0.8532 (mmt) cc_final: 0.7888 (mmt) REVERT: C 2512 MET cc_start: 0.8960 (tpp) cc_final: 0.8224 (tpp) REVERT: C 2605 MET cc_start: 0.8735 (tmm) cc_final: 0.8506 (tmm) REVERT: C 2890 GLN cc_start: 0.8218 (pt0) cc_final: 0.7628 (pp30) REVERT: C 3046 MET cc_start: 0.8457 (mmm) cc_final: 0.8189 (mmm) REVERT: C 3068 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8390 (tt) REVERT: C 3072 MET cc_start: 0.7578 (ttp) cc_final: 0.7262 (tmm) REVERT: C 3235 MET cc_start: 0.7310 (tpt) cc_final: 0.6753 (tpp) REVERT: C 3246 MET cc_start: 0.8360 (tpp) cc_final: 0.7979 (tpp) REVERT: C 3323 MET cc_start: 0.6333 (mmm) cc_final: 0.5990 (mmm) REVERT: C 3954 MET cc_start: 0.8968 (mmm) cc_final: 0.8679 (mmm) REVERT: C 4052 MET cc_start: 0.7882 (mmm) cc_final: 0.7509 (mmm) REVERT: C 4109 MET cc_start: 0.7440 (mtm) cc_final: 0.7084 (mtt) REVERT: C 4256 MET cc_start: 0.1886 (ppp) cc_final: 0.1239 (tmm) REVERT: C 4258 MET cc_start: -0.1361 (ptp) cc_final: -0.1948 (ttp) REVERT: C 4504 MET cc_start: 0.7395 (tmm) cc_final: 0.6975 (ppp) REVERT: C 4568 MET cc_start: 0.7892 (mmp) cc_final: 0.7351 (mmm) REVERT: C 4672 MET cc_start: 0.5355 (pmm) cc_final: 0.4580 (pmm) REVERT: C 4814 MET cc_start: 0.8275 (ttm) cc_final: 0.7932 (ttm) outliers start: 85 outliers final: 47 residues processed: 691 average time/residue: 1.1994 time to fit residues: 1521.8256 Evaluate side-chains 692 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 627 time to evaluate : 11.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain A residue 3978 MET Chi-restraints excluded: chain A residue 4009 ASN Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4557 VAL Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1552 VAL Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2589 LEU Chi-restraints excluded: chain D residue 2717 LEU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3272 HIS Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 4009 ASN Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4557 VAL Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2938 GLN Chi-restraints excluded: chain B residue 3272 HIS Chi-restraints excluded: chain B residue 3978 MET Chi-restraints excluded: chain B residue 4009 ASN Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4557 VAL Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2589 LEU Chi-restraints excluded: chain C residue 2618 TRP Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3122 ILE Chi-restraints excluded: chain C residue 4009 ASN Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 10.0000 chunk 665 optimal weight: 6.9990 chunk 994 optimal weight: 10.0000 chunk 501 optimal weight: 4.9990 chunk 327 optimal weight: 4.9990 chunk 322 optimal weight: 0.5980 chunk 1058 optimal weight: 5.9990 chunk 1134 optimal weight: 8.9990 chunk 823 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 1309 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2702 ASN A2704 GLN ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS G 106 ASN D 150 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2704 GLN C2978 HIS ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 141676 Z= 0.255 Angle : 0.559 14.902 191424 Z= 0.286 Chirality : 0.039 0.212 20988 Planarity : 0.004 0.138 24592 Dihedral : 5.322 87.844 19046 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.77 % Favored : 97.09 % Rotamer: Outliers : 0.57 % Allowed : 8.01 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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 (0.06), residues: 17212 helix: 2.06 (0.05), residues: 9180 sheet: 0.17 (0.14), residues: 1368 loop : -0.41 (0.07), residues: 6664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B2732 HIS 0.041 0.001 HIS F 26 PHE 0.024 0.001 PHE A3854 TYR 0.021 0.001 TYR C 462 ARG 0.012 0.000 ARG A2793 *********************** 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 713 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 628 time to evaluate : 11.664 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: H 58 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8323 (mtmm) REVERT: H 62 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: A 241 MET cc_start: 0.6738 (mpp) cc_final: 0.5888 (ptp) REVERT: A 494 MET cc_start: 0.8826 (mmm) cc_final: 0.8571 (mmm) REVERT: A 964 MET cc_start: 0.0828 (mpp) cc_final: 0.0457 (mtm) REVERT: A 1306 MET cc_start: 0.8591 (mtp) cc_final: 0.8320 (mtp) REVERT: A 1564 MET cc_start: 0.8340 (mmm) cc_final: 0.8031 (mmm) REVERT: A 1842 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8522 (mt) REVERT: A 1953 MET cc_start: 0.6770 (mpp) cc_final: 0.5890 (mpp) REVERT: A 2234 MET cc_start: 0.8341 (mmm) cc_final: 0.7945 (mtp) REVERT: A 2782 MET cc_start: 0.6703 (tmm) cc_final: 0.6274 (tmm) REVERT: A 3068 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8691 (tp) REVERT: A 3235 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7364 (mmm) REVERT: A 4274 MET cc_start: 0.0650 (mmp) cc_final: -0.0101 (mmm) REVERT: A 4292 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5132 (mmm) REVERT: A 4814 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7927 (ttm) REVERT: E 62 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: G 62 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: D 241 MET cc_start: 0.6832 (mpp) cc_final: 0.6125 (ptp) REVERT: D 393 MET cc_start: 0.7691 (mmm) cc_final: 0.7353 (mmm) REVERT: D 981 MET cc_start: 0.0083 (ptp) cc_final: -0.0243 (ptp) REVERT: D 1724 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: D 1842 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8488 (mt) REVERT: D 1975 MET cc_start: 0.8254 (ptm) cc_final: 0.7969 (ptt) REVERT: D 2142 MET cc_start: 0.8194 (mmm) cc_final: 0.7716 (mpp) REVERT: D 2214 MET cc_start: 0.8604 (mmm) cc_final: 0.8147 (mmm) REVERT: D 2234 MET cc_start: 0.8466 (mmm) cc_final: 0.8265 (mtp) REVERT: D 2442 MET cc_start: 0.7877 (mmm) cc_final: 0.7666 (mmm) REVERT: D 2512 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8862 (tpp) REVERT: D 2605 MET cc_start: 0.8316 (tmm) cc_final: 0.7995 (tmm) REVERT: D 2773 TRP cc_start: 0.7898 (t-100) cc_final: 0.7507 (t-100) REVERT: D 2828 MET cc_start: 0.7525 (mmt) cc_final: 0.7184 (mmt) REVERT: D 2844 MET cc_start: 0.8724 (tpp) cc_final: 0.8516 (mmm) REVERT: D 3003 MET cc_start: 0.8558 (mtp) cc_final: 0.8342 (ptp) REVERT: D 3072 MET cc_start: 0.7362 (ttp) cc_final: 0.6908 (tmm) REVERT: D 3231 MET cc_start: 0.8180 (tpp) cc_final: 0.7628 (tpp) REVERT: D 3954 MET cc_start: 0.8932 (mmm) cc_final: 0.8686 (mmt) REVERT: D 4258 MET cc_start: 0.2242 (ptp) cc_final: 0.0320 (mmm) REVERT: D 4274 MET cc_start: 0.1857 (mmp) cc_final: 0.1491 (mmm) REVERT: D 4279 MET cc_start: 0.3871 (mmp) cc_final: 0.3364 (mmt) REVERT: D 4292 MET cc_start: 0.5132 (mmm) cc_final: 0.4540 (mmm) REVERT: D 4504 MET cc_start: 0.7570 (tmm) cc_final: 0.7113 (tmm) REVERT: D 4707 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7691 (mmm) REVERT: D 4814 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7918 (ttm) REVERT: B 393 MET cc_start: 0.7401 (mmm) cc_final: 0.7090 (mmm) REVERT: B 655 MET cc_start: 0.8725 (mmm) cc_final: 0.8381 (mmt) REVERT: B 892 LEU cc_start: 0.7804 (mt) cc_final: 0.7581 (tp) REVERT: B 1165 MET cc_start: 0.8278 (mtt) cc_final: 0.7910 (mtm) REVERT: B 1168 MET cc_start: 0.7640 (mmm) cc_final: 0.7297 (mmm) REVERT: B 1564 MET cc_start: 0.8331 (mmm) cc_final: 0.8096 (mmm) REVERT: B 1724 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: B 1842 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8509 (mt) REVERT: B 1948 MET cc_start: 0.8008 (mmp) cc_final: 0.7735 (mmm) REVERT: B 1953 MET cc_start: 0.6673 (mpp) cc_final: 0.5601 (mpp) REVERT: B 2192 MET cc_start: 0.8646 (tpt) cc_final: 0.8435 (mmt) REVERT: B 2214 MET cc_start: 0.8605 (mmm) cc_final: 0.8187 (mmm) REVERT: B 2605 MET cc_start: 0.8596 (tmm) cc_final: 0.8353 (tmm) REVERT: B 2773 TRP cc_start: 0.8111 (t-100) cc_final: 0.7801 (t-100) REVERT: B 2828 MET cc_start: 0.7228 (mmt) cc_final: 0.6798 (mmt) REVERT: B 3246 MET cc_start: 0.8246 (tpp) cc_final: 0.7871 (tpp) REVERT: B 3605 MET cc_start: 0.2294 (ppp) cc_final: 0.2063 (ppp) REVERT: B 3954 MET cc_start: 0.8922 (mmm) cc_final: 0.8589 (mmm) REVERT: B 4052 MET cc_start: 0.7749 (mmm) cc_final: 0.7405 (mmm) REVERT: B 4256 MET cc_start: 0.2756 (ppp) cc_final: 0.1945 (tmm) REVERT: B 4258 MET cc_start: -0.0717 (ptp) cc_final: -0.1207 (mtp) REVERT: B 4279 MET cc_start: 0.2895 (mmm) cc_final: 0.2030 (mtt) REVERT: B 4502 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7440 (ttp) REVERT: B 4504 MET cc_start: 0.7532 (tmm) cc_final: 0.7051 (tmm) REVERT: B 4568 MET cc_start: 0.7714 (mmp) cc_final: 0.7029 (tpp) REVERT: B 4707 MET cc_start: 0.8057 (mmm) cc_final: 0.7741 (mmm) REVERT: B 4804 MET cc_start: 0.8460 (mmm) cc_final: 0.8165 (mmp) REVERT: B 4814 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7954 (ttm) REVERT: C 935 MET cc_start: 0.4810 (tmm) cc_final: 0.4337 (tpt) REVERT: C 1168 MET cc_start: 0.7600 (mmm) cc_final: 0.7390 (mmt) REVERT: C 1487 MET cc_start: 0.8340 (mtm) cc_final: 0.8068 (mtp) REVERT: C 1721 MET cc_start: 0.7989 (mmm) cc_final: 0.7506 (mmp) REVERT: C 1729 MET cc_start: 0.8356 (mmm) cc_final: 0.8069 (mmm) REVERT: C 1842 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 2214 MET cc_start: 0.8848 (mmm) cc_final: 0.8297 (mmm) REVERT: C 2279 MET cc_start: 0.8307 (tpp) cc_final: 0.7774 (tmm) REVERT: C 2456 MET cc_start: 0.8512 (mmt) cc_final: 0.7901 (mmt) REVERT: C 2512 MET cc_start: 0.9045 (tpp) cc_final: 0.8267 (tpp) REVERT: C 2605 MET cc_start: 0.8709 (tmm) cc_final: 0.8472 (tmm) REVERT: C 2840 MET cc_start: 0.8435 (mmp) cc_final: 0.8042 (mmp) REVERT: C 3046 MET cc_start: 0.8436 (mmm) cc_final: 0.8176 (mmm) REVERT: C 3068 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8381 (tt) REVERT: C 3072 MET cc_start: 0.7581 (ttp) cc_final: 0.7261 (tmm) REVERT: C 3246 MET cc_start: 0.8354 (tpp) cc_final: 0.8002 (tpp) REVERT: C 3323 MET cc_start: 0.6551 (mmm) cc_final: 0.6176 (mmm) REVERT: C 4052 MET cc_start: 0.7913 (mmm) cc_final: 0.7528 (mmm) REVERT: C 4109 MET cc_start: 0.7464 (mtm) cc_final: 0.7108 (mtt) REVERT: C 4186 MET cc_start: 0.8098 (mmm) cc_final: 0.7749 (mmm) REVERT: C 4256 MET cc_start: 0.1842 (ppp) cc_final: 0.1211 (tmm) REVERT: C 4258 MET cc_start: -0.1349 (ptp) cc_final: -0.1938 (ttp) REVERT: C 4504 MET cc_start: 0.7454 (tmm) cc_final: 0.7093 (tmm) REVERT: C 4568 MET cc_start: 0.7859 (mmp) cc_final: 0.7307 (mmm) REVERT: C 4672 MET cc_start: 0.5396 (pmm) cc_final: 0.4466 (pmm) REVERT: C 4814 MET cc_start: 0.8262 (ttm) cc_final: 0.7920 (ttm) outliers start: 85 outliers final: 44 residues processed: 686 average time/residue: 1.1758 time to fit residues: 1467.9643 Evaluate side-chains 686 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 623 time to evaluate : 11.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 4009 ASN Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4557 VAL Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1552 VAL Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2589 LEU Chi-restraints excluded: chain D residue 2717 LEU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3272 HIS Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 3978 MET Chi-restraints excluded: chain D residue 4009 ASN Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4557 VAL Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 3272 HIS Chi-restraints excluded: chain B residue 3978 MET Chi-restraints excluded: chain B residue 4009 ASN Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4557 VAL Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2589 LEU Chi-restraints excluded: chain C residue 2618 TRP Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3122 ILE Chi-restraints excluded: chain C residue 4009 ASN Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 9.9990 chunk 1595 optimal weight: 10.0000 chunk 1455 optimal weight: 1.9990 chunk 1552 optimal weight: 50.0000 chunk 934 optimal weight: 4.9990 chunk 676 optimal weight: 10.0000 chunk 1218 optimal weight: 5.9990 chunk 476 optimal weight: 30.0000 chunk 1402 optimal weight: 40.0000 chunk 1467 optimal weight: 0.0370 chunk 1546 optimal weight: 7.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 150 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS A2995 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4762 HIS F 26 HIS D 150 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2702 ASN B2704 GLN B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3964 GLN ** B4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1970 GLN ** C2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2702 ASN C2978 HIS C2995 HIS ** C4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 141676 Z= 0.236 Angle : 0.557 16.718 191424 Z= 0.284 Chirality : 0.039 0.224 20988 Planarity : 0.004 0.136 24592 Dihedral : 5.302 89.751 19046 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Rotamer: Outliers : 0.53 % Allowed : 8.10 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.48 (0.07), residues: 17212 helix: 2.10 (0.06), residues: 9140 sheet: 0.13 (0.14), residues: 1380 loop : -0.40 (0.07), residues: 6692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B2732 HIS 0.032 0.001 HIS F 26 PHE 0.022 0.001 PHE A3854 TYR 0.024 0.001 TYR A4939 ARG 0.011 0.000 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 703 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 624 time to evaluate : 11.597 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: H 58 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8297 (mtmm) REVERT: H 62 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: A 241 MET cc_start: 0.6721 (mpp) cc_final: 0.5881 (ptp) REVERT: A 964 MET cc_start: 0.0832 (mpp) cc_final: 0.0473 (mtm) REVERT: A 1306 MET cc_start: 0.8546 (mtp) cc_final: 0.8293 (mtp) REVERT: A 1564 MET cc_start: 0.8344 (mmm) cc_final: 0.8029 (mmm) REVERT: A 1842 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8509 (mt) REVERT: A 1953 MET cc_start: 0.6843 (mpp) cc_final: 0.6032 (mpp) REVERT: A 2234 MET cc_start: 0.8340 (mmm) cc_final: 0.7919 (mtp) REVERT: A 2512 MET cc_start: 0.9139 (tpp) cc_final: 0.8833 (tpp) REVERT: A 3046 MET cc_start: 0.8410 (mmm) cc_final: 0.8141 (mmm) REVERT: A 3068 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 3235 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7359 (mmm) REVERT: A 3246 MET cc_start: 0.8072 (mmm) cc_final: 0.7831 (mmm) REVERT: A 3954 MET cc_start: 0.8943 (mmm) cc_final: 0.8707 (mmt) REVERT: A 4274 MET cc_start: 0.0720 (mmp) cc_final: -0.0130 (mmm) REVERT: A 4292 MET cc_start: 0.5593 (OUTLIER) cc_final: 0.5140 (mmm) REVERT: A 4504 MET cc_start: 0.7490 (tmm) cc_final: 0.7112 (tmm) REVERT: A 4672 MET cc_start: 0.5792 (pmm) cc_final: 0.5203 (pmm) REVERT: A 4814 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7944 (ttm) REVERT: E 62 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: G 62 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: D 241 MET cc_start: 0.6768 (mpp) cc_final: 0.6071 (ptp) REVERT: D 393 MET cc_start: 0.7660 (mmm) cc_final: 0.7321 (mmm) REVERT: D 981 MET cc_start: 0.0085 (ptp) cc_final: -0.0247 (ptp) REVERT: D 1724 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: D 1842 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8487 (mt) REVERT: D 1975 MET cc_start: 0.8249 (ptm) cc_final: 0.7984 (ptt) REVERT: D 2142 MET cc_start: 0.8031 (mmm) cc_final: 0.7634 (tpp) REVERT: D 2214 MET cc_start: 0.8609 (mmm) cc_final: 0.8153 (mmm) REVERT: D 2512 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8729 (tpp) REVERT: D 2605 MET cc_start: 0.8343 (tmm) cc_final: 0.8039 (tmm) REVERT: D 2773 TRP cc_start: 0.7887 (t-100) cc_final: 0.7493 (t-100) REVERT: D 2828 MET cc_start: 0.7509 (mmt) cc_final: 0.7176 (mmt) REVERT: D 2840 MET cc_start: 0.8144 (mmm) cc_final: 0.7815 (mmm) REVERT: D 3072 MET cc_start: 0.7351 (ttp) cc_final: 0.6914 (tmm) REVERT: D 3231 MET cc_start: 0.8214 (tpp) cc_final: 0.7355 (tpp) REVERT: D 3246 MET cc_start: 0.7930 (mmm) cc_final: 0.7692 (mmm) REVERT: D 3954 MET cc_start: 0.8933 (mmm) cc_final: 0.8608 (mmm) REVERT: D 4012 MET cc_start: 0.8323 (ttm) cc_final: 0.8061 (ttp) REVERT: D 4258 MET cc_start: 0.2257 (ptp) cc_final: 0.0361 (mmm) REVERT: D 4274 MET cc_start: 0.1624 (mmp) cc_final: 0.1257 (mmm) REVERT: D 4279 MET cc_start: 0.3960 (mmp) cc_final: 0.3352 (mmt) REVERT: D 4292 MET cc_start: 0.5102 (mmm) cc_final: 0.4469 (mmm) REVERT: D 4502 MET cc_start: 0.8010 (ttp) cc_final: 0.7778 (ttp) REVERT: D 4504 MET cc_start: 0.7566 (tmm) cc_final: 0.7094 (tmm) REVERT: D 4672 MET cc_start: 0.5551 (pmm) cc_final: 0.4893 (pmm) REVERT: D 4707 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7677 (mmm) REVERT: D 4814 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7889 (ttm) REVERT: B 393 MET cc_start: 0.7408 (mmm) cc_final: 0.7090 (mmm) REVERT: B 655 MET cc_start: 0.8698 (mmm) cc_final: 0.8362 (mmt) REVERT: B 892 LEU cc_start: 0.7733 (mt) cc_final: 0.7517 (tp) REVERT: B 1165 MET cc_start: 0.8251 (mtt) cc_final: 0.7882 (mtm) REVERT: B 1168 MET cc_start: 0.7660 (mmm) cc_final: 0.7339 (mmm) REVERT: B 1564 MET cc_start: 0.8345 (mmm) cc_final: 0.8106 (mmm) REVERT: B 1724 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: B 1842 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8507 (mt) REVERT: B 1948 MET cc_start: 0.8010 (mmp) cc_final: 0.7729 (mmm) REVERT: B 1953 MET cc_start: 0.6683 (mpp) cc_final: 0.5565 (mpp) REVERT: B 2142 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7688 (tpp) REVERT: B 2214 MET cc_start: 0.8607 (mmm) cc_final: 0.8190 (mmm) REVERT: B 2512 MET cc_start: 0.9091 (tpp) cc_final: 0.8770 (tpp) REVERT: B 2773 TRP cc_start: 0.8119 (t-100) cc_final: 0.7796 (t-100) REVERT: B 2828 MET cc_start: 0.7220 (mmt) cc_final: 0.6771 (mmt) REVERT: B 3246 MET cc_start: 0.8224 (tpp) cc_final: 0.7839 (tpp) REVERT: B 3605 MET cc_start: 0.2321 (ppp) cc_final: 0.2102 (ppp) REVERT: B 3954 MET cc_start: 0.8910 (mmm) cc_final: 0.8579 (mmm) REVERT: B 4052 MET cc_start: 0.7755 (mmm) cc_final: 0.7404 (mmm) REVERT: B 4256 MET cc_start: 0.2749 (ppp) cc_final: 0.1934 (tmm) REVERT: B 4258 MET cc_start: -0.0727 (ptp) cc_final: -0.1235 (mtp) REVERT: B 4279 MET cc_start: 0.2752 (mmm) cc_final: 0.2007 (mtt) REVERT: B 4502 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7420 (ttp) REVERT: B 4504 MET cc_start: 0.7602 (tmm) cc_final: 0.7118 (tmm) REVERT: B 4568 MET cc_start: 0.7702 (mmp) cc_final: 0.7017 (tpp) REVERT: B 4707 MET cc_start: 0.8055 (mmm) cc_final: 0.7741 (mmm) REVERT: B 4804 MET cc_start: 0.8415 (mmm) cc_final: 0.8111 (mmp) REVERT: B 4814 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7932 (ttm) REVERT: C 935 MET cc_start: 0.5012 (tmm) cc_final: 0.4535 (tpt) REVERT: C 1168 MET cc_start: 0.7622 (mmm) cc_final: 0.7416 (mmt) REVERT: C 1487 MET cc_start: 0.8342 (mtm) cc_final: 0.8072 (mtp) REVERT: C 1721 MET cc_start: 0.7897 (mmm) cc_final: 0.7496 (mmp) REVERT: C 1729 MET cc_start: 0.8383 (mmm) cc_final: 0.8173 (mmp) REVERT: C 1842 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8500 (mt) REVERT: C 2214 MET cc_start: 0.8832 (mmm) cc_final: 0.8315 (mmm) REVERT: C 2279 MET cc_start: 0.8289 (tpp) cc_final: 0.7755 (tmm) REVERT: C 2456 MET cc_start: 0.8514 (mmt) cc_final: 0.7934 (mmt) REVERT: C 2512 MET cc_start: 0.9019 (tpp) cc_final: 0.8265 (tpp) REVERT: C 2605 MET cc_start: 0.8694 (tmm) cc_final: 0.8451 (tmm) REVERT: C 2840 MET cc_start: 0.8435 (mmp) cc_final: 0.7953 (mmp) REVERT: C 3046 MET cc_start: 0.8424 (mmm) cc_final: 0.8176 (mmm) REVERT: C 3068 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8387 (tt) REVERT: C 3072 MET cc_start: 0.7581 (ttp) cc_final: 0.7254 (tmm) REVERT: C 3246 MET cc_start: 0.8351 (tpp) cc_final: 0.8004 (tpp) REVERT: C 3323 MET cc_start: 0.6531 (mmm) cc_final: 0.6200 (mmm) REVERT: C 3954 MET cc_start: 0.8947 (mmm) cc_final: 0.8670 (mmm) REVERT: C 4052 MET cc_start: 0.7929 (mmm) cc_final: 0.7533 (mmm) REVERT: C 4109 MET cc_start: 0.7485 (mtm) cc_final: 0.7133 (mtt) REVERT: C 4186 MET cc_start: 0.8156 (mmm) cc_final: 0.7749 (mmm) REVERT: C 4256 MET cc_start: 0.1919 (ppp) cc_final: 0.1272 (tmm) REVERT: C 4258 MET cc_start: -0.1292 (ptp) cc_final: -0.1903 (ttp) REVERT: C 4504 MET cc_start: 0.7449 (tmm) cc_final: 0.7076 (tmm) REVERT: C 4568 MET cc_start: 0.7811 (mmp) cc_final: 0.7277 (mmm) REVERT: C 4672 MET cc_start: 0.5395 (pmm) cc_final: 0.4412 (pmm) REVERT: C 4814 MET cc_start: 0.8233 (ttm) cc_final: 0.7896 (ttm) outliers start: 79 outliers final: 44 residues processed: 680 average time/residue: 1.1176 time to fit residues: 1386.8727 Evaluate side-chains 688 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 624 time to evaluate : 11.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 4009 ASN Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4557 VAL Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1552 VAL Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2589 LEU Chi-restraints excluded: chain D residue 2717 LEU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3272 HIS Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 3978 MET Chi-restraints excluded: chain D residue 4009 ASN Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4557 VAL Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1174 MET Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 3272 HIS Chi-restraints excluded: chain B residue 3978 MET Chi-restraints excluded: chain B residue 4009 ASN Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4557 VAL Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2589 LEU Chi-restraints excluded: chain C residue 2618 TRP Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3122 ILE Chi-restraints excluded: chain C residue 4009 ASN Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 0.3980 chunk 1641 optimal weight: 8.9990 chunk 1001 optimal weight: 10.0000 chunk 778 optimal weight: 4.9990 chunk 1140 optimal weight: 7.9990 chunk 1721 optimal weight: 8.9990 chunk 1584 optimal weight: 8.9990 chunk 1370 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 1058 optimal weight: 5.9990 chunk 840 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS D 150 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1021 GLN C1970 GLN ** C2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2978 HIS ** C4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 141676 Z= 0.201 Angle : 0.549 15.102 191424 Z= 0.278 Chirality : 0.038 0.220 20988 Planarity : 0.004 0.077 24592 Dihedral : 5.238 88.404 19046 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 0.48 % Allowed : 8.25 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.53 (0.07), residues: 17212 helix: 2.14 (0.06), residues: 9136 sheet: 0.17 (0.14), residues: 1380 loop : -0.38 (0.07), residues: 6696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B2732 HIS 0.029 0.001 HIS F 26 PHE 0.019 0.001 PHE D4640 TYR 0.020 0.001 TYR C 462 ARG 0.011 0.000 ARG E 14 ********************** 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 700 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 629 time to evaluate : 11.660 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: H 58 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8285 (mtmm) REVERT: H 62 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: A 241 MET cc_start: 0.6641 (mpp) cc_final: 0.5822 (ptp) REVERT: A 964 MET cc_start: 0.0950 (mpp) cc_final: 0.0598 (mtm) REVERT: A 1306 MET cc_start: 0.8533 (mtp) cc_final: 0.8297 (mtp) REVERT: A 1564 MET cc_start: 0.8353 (mmm) cc_final: 0.8052 (mmm) REVERT: A 1953 MET cc_start: 0.6957 (mpp) cc_final: 0.6033 (mpp) REVERT: A 2172 MET cc_start: 0.8726 (mtp) cc_final: 0.8059 (mtp) REVERT: A 2214 MET cc_start: 0.8711 (mmm) cc_final: 0.8105 (mmm) REVERT: A 2406 MET cc_start: 0.7919 (mmp) cc_final: 0.7651 (mmp) REVERT: A 2782 MET cc_start: 0.6755 (tmm) cc_final: 0.6360 (tmm) REVERT: A 3046 MET cc_start: 0.8342 (mmm) cc_final: 0.8091 (mmm) REVERT: A 3068 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8657 (tp) REVERT: A 3235 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7331 (mmm) REVERT: A 3246 MET cc_start: 0.8088 (mmm) cc_final: 0.7861 (mmm) REVERT: A 3954 MET cc_start: 0.8935 (mmm) cc_final: 0.8592 (mmm) REVERT: A 4274 MET cc_start: 0.0586 (mmp) cc_final: -0.0075 (mmm) REVERT: A 4292 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4936 (mmm) REVERT: A 4672 MET cc_start: 0.5792 (pmm) cc_final: 0.5218 (pmm) REVERT: A 4814 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7939 (ttm) REVERT: E 62 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: G 62 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: D 241 MET cc_start: 0.6737 (mpp) cc_final: 0.6040 (ptp) REVERT: D 393 MET cc_start: 0.7668 (mmm) cc_final: 0.7296 (mmm) REVERT: D 981 MET cc_start: 0.0098 (ptp) cc_final: -0.0239 (ptp) REVERT: D 1165 MET cc_start: 0.8010 (mtp) cc_final: 0.7629 (mtt) REVERT: D 1300 MET cc_start: 0.8344 (mmm) cc_final: 0.8049 (mmm) REVERT: D 1724 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: D 1842 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8477 (mt) REVERT: D 1953 MET cc_start: 0.6036 (mpp) cc_final: 0.5138 (mpp) REVERT: D 2142 MET cc_start: 0.7903 (mmm) cc_final: 0.7630 (tpp) REVERT: D 2214 MET cc_start: 0.8622 (mmm) cc_final: 0.8167 (mmm) REVERT: D 2442 MET cc_start: 0.7734 (mmm) cc_final: 0.7522 (tpp) REVERT: D 2512 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8706 (tpp) REVERT: D 2605 MET cc_start: 0.8349 (tmm) cc_final: 0.8059 (tmm) REVERT: D 2681 MET cc_start: 0.7035 (mmm) cc_final: 0.6275 (mmt) REVERT: D 2773 TRP cc_start: 0.7875 (t-100) cc_final: 0.7480 (t-100) REVERT: D 2828 MET cc_start: 0.7576 (mmt) cc_final: 0.7254 (mmt) REVERT: D 2840 MET cc_start: 0.8115 (mmm) cc_final: 0.7857 (mmm) REVERT: D 2844 MET cc_start: 0.8675 (tpp) cc_final: 0.8421 (tmm) REVERT: D 3003 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8352 (ptp) REVERT: D 3072 MET cc_start: 0.7336 (ttp) cc_final: 0.6961 (tmm) REVERT: D 3231 MET cc_start: 0.8107 (tpp) cc_final: 0.7716 (tpp) REVERT: D 3235 MET cc_start: 0.7391 (mmm) cc_final: 0.7163 (mmt) REVERT: D 3246 MET cc_start: 0.7875 (mmm) cc_final: 0.7651 (mmm) REVERT: D 3954 MET cc_start: 0.8932 (mmm) cc_final: 0.8574 (mmm) REVERT: D 4012 MET cc_start: 0.8278 (ttm) cc_final: 0.8026 (ttp) REVERT: D 4258 MET cc_start: 0.2222 (ptp) cc_final: 0.0356 (mmm) REVERT: D 4274 MET cc_start: 0.1603 (mmp) cc_final: 0.1238 (mmm) REVERT: D 4279 MET cc_start: 0.3971 (mmp) cc_final: 0.3371 (mmt) REVERT: D 4292 MET cc_start: 0.5059 (mmm) cc_final: 0.4462 (mmm) REVERT: D 4502 MET cc_start: 0.7900 (ttp) cc_final: 0.7671 (ttp) REVERT: D 4504 MET cc_start: 0.7545 (tmm) cc_final: 0.7080 (tmm) REVERT: D 4707 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: D 4814 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7903 (ttm) REVERT: B 393 MET cc_start: 0.7421 (mmm) cc_final: 0.7122 (mmm) REVERT: B 892 LEU cc_start: 0.7754 (mt) cc_final: 0.7537 (tp) REVERT: B 964 MET cc_start: 0.0698 (mpp) cc_final: 0.0269 (mpp) REVERT: B 1165 MET cc_start: 0.8239 (mtt) cc_final: 0.7883 (mtm) REVERT: B 1168 MET cc_start: 0.7672 (mmm) cc_final: 0.7360 (mmm) REVERT: B 1564 MET cc_start: 0.8329 (mmm) cc_final: 0.8109 (mmm) REVERT: B 1724 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: B 1842 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8498 (mt) REVERT: B 1948 MET cc_start: 0.8000 (mmp) cc_final: 0.7699 (mmm) REVERT: B 1953 MET cc_start: 0.6614 (mpp) cc_final: 0.5450 (mpp) REVERT: B 2142 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7572 (tpp) REVERT: B 2214 MET cc_start: 0.8609 (mmm) cc_final: 0.8197 (mmm) REVERT: B 2234 MET cc_start: 0.8452 (mmm) cc_final: 0.8102 (mtp) REVERT: B 2442 MET cc_start: 0.7817 (mmm) cc_final: 0.7547 (tpp) REVERT: B 2773 TRP cc_start: 0.8106 (t-100) cc_final: 0.7796 (t-100) REVERT: B 2828 MET cc_start: 0.7183 (mmt) cc_final: 0.6728 (mmt) REVERT: B 3235 MET cc_start: 0.7956 (mmm) cc_final: 0.7425 (mmm) REVERT: B 3246 MET cc_start: 0.8217 (tpp) cc_final: 0.7818 (tpp) REVERT: B 3605 MET cc_start: 0.2310 (ppp) cc_final: 0.2055 (ppp) REVERT: B 3954 MET cc_start: 0.8907 (mmm) cc_final: 0.8576 (mmm) REVERT: B 4052 MET cc_start: 0.7739 (mmm) cc_final: 0.7393 (mmm) REVERT: B 4256 MET cc_start: 0.2693 (ppp) cc_final: 0.1865 (tmm) REVERT: B 4258 MET cc_start: -0.0734 (ptp) cc_final: -0.1230 (mtp) REVERT: B 4279 MET cc_start: 0.2744 (mmm) cc_final: 0.2005 (mtt) REVERT: B 4502 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7375 (ttp) REVERT: B 4504 MET cc_start: 0.7612 (tmm) cc_final: 0.7109 (tmm) REVERT: B 4568 MET cc_start: 0.7688 (mmp) cc_final: 0.7004 (tpp) REVERT: B 4707 MET cc_start: 0.8036 (mmm) cc_final: 0.7721 (mmm) REVERT: B 4804 MET cc_start: 0.8318 (mmm) cc_final: 0.8010 (mmp) REVERT: B 4814 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: C 935 MET cc_start: 0.4993 (tmm) cc_final: 0.4569 (tpt) REVERT: C 1168 MET cc_start: 0.7599 (mmm) cc_final: 0.7371 (mmt) REVERT: C 1487 MET cc_start: 0.8325 (mtm) cc_final: 0.8051 (mtp) REVERT: C 1729 MET cc_start: 0.8339 (mmm) cc_final: 0.8126 (mmp) REVERT: C 1842 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8492 (mt) REVERT: C 2142 MET cc_start: 0.8397 (mmm) cc_final: 0.7779 (mmt) REVERT: C 2214 MET cc_start: 0.8829 (mmm) cc_final: 0.8317 (mmm) REVERT: C 2279 MET cc_start: 0.8269 (tpp) cc_final: 0.7741 (tmm) REVERT: C 2456 MET cc_start: 0.8470 (mmt) cc_final: 0.7915 (mmt) REVERT: C 2512 MET cc_start: 0.9039 (tpp) cc_final: 0.8268 (tpp) REVERT: C 2605 MET cc_start: 0.8664 (tmm) cc_final: 0.8418 (tmm) REVERT: C 2840 MET cc_start: 0.8311 (mmp) cc_final: 0.8019 (mmp) REVERT: C 3046 MET cc_start: 0.8407 (mmm) cc_final: 0.8162 (mmm) REVERT: C 3068 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8381 (tt) REVERT: C 3072 MET cc_start: 0.7575 (ttp) cc_final: 0.7245 (tmm) REVERT: C 3246 MET cc_start: 0.8333 (tpp) cc_final: 0.8023 (tpp) REVERT: C 3323 MET cc_start: 0.6568 (mmm) cc_final: 0.6245 (mmm) REVERT: C 3954 MET cc_start: 0.8940 (mmm) cc_final: 0.8664 (mmm) REVERT: C 4012 MET cc_start: 0.8170 (mtp) cc_final: 0.7952 (ttp) REVERT: C 4109 MET cc_start: 0.7518 (mtm) cc_final: 0.7169 (mtt) REVERT: C 4186 MET cc_start: 0.8143 (mmm) cc_final: 0.7750 (mmm) REVERT: C 4256 MET cc_start: 0.1898 (ppp) cc_final: 0.1233 (tmm) REVERT: C 4258 MET cc_start: -0.1213 (ptp) cc_final: -0.1841 (ttp) REVERT: C 4504 MET cc_start: 0.7461 (tmm) cc_final: 0.7095 (tmm) REVERT: C 4568 MET cc_start: 0.7792 (mmp) cc_final: 0.7262 (mmm) REVERT: C 4814 MET cc_start: 0.8225 (ttm) cc_final: 0.7882 (ttm) REVERT: C 4943 MET cc_start: 0.8917 (mtt) cc_final: 0.8695 (mtp) outliers start: 71 outliers final: 43 residues processed: 680 average time/residue: 1.1512 time to fit residues: 1424.2879 Evaluate side-chains 688 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 625 time to evaluate : 11.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 4009 ASN Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4557 VAL Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 1174 MET Chi-restraints excluded: chain D residue 1552 VAL Chi-restraints excluded: chain D residue 1724 GLU Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2589 LEU Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3003 MET Chi-restraints excluded: chain D residue 3272 HIS Chi-restraints excluded: chain D residue 3772 THR Chi-restraints excluded: chain D residue 3978 MET Chi-restraints excluded: chain D residue 4009 ASN Chi-restraints excluded: chain D residue 4557 VAL Chi-restraints excluded: chain D residue 4707 MET Chi-restraints excluded: chain D residue 4814 MET Chi-restraints excluded: chain D residue 4819 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1724 GLU Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 3272 HIS Chi-restraints excluded: chain B residue 4009 ASN Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4557 VAL Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 1552 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2589 LEU Chi-restraints excluded: chain C residue 2618 TRP Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3122 ILE Chi-restraints excluded: chain C residue 4009 ASN Chi-restraints excluded: chain C residue 4819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 3.9990 chunk 1460 optimal weight: 9.9990 chunk 419 optimal weight: 7.9990 chunk 1264 optimal weight: 20.0000 chunk 202 optimal weight: 0.0020 chunk 380 optimal weight: 40.0000 chunk 1373 optimal weight: 10.0000 chunk 574 optimal weight: 20.0000 chunk 1409 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 252 optimal weight: 0.0770 overall best weight: 3.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS D 150 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1970 GLN ** C2118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2224 ASN C2867 ASN C2978 HIS ** C4638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.034810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.026986 restraints weight = 2527048.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.027980 restraints weight = 1169804.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.028309 restraints weight = 671261.139| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 141676 Z= 0.220 Angle : 0.555 15.647 191424 Z= 0.281 Chirality : 0.038 0.220 20988 Planarity : 0.004 0.077 24592 Dihedral : 5.205 86.488 19046 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.77 % Favored : 97.09 % Rotamer: Outliers : 0.45 % Allowed : 8.29 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.54 (0.07), residues: 17212 helix: 2.15 (0.06), residues: 9136 sheet: 0.16 (0.14), residues: 1380 loop : -0.37 (0.07), residues: 6696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C2732 HIS 0.025 0.001 HIS F 26 PHE 0.021 0.001 PHE A3854 TYR 0.020 0.001 TYR C 462 ARG 0.010 0.000 ARG E 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28919.25 seconds wall clock time: 511 minutes 3.79 seconds (30663.79 seconds total)