Starting phenix.real_space_refine on Thu Mar 21 09:41:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxl_42768/03_2024/8uxl_42768_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxl_42768/03_2024/8uxl_42768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxl_42768/03_2024/8uxl_42768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxl_42768/03_2024/8uxl_42768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxl_42768/03_2024/8uxl_42768_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxl_42768/03_2024/8uxl_42768_updated.pdb" } resolution = 3.12 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= 0.014 sd= 0.037 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 20 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 972 5.16 5 C 91232 2.51 5 N 24408 2.21 5 O 26840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1982": "OD1" <-> "OD2" Residue "A GLU 2314": "OE1" <-> "OE2" Residue "A GLU 2329": "OE1" <-> "OE2" Residue "A PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3062": "OD1" <-> "OD2" Residue "A PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3191": "OE1" <-> "OE2" Residue "A TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3822": "OE1" <-> "OE2" Residue "A GLU 4034": "OE1" <-> "OE2" Residue "A GLU 4184": "OE1" <-> "OE2" Residue "A TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4684": "OE1" <-> "OE2" Residue "A TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4963": "OE1" <-> "OE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "I ASP 21": "OD1" <-> "OD2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ASP 721": "OD1" <-> "OD2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B ARG 1100": "NH1" <-> "NH2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1982": "OD1" <-> "OD2" Residue "B GLU 2314": "OE1" <-> "OE2" Residue "B GLU 2329": "OE1" <-> "OE2" Residue "B PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3062": "OD1" <-> "OD2" Residue "B PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3191": "OE1" <-> "OE2" Residue "B TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3822": "OE1" <-> "OE2" Residue "B GLU 4034": "OE1" <-> "OE2" Residue "B GLU 4184": "OE1" <-> "OE2" Residue "B TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4684": "OE1" <-> "OE2" Residue "B TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4963": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "C ASP 721": "OD1" <-> "OD2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 920": "OE1" <-> "OE2" Residue "C ARG 1100": "NH1" <-> "NH2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1982": "OD1" <-> "OD2" Residue "C GLU 2314": "OE1" <-> "OE2" Residue "C GLU 2329": "OE1" <-> "OE2" Residue "C PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3062": "OD1" <-> "OD2" Residue "C PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3191": "OE1" <-> "OE2" Residue "C TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3822": "OE1" <-> "OE2" Residue "C GLU 4034": "OE1" <-> "OE2" Residue "C GLU 4184": "OE1" <-> "OE2" Residue "C TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4684": "OE1" <-> "OE2" Residue "C TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4963": "OE1" <-> "OE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D GLU 581": "OE1" <-> "OE2" Residue "D ASP 721": "OD1" <-> "OD2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 920": "OE1" <-> "OE2" Residue "D ARG 1100": "NH1" <-> "NH2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1982": "OD1" <-> "OD2" Residue "D GLU 2314": "OE1" <-> "OE2" Residue "D GLU 2329": "OE1" <-> "OE2" Residue "D PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3062": "OD1" <-> "OD2" Residue "D PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3191": "OE1" <-> "OE2" Residue "D TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3822": "OE1" <-> "OE2" Residue "D GLU 4034": "OE1" <-> "OE2" Residue "D GLU 4184": "OE1" <-> "OE2" Residue "D TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4684": "OE1" <-> "OE2" Residue "D TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4963": "OE1" <-> "OE2" Residue "J ASP 21": "OD1" <-> "OD2" Residue "J PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 21": "OD1" <-> "OD2" Residue "L PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 21": "OD1" <-> "OD2" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143500 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 33858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 34577 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "I" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 33858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 34577 Chain: "C" Number of atoms: 33858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 34577 Chain: "D" Number of atoms: 33858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 4232, 33850 Classifications: {'peptide': 4232} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4075} 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: 34577 Chain: "J" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "L" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "K" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33179 SG CYS A4888 178.873 204.017 86.896 1.00113.85 S ATOM 33204 SG CYS A4891 181.265 203.898 89.838 1.00104.23 S ATOM 71440 SG CYS B4888 177.232 178.906 86.490 1.00113.85 S ATOM 71465 SG CYS B4891 177.363 181.301 89.430 1.00104.23 S ATOM A0436 SG CYS C4888 202.509 177.279 86.553 1.00113.85 S ATOM A043V SG CYS C4891 200.104 177.405 89.484 1.00104.23 S ATOM A0U7O SG CYS D4888 203.995 202.890 86.835 1.00113.85 S ATOM A0U8D SG CYS D4891 203.860 200.500 89.778 1.00104.23 S Time building chain proxies: 98.75, per 1000 atoms: 0.69 Number of scatterers: 143500 At special positions: 0 Unit cell: (381.8, 381.8, 210.82, 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 20 19.99 S 972 16.00 P 24 15.00 O 26840 8.00 N 24408 7.00 C 91232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.63 Conformation dependent library (CDL) restraints added in 36.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33584 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: 732 helices and 84 sheets defined 59.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 47.27 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.978A 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 253 through 259 removed outlier: 4.427A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.711A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.645A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.921A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.831A pdb=" N VAL A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.711A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.663A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.150A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.705A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 removed outlier: 5.632A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.816A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.656A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.532A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.979A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.362A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 960 removed outlier: 4.484A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 4.658A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.476A pdb=" N ILE A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 987' Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.703A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.941A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.349A 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 1229 through 1235 removed outlier: 5.859A pdb=" N GLN A1233 " --> pdb=" O ILE A1229 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A1235 " --> pdb=" O GLY A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1229 through 1235' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.560A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 4.972A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1503 removed outlier: 4.406A pdb=" N ASN A1502 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1498 through 1503' Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.730A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1647 removed outlier: 4.529A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1666 removed outlier: 3.659A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.844A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.922A 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 removed outlier: 3.502A pdb=" N HIS A1710 " --> pdb=" O LEU A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.793A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 5.776A pdb=" N THR A1737 " --> pdb=" O THR A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 3.709A pdb=" N SER A1803 " --> pdb=" O VAL A1799 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A1805 " --> pdb=" O GLU A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1848 Proline residue: A1848 - end of helix Processing helix chain 'A' and resid 1899 through 1948 removed outlier: 4.266A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1959 removed outlier: 4.573A pdb=" N LEU A1957 " --> pdb=" O MET A1953 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A1959 " --> pdb=" O ALA A1955 " (cutoff:3.500A) Processing helix chain 'A' and resid 1960 through 1967 removed outlier: 4.159A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 removed outlier: 4.115A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.897A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.672A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.735A 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: 3.738A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.526A 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: 3.571A pdb=" N VAL A2178 " --> pdb=" O VAL A2174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.525A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.618A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.552A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.853A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (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 2377 through 2382 removed outlier: 5.607A pdb=" N ILE A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 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: 5.733A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.836A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2503 removed outlier: 3.768A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2504 through 2510 removed outlier: 4.740A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) Processing helix chain 'A' and resid 2511 through 2532 removed outlier: 5.513A 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: 3.878A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2581 removed outlier: 5.365A pdb=" N ARG A2581 " --> pdb=" O CYS A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2582 through 2596 removed outlier: 4.165A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.614A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.296A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 3.924A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) removed outlier: 3.928A 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: 4.516A pdb=" N GLU A2718 " --> pdb=" O PRO A2714 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 4.159A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix removed outlier: 3.949A pdb=" N MET A2782 " --> pdb=" O SER A2778 " (cutoff:3.500A) 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: 5.369A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.615A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2921 removed outlier: 4.498A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.813A 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 2948 removed outlier: 4.148A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2955 through 2979 removed outlier: 4.533A pdb=" N GLU A2959 " --> pdb=" O PRO A2955 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix removed outlier: 3.554A pdb=" N ARG A2979 " --> pdb=" O PHE A2975 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3017 removed outlier: 3.546A pdb=" N ARG A3016 " --> pdb=" O GLY A3012 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS A3017 " --> pdb=" O VAL A3013 " (cutoff:3.500A) Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.840A 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 3042 through 3047 Processing helix chain 'A' and resid 3050 through 3079 removed outlier: 3.681A pdb=" N GLN A3079 " --> pdb=" O LEU A3075 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.520A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3118 through 3123 removed outlier: 4.684A pdb=" N LEU A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3144 removed outlier: 6.206A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS A3144 " --> pdb=" O LEU A3140 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 Processing helix chain 'A' and resid 3153 through 3164 Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 4.096A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3188 Processing helix chain 'A' and resid 3189 through 3195 Processing helix chain 'A' and resid 3200 through 3206 Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 removed outlier: 3.648A pdb=" N ILE A3218 " --> pdb=" O LEU A3214 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 3.924A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3253 removed outlier: 5.124A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 3.666A pdb=" N TYR A3245 " --> pdb=" O MET A3241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A3247 " --> pdb=" O CYS A3243 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A3248 " --> pdb=" O SER A3244 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A3252 " --> pdb=" O ARG A3248 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 4.407A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.246A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 4.879A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3319 removed outlier: 5.407A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3329 removed outlier: 4.276A pdb=" N GLU A3324 " --> pdb=" O LEU A3320 " (cutoff:3.500A) Processing helix chain 'A' and resid 3586 through 3606 removed outlier: 3.890A pdb=" N GLN A3594 " --> pdb=" O LEU A3590 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3612 through 3628 Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.490A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.777A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 4.171A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.851A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.744A pdb=" N ILE A3744 " --> pdb=" O VAL A3740 " (cutoff:3.500A) removed outlier: 3.943A 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: 4.866A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.776A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.619A 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 3938 Processing helix chain 'A' and resid 3939 through 3958 removed outlier: 3.707A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) 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: 3.765A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.282A 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: 5.072A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 Proline residue: A4090 - end of helix Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4184 through 4209 removed outlier: 5.511A pdb=" N SER A4209 " --> pdb=" O GLN A4205 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4258 removed outlier: 4.139A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4274 removed outlier: 3.933A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A4273 " --> pdb=" O LYS A4269 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.721A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.341A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 4.191A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 3.987A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 4.016A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4701 removed outlier: 3.777A pdb=" N ILE A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.802A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.689A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4761 removed outlier: 4.068A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 5.214A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.711A 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: 4.092A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.038A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.144A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4929 removed outlier: 5.397A pdb=" N ASP A4929 " --> pdb=" O LEU A4925 " (cutoff:3.500A) Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 857 through 862 removed outlier: 3.597A pdb=" N ALA A 861 " --> pdb=" O THR A 858 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 4.370A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.978A 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 253 through 259 removed outlier: 4.426A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.711A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.645A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.921A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.830A pdb=" N VAL B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.712A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.663A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.150A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.705A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 removed outlier: 5.632A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.816A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.655A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.532A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 875 through 901 removed outlier: 4.980A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.361A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 960 removed outlier: 4.484A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 4.658A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.477A pdb=" N ILE B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 982 through 987' Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 4.704A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.941A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.348A 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 1229 through 1235 removed outlier: 5.859A pdb=" N GLN B1233 " --> pdb=" O ILE B1229 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B1235 " --> pdb=" O GLY B1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1229 through 1235' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.560A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 4.973A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1503 removed outlier: 4.406A pdb=" N ASN B1502 " --> pdb=" O GLN B1498 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1498 through 1503' Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.729A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1647 removed outlier: 4.529A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) Processing helix chain 'B' and resid 1648 through 1666 removed outlier: 3.660A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.844A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.922A 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 removed outlier: 3.502A pdb=" N HIS B1710 " --> pdb=" O LEU B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.793A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1737 removed outlier: 5.776A pdb=" N THR B1737 " --> pdb=" O THR B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 3.709A pdb=" N SER B1803 " --> pdb=" O VAL B1799 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS B1805 " --> pdb=" O GLU B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1848 Proline residue: B1848 - end of helix Processing helix chain 'B' and resid 1899 through 1948 removed outlier: 4.266A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1959 removed outlier: 4.574A pdb=" N LEU B1957 " --> pdb=" O MET B1953 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B1959 " --> pdb=" O ALA B1955 " (cutoff:3.500A) Processing helix chain 'B' and resid 1960 through 1967 removed outlier: 4.160A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 removed outlier: 4.115A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.898A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.673A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.735A 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: 3.738A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.526A 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: 3.571A pdb=" N VAL B2178 " --> pdb=" O VAL B2174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.525A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.619A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.552A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.853A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (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 2377 through 2382 removed outlier: 5.608A pdb=" N ILE B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 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: 5.733A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.836A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2503 removed outlier: 3.768A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2504 through 2510 removed outlier: 4.740A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) Processing helix chain 'B' and resid 2511 through 2532 removed outlier: 5.512A 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: 3.879A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2581 removed outlier: 5.366A pdb=" N ARG B2581 " --> pdb=" O CYS B2577 " (cutoff:3.500A) Processing helix chain 'B' and resid 2582 through 2596 removed outlier: 4.165A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.613A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.297A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2658 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 3.924A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) removed outlier: 3.929A 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: 4.515A pdb=" N GLU B2718 " --> pdb=" O PRO B2714 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B2719 " --> pdb=" O GLU B2715 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 4.159A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix removed outlier: 3.949A pdb=" N MET B2782 " --> pdb=" O SER B2778 " (cutoff:3.500A) 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: 5.368A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.615A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2921 removed outlier: 4.497A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.814A 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 2948 removed outlier: 4.148A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) Processing helix chain 'B' and resid 2955 through 2979 removed outlier: 4.532A pdb=" N GLU B2959 " --> pdb=" O PRO B2955 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix removed outlier: 3.554A pdb=" N ARG B2979 " --> pdb=" O PHE B2975 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3017 removed outlier: 3.546A pdb=" N ARG B3016 " --> pdb=" O GLY B3012 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N HIS B3017 " --> pdb=" O VAL B3013 " (cutoff:3.500A) Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.841A 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 3042 through 3047 Processing helix chain 'B' and resid 3050 through 3079 removed outlier: 3.682A pdb=" N GLN B3079 " --> pdb=" O LEU B3075 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.520A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3118 through 3123 removed outlier: 4.683A pdb=" N LEU B3123 " --> pdb=" O GLU B3119 " (cutoff:3.500A) Processing helix chain 'B' and resid 3124 through 3144 removed outlier: 6.205A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS B3144 " --> pdb=" O LEU B3140 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 Processing helix chain 'B' and resid 3153 through 3164 Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 4.096A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3182 through 3188 Processing helix chain 'B' and resid 3189 through 3195 Processing helix chain 'B' and resid 3200 through 3206 Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 removed outlier: 3.649A pdb=" N ILE B3218 " --> pdb=" O LEU B3214 " (cutoff:3.500A) Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 3.924A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3253 removed outlier: 5.125A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 3.666A pdb=" N TYR B3245 " --> pdb=" O MET B3241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B3247 " --> pdb=" O CYS B3243 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B3248 " --> pdb=" O SER B3244 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B3252 " --> pdb=" O ARG B3248 " (cutoff:3.500A) Processing helix chain 'B' and resid 3269 through 3289 removed outlier: 4.408A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.246A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 4.879A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3319 removed outlier: 5.407A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) Processing helix chain 'B' and resid 3320 through 3329 removed outlier: 4.276A pdb=" N GLU B3324 " --> pdb=" O LEU B3320 " (cutoff:3.500A) Processing helix chain 'B' and resid 3586 through 3606 removed outlier: 3.889A pdb=" N GLN B3594 " --> pdb=" O LEU B3590 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3612 through 3628 Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.489A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.777A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 4.171A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.850A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.744A pdb=" N ILE B3744 " --> pdb=" O VAL B3740 " (cutoff:3.500A) removed outlier: 3.943A 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: 4.866A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.776A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.620A 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 3938 Processing helix chain 'B' and resid 3939 through 3958 removed outlier: 3.707A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) 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: 3.764A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.282A 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: 5.072A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 Proline residue: B4090 - end of helix Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4184 through 4209 removed outlier: 5.511A pdb=" N SER B4209 " --> pdb=" O GLN B4205 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4258 removed outlier: 4.139A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4274 removed outlier: 3.933A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS B4273 " --> pdb=" O LYS B4269 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.721A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.341A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 4.190A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 3.988A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.886A 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 4657 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 4.016A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4701 removed outlier: 3.778A pdb=" N ILE B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) Processing helix chain 'B' and resid 4702 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.801A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.689A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4761 removed outlier: 4.068A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 5.214A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.712A 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: 4.091A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.038A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.144A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4929 removed outlier: 5.397A pdb=" N ASP B4929 " --> pdb=" O LEU B4925 " (cutoff:3.500A) Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 857 through 862 removed outlier: 3.597A pdb=" N ALA B 861 " --> pdb=" O THR B 858 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 862 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 4.371A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.979A 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 253 through 259 removed outlier: 4.428A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.712A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.645A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.921A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.831A pdb=" N VAL C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.711A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.664A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.150A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 removed outlier: 3.705A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 removed outlier: 5.632A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.815A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.657A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.532A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.980A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.361A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 960 removed outlier: 4.485A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 4.658A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 4.477A pdb=" N ILE C 986 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 987' Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 4.704A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.941A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.349A 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 1229 through 1235 removed outlier: 5.859A pdb=" N GLN C1233 " --> pdb=" O ILE C1229 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C1235 " --> pdb=" O GLY C1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1229 through 1235' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.560A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 4.972A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1498 through 1503 removed outlier: 4.406A pdb=" N ASN C1502 " --> pdb=" O GLN C1498 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1498 through 1503' Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.730A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1647 removed outlier: 4.529A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) Processing helix chain 'C' and resid 1648 through 1666 removed outlier: 3.659A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.844A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.923A 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 removed outlier: 3.502A pdb=" N HIS C1710 " --> pdb=" O LEU C1706 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.793A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1737 removed outlier: 5.776A pdb=" N THR C1737 " --> pdb=" O THR C1733 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 3.709A pdb=" N SER C1803 " --> pdb=" O VAL C1799 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C1805 " --> pdb=" O GLU C1801 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1848 Proline residue: C1848 - end of helix Processing helix chain 'C' and resid 1899 through 1948 removed outlier: 4.266A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1959 removed outlier: 4.573A pdb=" N LEU C1957 " --> pdb=" O MET C1953 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA C1959 " --> pdb=" O ALA C1955 " (cutoff:3.500A) Processing helix chain 'C' and resid 1960 through 1967 removed outlier: 4.160A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 removed outlier: 4.114A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.898A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.672A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.735A 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: 3.738A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.526A 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: 3.571A pdb=" N VAL C2178 " --> pdb=" O VAL C2174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.524A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.619A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.553A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.853A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (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 2377 through 2382 removed outlier: 5.608A pdb=" N ILE C2382 " --> pdb=" O GLU C2378 " (cutoff:3.500A) Processing helix chain 'C' and resid 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 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: 5.733A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.836A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2503 removed outlier: 3.768A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 2504 through 2510 removed outlier: 4.739A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) Processing helix chain 'C' and resid 2511 through 2532 removed outlier: 5.513A 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: 3.877A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2581 removed outlier: 5.365A pdb=" N ARG C2581 " --> pdb=" O CYS C2577 " (cutoff:3.500A) Processing helix chain 'C' and resid 2582 through 2596 removed outlier: 4.165A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.614A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.295A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2658 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 3.924A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) removed outlier: 3.928A 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: 4.516A pdb=" N GLU C2718 " --> pdb=" O PRO C2714 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR C2719 " --> pdb=" O GLU C2715 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 4.159A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix removed outlier: 3.949A pdb=" N MET C2782 " --> pdb=" O SER C2778 " (cutoff:3.500A) 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: 5.368A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.616A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2921 removed outlier: 4.497A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.813A 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 2948 removed outlier: 4.148A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) Processing helix chain 'C' and resid 2955 through 2979 removed outlier: 4.532A pdb=" N GLU C2959 " --> pdb=" O PRO C2955 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix removed outlier: 3.554A pdb=" N ARG C2979 " --> pdb=" O PHE C2975 " (cutoff:3.500A) Processing helix chain 'C' and resid 2997 through 3017 removed outlier: 3.546A pdb=" N ARG C3016 " --> pdb=" O GLY C3012 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS C3017 " --> pdb=" O VAL C3013 " (cutoff:3.500A) Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.841A 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 3042 through 3047 Processing helix chain 'C' and resid 3050 through 3079 removed outlier: 3.681A pdb=" N GLN C3079 " --> pdb=" O LEU C3075 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.519A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3118 through 3123 removed outlier: 4.683A pdb=" N LEU C3123 " --> pdb=" O GLU C3119 " (cutoff:3.500A) Processing helix chain 'C' and resid 3124 through 3144 removed outlier: 6.206A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS C3144 " --> pdb=" O LEU C3140 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 Processing helix chain 'C' and resid 3153 through 3164 Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 4.096A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3182 through 3188 Processing helix chain 'C' and resid 3189 through 3195 Processing helix chain 'C' and resid 3200 through 3206 Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 removed outlier: 3.648A pdb=" N ILE C3218 " --> pdb=" O LEU C3214 " (cutoff:3.500A) Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 3.925A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3253 removed outlier: 5.125A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 3.666A pdb=" N TYR C3245 " --> pdb=" O MET C3241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C3247 " --> pdb=" O CYS C3243 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C3248 " --> pdb=" O SER C3244 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C3252 " --> pdb=" O ARG C3248 " (cutoff:3.500A) Processing helix chain 'C' and resid 3269 through 3289 removed outlier: 4.407A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.246A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 4.880A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3319 removed outlier: 5.407A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) Processing helix chain 'C' and resid 3320 through 3329 removed outlier: 4.276A pdb=" N GLU C3324 " --> pdb=" O LEU C3320 " (cutoff:3.500A) Processing helix chain 'C' and resid 3586 through 3606 removed outlier: 3.890A pdb=" N GLN C3594 " --> pdb=" O LEU C3590 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3612 through 3628 Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.490A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.777A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 4.172A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.851A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.744A pdb=" N ILE C3744 " --> pdb=" O VAL C3740 " (cutoff:3.500A) removed outlier: 3.943A 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: 4.866A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.775A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.620A 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 3938 Processing helix chain 'C' and resid 3939 through 3958 removed outlier: 3.707A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) 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: 3.764A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.281A 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: 5.072A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 Proline residue: C4090 - end of helix Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4184 through 4209 removed outlier: 5.511A pdb=" N SER C4209 " --> pdb=" O GLN C4205 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4258 removed outlier: 4.140A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4274 removed outlier: 3.932A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS C4273 " --> pdb=" O LYS C4269 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.720A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.341A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 4.191A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 3.987A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.886A 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 4657 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 4.016A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4701 removed outlier: 3.777A pdb=" N ILE C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) Processing helix chain 'C' and resid 4702 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.802A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.690A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4761 removed outlier: 4.068A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 5.214A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.711A 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: 4.092A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.038A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.145A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4929 removed outlier: 5.398A pdb=" N ASP C4929 " --> pdb=" O LEU C4925 " (cutoff:3.500A) Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 857 through 862 removed outlier: 3.597A pdb=" N ALA C 861 " --> pdb=" O THR C 858 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 862 " --> pdb=" O GLN C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 4.370A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.978A 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 253 through 259 removed outlier: 4.428A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.711A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.645A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.921A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.831A pdb=" N VAL D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.711A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.664A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.150A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.705A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 590 removed outlier: 5.632A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.815A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.655A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.533A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.979A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.362A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 960 removed outlier: 4.484A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 4.658A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.476A pdb=" N ILE D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS D 987 " --> pdb=" O LEU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 982 through 987' Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 4.703A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.941A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.349A 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 1229 through 1235 removed outlier: 5.859A pdb=" N GLN D1233 " --> pdb=" O ILE D1229 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D1235 " --> pdb=" O GLY D1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1229 through 1235' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.560A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 4.972A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1498 through 1503 removed outlier: 4.406A pdb=" N ASN D1502 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1498 through 1503' Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.730A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1647 removed outlier: 4.529A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) Processing helix chain 'D' and resid 1648 through 1666 removed outlier: 3.660A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.843A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.922A 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 removed outlier: 3.502A pdb=" N HIS D1710 " --> pdb=" O LEU D1706 " (cutoff:3.500A) Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.793A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1737 removed outlier: 5.776A pdb=" N THR D1737 " --> pdb=" O THR D1733 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 3.709A pdb=" N SER D1803 " --> pdb=" O VAL D1799 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D1805 " --> pdb=" O GLU D1801 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1848 Proline residue: D1848 - end of helix Processing helix chain 'D' and resid 1899 through 1948 removed outlier: 4.265A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1959 removed outlier: 4.572A pdb=" N LEU D1957 " --> pdb=" O MET D1953 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR D1958 " --> pdb=" O SER D1954 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D1959 " --> pdb=" O ALA D1955 " (cutoff:3.500A) Processing helix chain 'D' and resid 1960 through 1967 removed outlier: 4.159A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 removed outlier: 4.115A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.897A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.672A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.735A 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: 3.738A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.527A 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: 3.570A pdb=" N VAL D2178 " --> pdb=" O VAL D2174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.525A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.618A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.553A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.852A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (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 2377 through 2382 removed outlier: 5.608A pdb=" N ILE D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) Processing helix chain 'D' and resid 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 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: 5.733A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.836A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2503 removed outlier: 3.768A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2504 through 2510 removed outlier: 4.739A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) Processing helix chain 'D' and resid 2511 through 2532 removed outlier: 5.513A 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: 3.878A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2581 removed outlier: 5.365A pdb=" N ARG D2581 " --> pdb=" O CYS D2577 " (cutoff:3.500A) Processing helix chain 'D' and resid 2582 through 2596 removed outlier: 4.165A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.614A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.297A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2658 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 3.925A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) removed outlier: 3.928A 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: 4.516A pdb=" N GLU D2718 " --> pdb=" O PRO D2714 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR D2719 " --> pdb=" O GLU D2715 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 4.159A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix removed outlier: 3.949A pdb=" N MET D2782 " --> pdb=" O SER D2778 " (cutoff:3.500A) 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: 5.369A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.616A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2921 removed outlier: 4.498A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.814A 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 2948 removed outlier: 4.147A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) Processing helix chain 'D' and resid 2955 through 2979 removed outlier: 4.532A pdb=" N GLU D2959 " --> pdb=" O PRO D2955 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix removed outlier: 3.555A pdb=" N ARG D2979 " --> pdb=" O PHE D2975 " (cutoff:3.500A) Processing helix chain 'D' and resid 2997 through 3017 removed outlier: 3.545A pdb=" N ARG D3016 " --> pdb=" O GLY D3012 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N HIS D3017 " --> pdb=" O VAL D3013 " (cutoff:3.500A) Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.840A 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 3042 through 3047 Processing helix chain 'D' and resid 3050 through 3079 removed outlier: 3.681A pdb=" N GLN D3079 " --> pdb=" O LEU D3075 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.520A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3118 through 3123 removed outlier: 4.684A pdb=" N LEU D3123 " --> pdb=" O GLU D3119 " (cutoff:3.500A) Processing helix chain 'D' and resid 3124 through 3144 removed outlier: 6.205A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS D3144 " --> pdb=" O LEU D3140 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 Processing helix chain 'D' and resid 3153 through 3164 Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 4.096A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3182 through 3188 Processing helix chain 'D' and resid 3189 through 3195 Processing helix chain 'D' and resid 3200 through 3206 Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 removed outlier: 3.648A pdb=" N ILE D3218 " --> pdb=" O LEU D3214 " (cutoff:3.500A) Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 3.925A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3253 removed outlier: 5.124A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 3.666A pdb=" N TYR D3245 " --> pdb=" O MET D3241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D3247 " --> pdb=" O CYS D3243 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG D3248 " --> pdb=" O SER D3244 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS D3252 " --> pdb=" O ARG D3248 " (cutoff:3.500A) Processing helix chain 'D' and resid 3269 through 3289 removed outlier: 4.407A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.246A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 4.879A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3319 removed outlier: 5.407A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) Processing helix chain 'D' and resid 3320 through 3329 removed outlier: 4.275A pdb=" N GLU D3324 " --> pdb=" O LEU D3320 " (cutoff:3.500A) Processing helix chain 'D' and resid 3586 through 3606 removed outlier: 3.890A pdb=" N GLN D3594 " --> pdb=" O LEU D3590 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3612 through 3628 Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.489A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.777A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 4.171A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.851A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.744A pdb=" N ILE D3744 " --> pdb=" O VAL D3740 " (cutoff:3.500A) removed outlier: 3.943A 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: 4.866A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.776A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.619A 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 3938 Processing helix chain 'D' and resid 3939 through 3958 removed outlier: 3.707A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) 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: 3.764A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.282A 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: 5.071A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 Proline residue: D4090 - end of helix Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4184 through 4209 removed outlier: 5.511A pdb=" N SER D4209 " --> pdb=" O GLN D4205 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4258 removed outlier: 4.139A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4274 removed outlier: 3.933A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS D4273 " --> pdb=" O LYS D4269 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.721A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.341A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 4.191A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 3.987A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 4.015A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4701 removed outlier: 3.777A pdb=" N ILE D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) Processing helix chain 'D' and resid 4702 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.801A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.690A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4761 removed outlier: 4.068A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 5.214A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.711A 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: 4.092A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.039A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.145A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4929 removed outlier: 5.397A pdb=" N ASP D4929 " --> pdb=" O LEU D4925 " (cutoff:3.500A) Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 857 through 862 removed outlier: 3.597A pdb=" N ALA D 861 " --> pdb=" O THR D 858 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE D 862 " --> pdb=" O GLN D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 4.370A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.859A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 4.784A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.088A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.860A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 4.784A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.087A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.860A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 4.784A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.087A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.860A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 4.784A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.087A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 22 removed outlier: 3.588A pdb=" N PHE I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS I 22 " --> pdb=" O SER I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 41 removed outlier: 3.904A pdb=" N VAL I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 57 removed outlier: 3.612A pdb=" N VAL I 56 " --> pdb=" O MET I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 removed outlier: 4.914A pdb=" N MET I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 95 removed outlier: 4.194A pdb=" N LYS I 95 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 114 removed outlier: 3.778A pdb=" N ARG I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HIS I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR I 111 " --> pdb=" O ARG I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 130 removed outlier: 3.809A pdb=" N GLU I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 Processing helix chain 'J' and resid 6 through 22 removed outlier: 3.588A pdb=" N PHE J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.904A pdb=" N VAL J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 57 removed outlier: 3.612A pdb=" N VAL J 56 " --> pdb=" O MET J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 77 removed outlier: 4.914A pdb=" N MET J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 95 removed outlier: 4.193A pdb=" N LYS J 95 " --> pdb=" O ARG J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 114 removed outlier: 3.778A pdb=" N ARG J 107 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HIS J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR J 111 " --> pdb=" O ARG J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 removed outlier: 3.809A pdb=" N GLU J 128 " --> pdb=" O GLU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 146 Processing helix chain 'L' and resid 6 through 22 removed outlier: 3.588A pdb=" N PHE L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS L 22 " --> pdb=" O SER L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 41 removed outlier: 3.904A pdb=" N VAL L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 57 removed outlier: 3.613A pdb=" N VAL L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 4.914A pdb=" N MET L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 95 removed outlier: 4.193A pdb=" N LYS L 95 " --> pdb=" O ARG L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 114 removed outlier: 3.778A pdb=" N ARG L 107 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 130 removed outlier: 3.809A pdb=" N GLU L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 146 Processing helix chain 'K' and resid 6 through 22 removed outlier: 3.588A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 41 removed outlier: 3.904A pdb=" N VAL K 36 " --> pdb=" O GLU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 removed outlier: 3.612A pdb=" N VAL K 56 " --> pdb=" O MET K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 77 removed outlier: 4.914A pdb=" N MET K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 95 removed outlier: 4.194A pdb=" N LYS K 95 " --> pdb=" O ARG K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 114 removed outlier: 3.778A pdb=" N ARG K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HIS K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR K 111 " --> pdb=" O ARG K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 130 removed outlier: 3.809A pdb=" N GLU K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 146 Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.359A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.269A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.577A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.747A pdb=" N HIS A 202 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 243 through 247 Processing sheet with id= 5, first strand: chain 'A' and resid 295 through 299 removed outlier: 4.023A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 7, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 8, first strand: chain 'A' and resid 737 through 740 removed outlier: 5.535A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.810A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 11, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.433A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 3.534A pdb=" N GLY A1019 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 4.260A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.812A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A1433 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.778A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 3.597A pdb=" N THR A2444 " --> pdb=" O VAL A2452 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2741 through 2744 removed outlier: 3.517A pdb=" N GLY A2744 " --> pdb=" O GLN A2754 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2787 through 2791 Processing sheet with id= 19, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.826A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 21, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.359A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.269A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.577A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.747A pdb=" N HIS B 202 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 243 through 247 Processing sheet with id= 25, first strand: chain 'B' and resid 295 through 299 removed outlier: 4.023A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 27, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 28, first strand: chain 'B' and resid 737 through 740 removed outlier: 5.535A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.810A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 31, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.433A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 3.534A pdb=" N GLY B1019 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 4.261A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.812A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B1433 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.777A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 3.597A pdb=" N THR B2444 " --> pdb=" O VAL B2452 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 2741 through 2744 removed outlier: 3.517A pdb=" N GLY B2744 " --> pdb=" O GLN B2754 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 2787 through 2791 Processing sheet with id= 39, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.826A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 41, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.358A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.270A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.576A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.747A pdb=" N HIS C 202 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 243 through 247 Processing sheet with id= 45, first strand: chain 'C' and resid 295 through 299 removed outlier: 4.023A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 47, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 48, first strand: chain 'C' and resid 737 through 740 removed outlier: 5.535A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.810A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 51, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.433A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 3.534A pdb=" N GLY C1019 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 4.260A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.812A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C1433 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.777A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 3.598A pdb=" N THR C2444 " --> pdb=" O VAL C2452 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 2741 through 2744 removed outlier: 3.517A pdb=" N GLY C2744 " --> pdb=" O GLN C2754 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 2787 through 2791 Processing sheet with id= 59, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.825A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 61, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.359A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.270A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.577A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 193 through 196 removed outlier: 3.746A pdb=" N HIS D 202 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 243 through 247 Processing sheet with id= 65, first strand: chain 'D' and resid 295 through 299 removed outlier: 4.023A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 67, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 68, first strand: chain 'D' and resid 737 through 740 removed outlier: 5.535A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.811A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 71, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.433A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 3.534A pdb=" N GLY D1019 " --> pdb=" O ASN D1029 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 4.261A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.812A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D1433 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.778A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 3.597A pdb=" N THR D2444 " --> pdb=" O VAL D2452 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 2741 through 2744 removed outlier: 3.517A pdb=" N GLY D2744 " --> pdb=" O GLN D2754 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 2787 through 2791 Processing sheet with id= 79, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.826A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 81, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.892A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.892A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.893A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.892A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 7656 hydrogen bonds defined for protein. 22828 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: 114.86 Time building geometry restraints manager: 47.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 24425 1.32 - 1.45: 40497 1.45 - 1.59: 80010 1.59 - 1.72: 52 1.72 - 1.85: 1584 Bond restraints: 146568 Sorted by residual: bond pdb=" CA SER D3244 " pdb=" C SER D3244 " ideal model delta sigma weight residual 1.523 1.682 -0.159 1.34e-02 5.57e+03 1.40e+02 bond pdb=" CA SER A3244 " pdb=" C SER A3244 " ideal model delta sigma weight residual 1.523 1.681 -0.158 1.34e-02 5.57e+03 1.39e+02 bond pdb=" CA SER C3244 " pdb=" C SER C3244 " ideal model delta sigma weight residual 1.523 1.681 -0.158 1.34e-02 5.57e+03 1.39e+02 bond pdb=" CA SER B3244 " pdb=" C SER B3244 " ideal model delta sigma weight residual 1.523 1.681 -0.158 1.34e-02 5.57e+03 1.39e+02 bond pdb=" CA GLY B3164 " pdb=" C GLY B3164 " ideal model delta sigma weight residual 1.514 1.659 -0.145 1.41e-02 5.03e+03 1.05e+02 ... (remaining 146563 not shown) Histogram of bond angle deviations from ideal: 93.40 - 103.57: 1943 103.57 - 113.74: 82437 113.74 - 123.91: 110095 123.91 - 134.08: 3453 134.08 - 144.26: 44 Bond angle restraints: 197972 Sorted by residual: angle pdb=" C SER D3247 " pdb=" N ARG D3248 " pdb=" CA ARG D3248 " ideal model delta sigma weight residual 120.28 100.28 20.00 1.34e+00 5.57e-01 2.23e+02 angle pdb=" C SER A3247 " pdb=" N ARG A3248 " pdb=" CA ARG A3248 " ideal model delta sigma weight residual 120.28 100.30 19.98 1.34e+00 5.57e-01 2.22e+02 angle pdb=" C SER B3247 " pdb=" N ARG B3248 " pdb=" CA ARG B3248 " ideal model delta sigma weight residual 120.28 100.31 19.97 1.34e+00 5.57e-01 2.22e+02 angle pdb=" C SER C3247 " pdb=" N ARG C3248 " pdb=" CA ARG C3248 " ideal model delta sigma weight residual 120.28 100.33 19.95 1.34e+00 5.57e-01 2.22e+02 angle pdb=" O SER B3244 " pdb=" C SER B3244 " pdb=" N TYR B3245 " ideal model delta sigma weight residual 122.25 108.10 14.15 1.19e+00 7.06e-01 1.41e+02 ... (remaining 197967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 78928 17.61 - 35.23: 7552 35.23 - 52.84: 1327 52.84 - 70.45: 453 70.45 - 88.07: 176 Dihedral angle restraints: 88436 sinusoidal: 36348 harmonic: 52088 Sorted by residual: dihedral pdb=" CA PHE D4640 " pdb=" C PHE D4640 " pdb=" N PRO D4641 " pdb=" CA PRO D4641 " ideal model delta harmonic sigma weight residual -180.00 -133.21 -46.79 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual -180.00 -133.23 -46.77 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CA PHE C4640 " pdb=" C PHE C4640 " pdb=" N PRO C4641 " pdb=" CA PRO C4641 " ideal model delta harmonic sigma weight residual 180.00 -133.23 -46.77 0 5.00e+00 4.00e-02 8.75e+01 ... (remaining 88433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 20347 0.088 - 0.177: 1234 0.177 - 0.265: 91 0.265 - 0.354: 8 0.354 - 0.442: 8 Chirality restraints: 21688 Sorted by residual: chirality pdb=" CA SER D3244 " pdb=" N SER D3244 " pdb=" C SER D3244 " pdb=" CB SER D3244 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA SER C3244 " pdb=" N SER C3244 " pdb=" C SER C3244 " pdb=" CB SER C3244 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA SER B3244 " pdb=" N SER B3244 " pdb=" C SER B3244 " pdb=" CB SER B3244 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 21685 not shown) Planarity restraints: 25472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B3058 " 1.032 9.50e-02 1.11e+02 4.63e-01 1.30e+02 pdb=" NE ARG B3058 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B3058 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B3058 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B3058 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C3058 " 1.032 9.50e-02 1.11e+02 4.63e-01 1.30e+02 pdb=" NE ARG C3058 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C3058 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C3058 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C3058 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D3058 " 1.032 9.50e-02 1.11e+02 4.63e-01 1.29e+02 pdb=" NE ARG D3058 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG D3058 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D3058 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D3058 " 0.015 2.00e-02 2.50e+03 ... (remaining 25469 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 171 2.28 - 2.94: 61244 2.94 - 3.59: 227617 3.59 - 4.25: 346206 4.25 - 4.90: 574488 Nonbonded interactions: 1209726 Sorted by model distance: nonbonded pdb=" N ALA B3165 " pdb=" O SER B3244 " model vdw 1.627 2.520 nonbonded pdb=" N ALA C3165 " pdb=" O SER C3244 " model vdw 1.627 2.520 nonbonded pdb=" N ALA A3165 " pdb=" O SER A3244 " model vdw 1.627 2.520 nonbonded pdb=" N ALA D3165 " pdb=" O SER D3244 " model vdw 1.628 2.520 nonbonded pdb=" OD1 ASP I 130 " pdb="CA CA I 204 " model vdw 1.714 2.510 ... (remaining 1209721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 30.500 Check model and map are aligned: 1.580 Set scattering table: 0.960 Process input model: 478.880 Find NCS groups from input model: 8.610 Set up NCS constraints: 1.300 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: 0.030 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 531.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 146568 Z= 0.273 Angle : 0.889 31.556 197972 Z= 0.491 Chirality : 0.045 0.442 21688 Planarity : 0.010 0.463 25472 Dihedral : 14.915 88.068 54840 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 1.53 % Allowed : 1.06 % Favored : 97.42 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.06), residues: 17808 helix: 1.29 (0.05), residues: 9428 sheet: -0.02 (0.13), residues: 1636 loop : -0.44 (0.07), residues: 6744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP C 893 HIS 0.016 0.001 HIS C3034 PHE 0.060 0.002 PHE D4640 TYR 0.055 0.002 TYR A3138 ARG 0.025 0.001 ARG B3298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 881 time to evaluate : 12.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8883 (tp) REVERT: A 935 MET cc_start: 0.9243 (ptp) cc_final: 0.8934 (ppp) REVERT: A 946 LEU cc_start: 0.8953 (mt) cc_final: 0.8334 (tt) REVERT: A 1044 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8830 (tppt) REVERT: A 1165 MET cc_start: 0.8611 (mtp) cc_final: 0.8293 (mtt) REVERT: A 2192 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8627 (tpt) REVERT: A 2347 MET cc_start: 0.8786 (mmm) cc_final: 0.8496 (mmt) REVERT: A 2688 MET cc_start: 0.5171 (tmm) cc_final: 0.4730 (tmm) REVERT: A 2757 MET cc_start: 0.8146 (mmp) cc_final: 0.6868 (mmm) REVERT: A 3235 MET cc_start: 0.8670 (pmm) cc_final: 0.8403 (pmm) REVERT: A 3302 PHE cc_start: 0.8666 (t80) cc_final: 0.8453 (t80) REVERT: A 4046 ARG cc_start: 0.9166 (tpm170) cc_final: 0.8868 (tpp-160) REVERT: A 4052 MET cc_start: 0.8206 (mtp) cc_final: 0.7978 (mtp) REVERT: A 4943 MET cc_start: 0.8981 (mtp) cc_final: 0.8727 (ttp) REVERT: E 19 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8852 (tppt) REVERT: E 54 GLN cc_start: 0.8984 (mp10) cc_final: 0.8642 (mp10) REVERT: E 58 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8022 (ptpp) REVERT: E 62 GLU cc_start: 0.7977 (mp0) cc_final: 0.7773 (pm20) REVERT: F 19 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8742 (tppt) REVERT: F 54 GLN cc_start: 0.8892 (mp10) cc_final: 0.8595 (mp10) REVERT: F 67 MET cc_start: 0.9127 (ttp) cc_final: 0.8907 (mtp) REVERT: G 54 GLN cc_start: 0.9056 (mp10) cc_final: 0.8689 (mp10) REVERT: G 58 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8233 (ptpp) REVERT: H 54 GLN cc_start: 0.9117 (mp10) cc_final: 0.8699 (mp10) REVERT: H 58 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8139 (pttm) REVERT: H 62 GLU cc_start: 0.8091 (mp0) cc_final: 0.7855 (pm20) REVERT: H 67 MET cc_start: 0.9180 (ttp) cc_final: 0.8965 (ttm) REVERT: I 9 GLN cc_start: 0.9204 (mt0) cc_final: 0.8956 (mt0) REVERT: I 14 LYS cc_start: 0.9247 (mmpt) cc_final: 0.8856 (mmmt) REVERT: I 73 MET cc_start: 0.8595 (mmp) cc_final: 0.8107 (mmm) REVERT: I 130 ASP cc_start: 0.3645 (OUTLIER) cc_final: 0.3135 (t0) REVERT: B 309 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7654 (mmp) REVERT: B 878 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8923 (tp) REVERT: B 935 MET cc_start: 0.9219 (ptp) cc_final: 0.8997 (ppp) REVERT: B 995 MET cc_start: 0.8806 (ptp) cc_final: 0.8334 (ptp) REVERT: B 2192 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8628 (tpt) REVERT: B 2732 TRP cc_start: 0.8681 (t60) cc_final: 0.8264 (t60) REVERT: B 3243 CYS cc_start: 0.8340 (m) cc_final: 0.8063 (m) REVERT: B 3302 PHE cc_start: 0.8748 (t80) cc_final: 0.8367 (t80) REVERT: B 3719 MET cc_start: 0.8557 (mmp) cc_final: 0.8322 (mmp) REVERT: B 3956 MET cc_start: 0.8305 (mmt) cc_final: 0.8055 (mmt) REVERT: B 4139 MET cc_start: 0.9063 (tpp) cc_final: 0.8767 (tpt) REVERT: B 4186 MET cc_start: 0.8751 (mmp) cc_final: 0.8519 (mmp) REVERT: B 4268 MET cc_start: 0.8360 (tpp) cc_final: 0.7867 (tpp) REVERT: B 4809 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (tpt) REVERT: C 878 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8893 (tp) REVERT: C 935 MET cc_start: 0.9246 (ptp) cc_final: 0.9028 (ppp) REVERT: C 946 LEU cc_start: 0.9015 (mt) cc_final: 0.8445 (tt) REVERT: C 981 MET cc_start: 0.7821 (ppp) cc_final: 0.7579 (ppp) REVERT: C 995 MET cc_start: 0.8817 (ptp) cc_final: 0.8601 (ptp) REVERT: C 1044 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8944 (tppt) REVERT: C 1168 MET cc_start: 0.8698 (mmm) cc_final: 0.8377 (mmm) REVERT: C 1174 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8619 (ptp) REVERT: C 2732 TRP cc_start: 0.8323 (t60) cc_final: 0.7438 (t60) REVERT: C 2757 MET cc_start: 0.8691 (mmp) cc_final: 0.8144 (mmm) REVERT: C 2782 MET cc_start: 0.9185 (ptp) cc_final: 0.8702 (ppp) REVERT: C 2783 LEU cc_start: 0.9342 (mt) cc_final: 0.8331 (mt) REVERT: C 2840 MET cc_start: 0.8968 (mmm) cc_final: 0.8721 (mmm) REVERT: C 2843 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8210 (mtm) REVERT: C 2943 PHE cc_start: 0.8119 (m-80) cc_final: 0.7735 (m-80) REVERT: C 3134 LEU cc_start: 0.9529 (tp) cc_final: 0.9183 (tt) REVERT: C 3719 MET cc_start: 0.8439 (mmp) cc_final: 0.8209 (mmp) REVERT: C 4052 MET cc_start: 0.8446 (mtp) cc_final: 0.8170 (mtp) REVERT: C 4067 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9094 (mt) REVERT: C 4268 MET cc_start: 0.8129 (tpp) cc_final: 0.7472 (tpp) REVERT: C 4728 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8834 (mmp) REVERT: C 4809 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8675 (tpt) REVERT: C 4963 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: D 393 MET cc_start: 0.7687 (tpt) cc_final: 0.7439 (tpt) REVERT: D 878 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9067 (tp) REVERT: D 949 HIS cc_start: 0.7931 (t-90) cc_final: 0.7685 (t-90) REVERT: D 981 MET cc_start: 0.7009 (ppp) cc_final: 0.6784 (ppp) REVERT: D 995 MET cc_start: 0.8467 (ptp) cc_final: 0.8226 (ptp) REVERT: D 1044 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8788 (tppt) REVERT: D 1113 MET cc_start: 0.8615 (mtm) cc_final: 0.8352 (mtp) REVERT: D 1162 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8764 (m) REVERT: D 1165 MET cc_start: 0.8150 (mtp) cc_final: 0.7566 (mtp) REVERT: D 2757 MET cc_start: 0.7075 (mmp) cc_final: 0.6584 (mmt) REVERT: D 2793 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8249 (pmt-80) REVERT: D 2943 PHE cc_start: 0.7681 (m-80) cc_final: 0.7478 (m-80) REVERT: D 3281 LEU cc_start: 0.9651 (pt) cc_final: 0.9318 (pt) REVERT: D 3302 PHE cc_start: 0.8806 (t80) cc_final: 0.8372 (t80) REVERT: D 4943 MET cc_start: 0.8815 (mtp) cc_final: 0.8503 (ttm) REVERT: J 14 LYS cc_start: 0.9252 (mmpt) cc_final: 0.8900 (mmmt) REVERT: J 37 MET cc_start: 0.9431 (mtp) cc_final: 0.9135 (mtp) REVERT: J 73 MET cc_start: 0.8673 (mmp) cc_final: 0.8039 (mmm) REVERT: J 130 ASP cc_start: 0.4450 (OUTLIER) cc_final: 0.3956 (t0) REVERT: L 9 GLN cc_start: 0.9253 (mt0) cc_final: 0.8956 (mt0) REVERT: L 14 LYS cc_start: 0.9262 (mmpt) cc_final: 0.8846 (mmmt) REVERT: L 73 MET cc_start: 0.8542 (mmp) cc_final: 0.8287 (mmm) REVERT: L 130 ASP cc_start: 0.2943 (OUTLIER) cc_final: 0.2401 (t70) REVERT: K 9 GLN cc_start: 0.9291 (mt0) cc_final: 0.9091 (mt0) REVERT: K 14 LYS cc_start: 0.9304 (mmpt) cc_final: 0.8943 (mmmt) REVERT: K 37 MET cc_start: 0.9420 (mtp) cc_final: 0.9215 (mtp) REVERT: K 73 MET cc_start: 0.8660 (mmp) cc_final: 0.8439 (mmm) REVERT: K 107 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8051 (mmt180) REVERT: K 130 ASP cc_start: 0.4711 (OUTLIER) cc_final: 0.4356 (t0) outliers start: 232 outliers final: 60 residues processed: 979 average time/residue: 1.2546 time to fit residues: 2157.8778 Evaluate side-chains 873 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 784 time to evaluate : 12.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 807 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1729 MET Chi-restraints excluded: chain A residue 1953 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2214 MET Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2844 MET Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3299 LEU Chi-restraints excluded: chain A residue 3583 LYS Chi-restraints excluded: chain A residue 3589 LYS Chi-restraints excluded: chain A residue 4728 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 807 ARG Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1953 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2214 MET Chi-restraints excluded: chain B residue 2456 MET Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 2737 LEU Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 3241 MET Chi-restraints excluded: chain B residue 3583 LYS Chi-restraints excluded: chain B residue 3589 LYS Chi-restraints excluded: chain B residue 4753 LEU Chi-restraints excluded: chain B residue 4809 MET Chi-restraints excluded: chain B residue 4884 MET Chi-restraints excluded: chain B residue 4963 GLU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 807 ARG Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1174 MET Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2214 MET Chi-restraints excluded: chain C residue 2456 MET Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 3241 MET Chi-restraints excluded: chain C residue 3583 LYS Chi-restraints excluded: chain C residue 3589 LYS Chi-restraints excluded: chain C residue 4067 LEU Chi-restraints excluded: chain C residue 4728 MET Chi-restraints excluded: chain C residue 4809 MET Chi-restraints excluded: chain C residue 4963 GLU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1953 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2214 MET Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 2793 ARG Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 3241 MET Chi-restraints excluded: chain D residue 3583 LYS Chi-restraints excluded: chain D residue 3589 LYS Chi-restraints excluded: chain D residue 4728 MET Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 5.9990 chunk 1355 optimal weight: 5.9990 chunk 751 optimal weight: 40.0000 chunk 462 optimal weight: 4.9990 chunk 914 optimal weight: 10.0000 chunk 724 optimal weight: 50.0000 chunk 1401 optimal weight: 9.9990 chunk 542 optimal weight: 10.0000 chunk 852 optimal weight: 9.9990 chunk 1043 optimal weight: 9.9990 chunk 1623 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 ASN A 992 GLN ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN A1656 HIS ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2309 ASN A2847 ASN ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS A3233 HIS ** A3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN B 888 ASN B 992 GLN ** B1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2309 ASN B2847 ASN ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS B3233 HIS ** B3313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN C 888 ASN C 992 GLN ** C1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1656 HIS ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2309 ASN C2729 HIS C2847 ASN ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2978 HIS C3233 HIS ** C3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN D 992 GLN ** D1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1126 GLN ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2309 ASN ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2978 HIS ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3233 HIS ** D3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.564 146568 Z= 0.470 Angle : 0.738 22.898 197972 Z= 0.381 Chirality : 0.045 0.389 21688 Planarity : 0.006 0.196 25472 Dihedral : 6.678 87.760 19934 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 4.04 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.06), residues: 17808 helix: 1.46 (0.05), residues: 9472 sheet: -0.21 (0.13), residues: 1688 loop : -0.41 (0.08), residues: 6648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 893 HIS 0.012 0.002 HIS A3034 PHE 0.046 0.002 PHE A4640 TYR 0.082 0.002 TYR C3245 ARG 0.022 0.001 ARG C3298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 842 time to evaluate : 10.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8058 (tpt) cc_final: 0.7762 (tpt) REVERT: A 878 LEU cc_start: 0.9408 (tp) cc_final: 0.9000 (tp) REVERT: A 2150 MET cc_start: 0.8406 (mmm) cc_final: 0.8138 (mtt) REVERT: A 2757 MET cc_start: 0.7837 (mmp) cc_final: 0.7252 (mmm) REVERT: A 2782 MET cc_start: 0.9347 (ptt) cc_final: 0.9142 (ptm) REVERT: A 2840 MET cc_start: 0.9163 (mmm) cc_final: 0.8724 (mmm) REVERT: A 2843 MET cc_start: 0.8684 (ttt) cc_final: 0.8376 (tmm) REVERT: A 3138 TYR cc_start: 0.8807 (m-80) cc_final: 0.8505 (m-80) REVERT: A 3235 MET cc_start: 0.8732 (pmm) cc_final: 0.8500 (pmm) REVERT: A 3252 HIS cc_start: 0.8965 (t-90) cc_final: 0.8543 (t-90) REVERT: A 3719 MET cc_start: 0.8213 (mmp) cc_final: 0.7969 (mmp) REVERT: A 3819 MET cc_start: 0.6804 (mtt) cc_final: 0.6601 (mmm) REVERT: A 3981 MET cc_start: 0.8856 (tmm) cc_final: 0.8138 (ttp) REVERT: A 4046 ARG cc_start: 0.9192 (tpm170) cc_final: 0.8899 (tpp-160) REVERT: A 4256 MET cc_start: 0.8700 (mtm) cc_final: 0.8418 (mtp) REVERT: A 4268 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7276 (ptt) REVERT: E 30 MET cc_start: 0.7816 (mmm) cc_final: 0.7488 (tpp) REVERT: E 54 GLN cc_start: 0.9077 (mp10) cc_final: 0.8703 (mp10) REVERT: E 58 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7792 (ptpp) REVERT: E 62 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7733 (mp0) REVERT: E 108 GLU cc_start: 0.8474 (pp20) cc_final: 0.8086 (pm20) REVERT: F 54 GLN cc_start: 0.9016 (mp10) cc_final: 0.8667 (mp10) REVERT: G 18 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8741 (mtmm) REVERT: G 53 LYS cc_start: 0.8894 (mppt) cc_final: 0.8621 (mptt) REVERT: G 54 GLN cc_start: 0.9145 (mp10) cc_final: 0.8753 (mp10) REVERT: H 14 ARG cc_start: 0.8929 (mtm110) cc_final: 0.8664 (mtm110) REVERT: H 30 MET cc_start: 0.8097 (tpp) cc_final: 0.7841 (mmm) REVERT: H 54 GLN cc_start: 0.9165 (mp10) cc_final: 0.8712 (mp10) REVERT: H 58 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.7880 (ptpp) REVERT: H 62 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7798 (mp0) REVERT: H 108 GLU cc_start: 0.8392 (pp20) cc_final: 0.8045 (pm20) REVERT: I 14 LYS cc_start: 0.9318 (mmpt) cc_final: 0.8869 (mmmm) REVERT: I 72 MET cc_start: 0.9347 (tmm) cc_final: 0.8831 (ppp) REVERT: B 309 MET cc_start: 0.8131 (mmp) cc_final: 0.7750 (mmp) REVERT: B 878 LEU cc_start: 0.9409 (tp) cc_final: 0.9079 (tp) REVERT: B 995 MET cc_start: 0.8853 (ptp) cc_final: 0.8459 (ptp) REVERT: B 1174 MET cc_start: 0.8501 (ptp) cc_final: 0.8161 (pmm) REVERT: B 1953 MET cc_start: 0.8983 (tpt) cc_final: 0.8739 (tpp) REVERT: B 2732 TRP cc_start: 0.8942 (t60) cc_final: 0.8549 (t60) REVERT: B 2757 MET cc_start: 0.8628 (mmp) cc_final: 0.7716 (mmm) REVERT: B 2782 MET cc_start: 0.9349 (ptt) cc_final: 0.9129 (ptm) REVERT: B 2840 MET cc_start: 0.9209 (mmm) cc_final: 0.9004 (mmm) REVERT: B 3243 CYS cc_start: 0.7886 (m) cc_final: 0.7122 (m) REVERT: B 3302 PHE cc_start: 0.8782 (t80) cc_final: 0.8449 (t80) REVERT: B 3719 MET cc_start: 0.8515 (mmp) cc_final: 0.8279 (mmp) REVERT: B 3819 MET cc_start: 0.6864 (mtt) cc_final: 0.6535 (mtt) REVERT: B 4080 TYR cc_start: 0.7857 (p90) cc_final: 0.7365 (p90) REVERT: B 4139 MET cc_start: 0.9143 (tpp) cc_final: 0.8928 (tpt) REVERT: B 4258 MET cc_start: 0.6370 (ttt) cc_final: 0.5874 (ptt) REVERT: B 4268 MET cc_start: 0.8225 (tpp) cc_final: 0.7906 (tpp) REVERT: C 128 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8594 (mtm) REVERT: C 878 LEU cc_start: 0.9387 (tp) cc_final: 0.8992 (tp) REVERT: C 981 MET cc_start: 0.7948 (ppp) cc_final: 0.7691 (ppp) REVERT: C 995 MET cc_start: 0.8885 (ptp) cc_final: 0.8523 (ptp) REVERT: C 1487 MET cc_start: 0.8729 (mtp) cc_final: 0.8521 (mtp) REVERT: C 2192 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8778 (tpp) REVERT: C 2585 MET cc_start: 0.8283 (mtm) cc_final: 0.8068 (mtm) REVERT: C 2732 TRP cc_start: 0.8778 (t60) cc_final: 0.8241 (t60) REVERT: C 2757 MET cc_start: 0.8258 (mmp) cc_final: 0.7767 (mmm) REVERT: C 2782 MET cc_start: 0.9254 (ptp) cc_final: 0.9037 (ptm) REVERT: C 2783 LEU cc_start: 0.9360 (mt) cc_final: 0.9111 (mt) REVERT: C 2943 PHE cc_start: 0.8309 (m-80) cc_final: 0.7718 (m-80) REVERT: C 3235 MET cc_start: 0.8706 (pmm) cc_final: 0.8060 (pmm) REVERT: C 4268 MET cc_start: 0.8177 (tpp) cc_final: 0.7600 (tpp) REVERT: D 393 MET cc_start: 0.7969 (tpt) cc_final: 0.7427 (tpt) REVERT: D 878 LEU cc_start: 0.9501 (tp) cc_final: 0.9171 (tp) REVERT: D 949 HIS cc_start: 0.8027 (t-90) cc_final: 0.7768 (t-90) REVERT: D 1113 MET cc_start: 0.8816 (mtm) cc_final: 0.8490 (mtm) REVERT: D 1165 MET cc_start: 0.8667 (mtp) cc_final: 0.8237 (mtp) REVERT: D 1168 MET cc_start: 0.8554 (mmm) cc_final: 0.8102 (mmm) REVERT: D 1953 MET cc_start: 0.8920 (tpt) cc_final: 0.8646 (tpp) REVERT: D 2192 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8708 (tpt) REVERT: D 2757 MET cc_start: 0.7307 (mmp) cc_final: 0.6720 (mmm) REVERT: D 3302 PHE cc_start: 0.8835 (t80) cc_final: 0.8548 (t80) REVERT: D 3719 MET cc_start: 0.8249 (mmp) cc_final: 0.7997 (mmp) REVERT: D 4728 MET cc_start: 0.9148 (mmm) cc_final: 0.8846 (mmt) REVERT: J 14 LYS cc_start: 0.9348 (mmpt) cc_final: 0.8911 (mmmm) REVERT: J 50 GLN cc_start: 0.9054 (mt0) cc_final: 0.8562 (mm-40) REVERT: J 72 MET cc_start: 0.9342 (tmm) cc_final: 0.8789 (ppp) REVERT: J 73 MET cc_start: 0.8930 (mmp) cc_final: 0.8723 (mmm) REVERT: J 101 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8522 (mt) REVERT: J 145 MET cc_start: 0.9288 (mmp) cc_final: 0.8187 (mmp) REVERT: L 14 LYS cc_start: 0.9353 (mmpt) cc_final: 0.8875 (mmmm) REVERT: L 72 MET cc_start: 0.9390 (tmm) cc_final: 0.8908 (ppp) REVERT: L 77 MET cc_start: 0.7277 (ppp) cc_final: 0.6755 (pmm) REVERT: L 101 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8551 (mt) REVERT: K 14 LYS cc_start: 0.9405 (mmpt) cc_final: 0.8971 (mmmm) REVERT: K 50 GLN cc_start: 0.9103 (mt0) cc_final: 0.8756 (mm110) REVERT: K 72 MET cc_start: 0.9342 (tmm) cc_final: 0.9078 (ppp) REVERT: K 73 MET cc_start: 0.8876 (mmp) cc_final: 0.8551 (mmm) REVERT: K 107 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8191 (mmt180) REVERT: K 130 ASP cc_start: 0.3994 (OUTLIER) cc_final: 0.3745 (t0) REVERT: K 145 MET cc_start: 0.9260 (mmp) cc_final: 0.7966 (mmp) outliers start: 89 outliers final: 40 residues processed: 878 average time/residue: 1.1770 time to fit residues: 1840.2591 Evaluate side-chains 839 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 789 time to evaluate : 12.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3241 MET Chi-restraints excluded: chain A residue 3583 LYS Chi-restraints excluded: chain A residue 4268 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3241 MET Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3583 LYS Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3241 MET Chi-restraints excluded: chain C residue 3583 LYS Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3326 LEU Chi-restraints excluded: chain D residue 3583 LYS Chi-restraints excluded: chain D residue 4753 LEU Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 130 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 6.9990 chunk 503 optimal weight: 10.0000 chunk 1351 optimal weight: 7.9990 chunk 1105 optimal weight: 6.9990 chunk 447 optimal weight: 5.9990 chunk 1626 optimal weight: 0.9990 chunk 1757 optimal weight: 50.0000 chunk 1448 optimal weight: 7.9990 chunk 1613 optimal weight: 30.0000 chunk 554 optimal weight: 5.9990 chunk 1304 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS A 388 GLN A1005 ASN ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2927 GLN A3252 HIS ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN B1063 ASN ** B1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2927 GLN B3252 HIS ** B3313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2927 GLN ** C3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS D 388 GLN D1005 ASN ** D1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.395 146568 Z= 0.338 Angle : 0.653 23.865 197972 Z= 0.334 Chirality : 0.042 0.310 21688 Planarity : 0.005 0.148 25472 Dihedral : 5.995 89.358 19717 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 0.70 % Allowed : 5.61 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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: 1.07 (0.06), residues: 17808 helix: 1.69 (0.05), residues: 9476 sheet: -0.31 (0.12), residues: 1736 loop : -0.38 (0.08), residues: 6596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 893 HIS 0.012 0.001 HIS A3034 PHE 0.030 0.001 PHE A4640 TYR 0.060 0.001 TYR D3245 ARG 0.009 0.001 ARG B3298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 812 time to evaluate : 12.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8010 (tpt) cc_final: 0.7473 (mmm) REVERT: A 878 LEU cc_start: 0.9392 (tp) cc_final: 0.9014 (tp) REVERT: A 935 MET cc_start: 0.8964 (ppp) cc_final: 0.8612 (ppp) REVERT: A 981 MET cc_start: 0.7838 (ppp) cc_final: 0.7318 (ppp) REVERT: A 2757 MET cc_start: 0.7733 (mmp) cc_final: 0.7311 (mmm) REVERT: A 2840 MET cc_start: 0.9161 (mmm) cc_final: 0.8782 (mmm) REVERT: A 2843 MET cc_start: 0.8494 (ttt) cc_final: 0.8095 (tmm) REVERT: A 2844 MET cc_start: 0.8823 (ppp) cc_final: 0.8610 (ppp) REVERT: A 3138 TYR cc_start: 0.8838 (m-80) cc_final: 0.8504 (m-80) REVERT: A 3162 PHE cc_start: 0.8622 (m-10) cc_final: 0.8415 (m-10) REVERT: A 3215 MET cc_start: 0.9541 (ppp) cc_final: 0.9167 (tpp) REVERT: A 3231 MET cc_start: 0.9150 (tpp) cc_final: 0.8589 (tmm) REVERT: A 3243 CYS cc_start: 0.8571 (m) cc_final: 0.8019 (m) REVERT: A 3249 TRP cc_start: 0.8078 (m-90) cc_final: 0.7836 (m-90) REVERT: A 3302 PHE cc_start: 0.8633 (t80) cc_final: 0.8362 (t80) REVERT: A 3605 MET cc_start: 0.9225 (ttm) cc_final: 0.8954 (mtm) REVERT: A 3719 MET cc_start: 0.8288 (mmp) cc_final: 0.8035 (mmp) REVERT: A 3819 MET cc_start: 0.6816 (mtt) cc_final: 0.6597 (mmm) REVERT: A 3981 MET cc_start: 0.8969 (tmm) cc_final: 0.8019 (ttp) REVERT: A 4268 MET cc_start: 0.7660 (mmp) cc_final: 0.7191 (ptm) REVERT: E 54 GLN cc_start: 0.9113 (mp10) cc_final: 0.8704 (mp10) REVERT: E 108 GLU cc_start: 0.8450 (pp20) cc_final: 0.8062 (pm20) REVERT: F 54 GLN cc_start: 0.9063 (mp10) cc_final: 0.8678 (mp10) REVERT: F 62 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: G 53 LYS cc_start: 0.8976 (mppt) cc_final: 0.8715 (mptt) REVERT: G 54 GLN cc_start: 0.9151 (mp10) cc_final: 0.8726 (mp10) REVERT: G 58 LYS cc_start: 0.8652 (ptpp) cc_final: 0.8450 (pttm) REVERT: H 53 LYS cc_start: 0.9003 (mppt) cc_final: 0.8660 (mptt) REVERT: H 54 GLN cc_start: 0.9182 (mp10) cc_final: 0.8710 (mp10) REVERT: H 108 GLU cc_start: 0.8405 (pp20) cc_final: 0.8060 (pm20) REVERT: I 31 LYS cc_start: 0.9477 (mmmt) cc_final: 0.9195 (mmmt) REVERT: I 73 MET cc_start: 0.8527 (mmm) cc_final: 0.8163 (mmm) REVERT: I 101 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8615 (mt) REVERT: I 125 MET cc_start: 0.9098 (ppp) cc_final: 0.8775 (ppp) REVERT: B 878 LEU cc_start: 0.9396 (tp) cc_final: 0.9080 (tp) REVERT: B 935 MET cc_start: 0.9010 (ppp) cc_final: 0.8666 (ppp) REVERT: B 995 MET cc_start: 0.8853 (ptp) cc_final: 0.8364 (ptp) REVERT: B 1174 MET cc_start: 0.8472 (ptp) cc_final: 0.8196 (pmm) REVERT: B 1953 MET cc_start: 0.9068 (tpt) cc_final: 0.8768 (tpp) REVERT: B 2162 MET cc_start: 0.9102 (mmp) cc_final: 0.8868 (mmp) REVERT: B 2732 TRP cc_start: 0.9061 (t60) cc_final: 0.8595 (t60) REVERT: B 2757 MET cc_start: 0.8597 (mmp) cc_final: 0.7845 (mmm) REVERT: B 2840 MET cc_start: 0.9272 (mmm) cc_final: 0.8997 (mmm) REVERT: B 3231 MET cc_start: 0.8992 (tpp) cc_final: 0.8458 (tmm) REVERT: B 3243 CYS cc_start: 0.8144 (m) cc_final: 0.7540 (m) REVERT: B 3302 PHE cc_start: 0.8692 (t80) cc_final: 0.8308 (t80) REVERT: B 3719 MET cc_start: 0.8474 (mmp) cc_final: 0.8259 (mmp) REVERT: B 4258 MET cc_start: 0.6692 (ttt) cc_final: 0.6212 (ptt) REVERT: C 128 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8607 (mtm) REVERT: C 309 MET cc_start: 0.7954 (mmp) cc_final: 0.7570 (mmt) REVERT: C 878 LEU cc_start: 0.9370 (tp) cc_final: 0.9055 (tp) REVERT: C 935 MET cc_start: 0.8980 (ppp) cc_final: 0.8695 (ppp) REVERT: C 981 MET cc_start: 0.7880 (ppp) cc_final: 0.7646 (ppp) REVERT: C 995 MET cc_start: 0.8873 (ptp) cc_final: 0.8449 (ptp) REVERT: C 2585 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8131 (mtm) REVERT: C 2732 TRP cc_start: 0.8793 (t60) cc_final: 0.8233 (t60) REVERT: C 2757 MET cc_start: 0.8395 (mmp) cc_final: 0.7972 (mmm) REVERT: C 2782 MET cc_start: 0.9266 (ptp) cc_final: 0.9061 (ptm) REVERT: C 2783 LEU cc_start: 0.9346 (mt) cc_final: 0.9086 (mt) REVERT: C 2828 MET cc_start: 0.8982 (tpp) cc_final: 0.8722 (tpp) REVERT: C 2844 MET cc_start: 0.8723 (tmm) cc_final: 0.8404 (tmm) REVERT: C 2848 TYR cc_start: 0.8043 (m-80) cc_final: 0.7833 (m-80) REVERT: C 2935 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: C 2943 PHE cc_start: 0.8332 (m-80) cc_final: 0.7757 (m-80) REVERT: C 3235 MET cc_start: 0.8654 (pmm) cc_final: 0.7997 (pmm) REVERT: C 3243 CYS cc_start: 0.8649 (m) cc_final: 0.8287 (m) REVERT: C 3263 MET cc_start: 0.9049 (mmp) cc_final: 0.8587 (mpp) REVERT: C 3819 MET cc_start: 0.6271 (mmm) cc_final: 0.6049 (mmm) REVERT: C 4268 MET cc_start: 0.8246 (tpp) cc_final: 0.7601 (tpp) REVERT: C 4274 MET cc_start: 0.5927 (ttp) cc_final: 0.5387 (tpp) REVERT: D 309 MET cc_start: 0.8397 (mmm) cc_final: 0.8095 (mmp) REVERT: D 317 MET cc_start: 0.7683 (ptt) cc_final: 0.7275 (ptt) REVERT: D 878 LEU cc_start: 0.9501 (tp) cc_final: 0.9181 (tp) REVERT: D 935 MET cc_start: 0.9115 (ppp) cc_final: 0.8709 (ppp) REVERT: D 949 HIS cc_start: 0.8025 (t-90) cc_final: 0.7768 (t-90) REVERT: D 1165 MET cc_start: 0.8667 (mtp) cc_final: 0.8457 (mtp) REVERT: D 1953 MET cc_start: 0.8955 (tpt) cc_final: 0.8660 (tpp) REVERT: D 2192 MET cc_start: 0.9050 (tpp) cc_final: 0.8838 (tpt) REVERT: D 2214 MET cc_start: 0.9307 (mmm) cc_final: 0.8917 (mmm) REVERT: D 2688 MET cc_start: 0.7805 (tmm) cc_final: 0.6736 (tmm) REVERT: D 2757 MET cc_start: 0.7072 (mmp) cc_final: 0.6852 (mmm) REVERT: D 2840 MET cc_start: 0.8760 (mmm) cc_final: 0.8547 (mmt) REVERT: D 2943 PHE cc_start: 0.7960 (m-80) cc_final: 0.7409 (m-80) REVERT: D 3263 MET cc_start: 0.8081 (mmp) cc_final: 0.7795 (mpp) REVERT: D 3302 PHE cc_start: 0.8856 (t80) cc_final: 0.8571 (t80) REVERT: D 3719 MET cc_start: 0.8197 (mmp) cc_final: 0.7979 (mmp) REVERT: D 3819 MET cc_start: 0.6589 (mtt) cc_final: 0.6225 (mmm) REVERT: J 50 GLN cc_start: 0.9069 (mt0) cc_final: 0.8580 (mm-40) REVERT: J 72 MET cc_start: 0.9329 (tmm) cc_final: 0.8626 (tmm) REVERT: J 73 MET cc_start: 0.8838 (mmp) cc_final: 0.8586 (mmm) REVERT: J 125 MET cc_start: 0.8929 (ppp) cc_final: 0.8382 (ppp) REVERT: L 9 GLN cc_start: 0.9228 (mt0) cc_final: 0.8939 (mt0) REVERT: L 73 MET cc_start: 0.8547 (mmm) cc_final: 0.8250 (mmm) REVERT: L 125 MET cc_start: 0.9012 (ppp) cc_final: 0.8624 (ppp) REVERT: K 50 GLN cc_start: 0.9173 (mt0) cc_final: 0.8777 (mm110) REVERT: K 72 MET cc_start: 0.9363 (tmm) cc_final: 0.8986 (ppp) REVERT: K 73 MET cc_start: 0.8776 (mmp) cc_final: 0.8472 (mmm) REVERT: K 77 MET cc_start: 0.7481 (ppp) cc_final: 0.7231 (pmm) REVERT: K 101 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8729 (mt) REVERT: K 145 MET cc_start: 0.9086 (mmp) cc_final: 0.8795 (mmp) outliers start: 102 outliers final: 51 residues processed: 862 average time/residue: 1.2374 time to fit residues: 1900.1695 Evaluate side-chains 844 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 787 time to evaluate : 12.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2737 LEU Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3583 LYS Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 1052 GLU Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2734 MET Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 3583 LYS Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3326 LEU Chi-restraints excluded: chain D residue 3583 LYS Chi-restraints excluded: chain D residue 4753 LEU Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 101 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 30.0000 chunk 1222 optimal weight: 6.9990 chunk 844 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 776 optimal weight: 50.0000 chunk 1092 optimal weight: 9.9990 chunk 1632 optimal weight: 20.0000 chunk 1728 optimal weight: 6.9990 chunk 852 optimal weight: 8.9990 chunk 1547 optimal weight: 3.9990 chunk 465 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3063 ASN ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS G 26 HIS H 26 HIS ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN B1063 ASN ** B1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3063 ASN ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3063 ASN C3588 HIS C3770 ASN ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2927 GLN D3063 ASN ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.406 146568 Z= 0.439 Angle : 0.671 23.802 197972 Z= 0.342 Chirality : 0.043 0.376 21688 Planarity : 0.005 0.145 25472 Dihedral : 5.812 89.277 19682 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.58 % Rotamer: Outliers : 0.89 % Allowed : 6.20 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.06), residues: 17808 helix: 1.74 (0.05), residues: 9464 sheet: -0.26 (0.12), residues: 1700 loop : -0.35 (0.08), residues: 6644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 893 HIS 0.010 0.001 HIS A3034 PHE 0.035 0.002 PHE C3854 TYR 0.054 0.002 TYR B3245 ARG 0.010 0.001 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 810 time to evaluate : 12.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8071 (tpt) cc_final: 0.7811 (mmm) REVERT: A 878 LEU cc_start: 0.9401 (tp) cc_final: 0.9033 (tp) REVERT: A 2757 MET cc_start: 0.7807 (mmp) cc_final: 0.7508 (mmm) REVERT: A 2828 MET cc_start: 0.8858 (ttm) cc_final: 0.8507 (ttt) REVERT: A 2840 MET cc_start: 0.9157 (mmm) cc_final: 0.8848 (mmm) REVERT: A 2843 MET cc_start: 0.8547 (ttt) cc_final: 0.8202 (tmm) REVERT: A 2844 MET cc_start: 0.8826 (ppp) cc_final: 0.8467 (tmm) REVERT: A 3138 TYR cc_start: 0.8840 (m-80) cc_final: 0.8546 (m-80) REVERT: A 3162 PHE cc_start: 0.8600 (m-10) cc_final: 0.8277 (m-10) REVERT: A 3235 MET cc_start: 0.8297 (pmm) cc_final: 0.7679 (pmm) REVERT: A 3241 MET cc_start: 0.9181 (ttp) cc_final: 0.8917 (tmm) REVERT: A 3243 CYS cc_start: 0.8518 (m) cc_final: 0.7986 (m) REVERT: A 3263 MET cc_start: 0.8850 (mmp) cc_final: 0.8430 (mpp) REVERT: A 3605 MET cc_start: 0.9277 (ttm) cc_final: 0.8964 (mtm) REVERT: A 3719 MET cc_start: 0.8301 (mmp) cc_final: 0.8040 (mmp) REVERT: A 3981 MET cc_start: 0.8980 (tmm) cc_final: 0.8108 (ttp) REVERT: A 4268 MET cc_start: 0.7683 (mmp) cc_final: 0.7195 (ptm) REVERT: E 54 GLN cc_start: 0.9149 (mp10) cc_final: 0.8685 (mp10) REVERT: E 108 GLU cc_start: 0.8428 (pp20) cc_final: 0.8029 (pm20) REVERT: F 54 GLN cc_start: 0.9072 (mp10) cc_final: 0.8689 (mp10) REVERT: F 58 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8049 (mtmm) REVERT: F 62 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: G 53 LYS cc_start: 0.9051 (mppt) cc_final: 0.8676 (mptt) REVERT: G 54 GLN cc_start: 0.9166 (mp10) cc_final: 0.8716 (mp10) REVERT: G 58 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8084 (ptpp) REVERT: G 62 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: G 108 GLU cc_start: 0.8465 (pp20) cc_final: 0.8189 (pm20) REVERT: H 53 LYS cc_start: 0.9063 (mppt) cc_final: 0.8679 (mptt) REVERT: H 54 GLN cc_start: 0.9207 (mp10) cc_final: 0.8733 (mp10) REVERT: H 108 GLU cc_start: 0.8407 (pp20) cc_final: 0.8070 (pm20) REVERT: I 14 LYS cc_start: 0.9372 (mmpt) cc_final: 0.9139 (tppt) REVERT: I 31 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9211 (mmmt) REVERT: I 72 MET cc_start: 0.9178 (tmm) cc_final: 0.8863 (tmm) REVERT: I 73 MET cc_start: 0.8722 (mmm) cc_final: 0.7882 (mmm) REVERT: B 393 MET cc_start: 0.7955 (mmm) cc_final: 0.7101 (mmm) REVERT: B 655 MET cc_start: 0.8716 (mmm) cc_final: 0.8483 (mmm) REVERT: B 878 LEU cc_start: 0.9419 (tp) cc_final: 0.9041 (tp) REVERT: B 995 MET cc_start: 0.8864 (ptp) cc_final: 0.8384 (ptp) REVERT: B 1050 LEU cc_start: 0.9591 (mp) cc_final: 0.9210 (pt) REVERT: B 1174 MET cc_start: 0.8406 (ptp) cc_final: 0.8110 (pmm) REVERT: B 1300 MET cc_start: 0.8837 (mmp) cc_final: 0.8618 (mmp) REVERT: B 1564 MET cc_start: 0.8749 (mmm) cc_final: 0.8504 (mmt) REVERT: B 1953 MET cc_start: 0.9049 (tpt) cc_final: 0.8808 (tpp) REVERT: B 2732 TRP cc_start: 0.9080 (t60) cc_final: 0.8580 (t60) REVERT: B 2844 MET cc_start: 0.8973 (ppp) cc_final: 0.8738 (tmm) REVERT: B 3138 TYR cc_start: 0.8798 (m-80) cc_final: 0.8562 (m-80) REVERT: B 3162 PHE cc_start: 0.8506 (m-10) cc_final: 0.8243 (m-10) REVERT: B 3241 MET cc_start: 0.9044 (ttp) cc_final: 0.8782 (tmm) REVERT: B 3243 CYS cc_start: 0.8082 (m) cc_final: 0.7480 (m) REVERT: B 3263 MET cc_start: 0.8612 (mmp) cc_final: 0.8314 (mpp) REVERT: B 3302 PHE cc_start: 0.8627 (t80) cc_final: 0.8270 (t80) REVERT: B 3719 MET cc_start: 0.8434 (mmp) cc_final: 0.8179 (mmp) REVERT: B 3819 MET cc_start: 0.7017 (mtt) cc_final: 0.6792 (mtt) REVERT: B 4258 MET cc_start: 0.6691 (ttt) cc_final: 0.6255 (ptt) REVERT: B 4268 MET cc_start: 0.8314 (tpp) cc_final: 0.7977 (ptm) REVERT: C 128 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8639 (mtm) REVERT: C 309 MET cc_start: 0.7997 (mmp) cc_final: 0.7729 (mmt) REVERT: C 393 MET cc_start: 0.8176 (mmm) cc_final: 0.7537 (mmm) REVERT: C 878 LEU cc_start: 0.9389 (tp) cc_final: 0.9007 (tp) REVERT: C 981 MET cc_start: 0.7919 (ppp) cc_final: 0.7609 (ppp) REVERT: C 995 MET cc_start: 0.8886 (ptp) cc_final: 0.8424 (ptp) REVERT: C 1165 MET cc_start: 0.8769 (mtt) cc_final: 0.8375 (mtp) REVERT: C 1487 MET cc_start: 0.8617 (mtp) cc_final: 0.8278 (mtp) REVERT: C 2732 TRP cc_start: 0.8831 (t60) cc_final: 0.8441 (t60) REVERT: C 2734 MET cc_start: 0.9433 (mtt) cc_final: 0.9214 (mpp) REVERT: C 2737 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9338 (pp) REVERT: C 2757 MET cc_start: 0.8268 (mmp) cc_final: 0.7964 (mmm) REVERT: C 2783 LEU cc_start: 0.9372 (mt) cc_final: 0.9142 (mt) REVERT: C 2828 MET cc_start: 0.9068 (tpp) cc_final: 0.8827 (tpp) REVERT: C 2843 MET cc_start: 0.8473 (tpp) cc_final: 0.8268 (tpp) REVERT: C 2844 MET cc_start: 0.8697 (tmm) cc_final: 0.8353 (tmm) REVERT: C 2848 TYR cc_start: 0.8166 (m-80) cc_final: 0.7953 (m-80) REVERT: C 2935 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: C 2943 PHE cc_start: 0.8321 (m-80) cc_final: 0.7768 (m-80) REVERT: C 3235 MET cc_start: 0.8750 (pmm) cc_final: 0.8253 (pmm) REVERT: C 3243 CYS cc_start: 0.8579 (m) cc_final: 0.8302 (m) REVERT: C 3263 MET cc_start: 0.9120 (mmp) cc_final: 0.8671 (mpp) REVERT: C 3719 MET cc_start: 0.8221 (mmp) cc_final: 0.7932 (mmp) REVERT: C 3819 MET cc_start: 0.6547 (mmm) cc_final: 0.6308 (mmm) REVERT: C 4268 MET cc_start: 0.8257 (tpp) cc_final: 0.7506 (tpt) REVERT: D 309 MET cc_start: 0.8421 (mmm) cc_final: 0.7859 (mmt) REVERT: D 317 MET cc_start: 0.7778 (ptt) cc_final: 0.7446 (ptt) REVERT: D 393 MET cc_start: 0.8079 (tpt) cc_final: 0.7588 (mmm) REVERT: D 655 MET cc_start: 0.8704 (mmm) cc_final: 0.8438 (mmm) REVERT: D 878 LEU cc_start: 0.9504 (tp) cc_final: 0.9194 (tp) REVERT: D 949 HIS cc_start: 0.8095 (t-90) cc_final: 0.7826 (t-90) REVERT: D 981 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6776 (ppp) REVERT: D 995 MET cc_start: 0.8710 (ptp) cc_final: 0.8110 (ptp) REVERT: D 1113 MET cc_start: 0.8891 (mtm) cc_final: 0.8654 (mtp) REVERT: D 1953 MET cc_start: 0.8980 (tpt) cc_final: 0.8744 (tpp) REVERT: D 2757 MET cc_start: 0.7454 (mmp) cc_final: 0.7163 (mmm) REVERT: D 2939 TYR cc_start: 0.8730 (m-10) cc_final: 0.8280 (m-80) REVERT: D 2943 PHE cc_start: 0.7980 (m-80) cc_final: 0.7502 (m-80) REVERT: D 3263 MET cc_start: 0.8180 (mmp) cc_final: 0.7863 (mpp) REVERT: D 3302 PHE cc_start: 0.8789 (t80) cc_final: 0.8491 (t80) REVERT: D 3819 MET cc_start: 0.6742 (mtt) cc_final: 0.6506 (mmm) REVERT: J 14 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9140 (tppt) REVERT: J 50 GLN cc_start: 0.9083 (mt0) cc_final: 0.8554 (mm110) REVERT: J 72 MET cc_start: 0.9298 (tmm) cc_final: 0.8645 (tmm) REVERT: J 73 MET cc_start: 0.8915 (mmp) cc_final: 0.8541 (mmm) REVERT: J 101 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8562 (mt) REVERT: L 72 MET cc_start: 0.9126 (ppp) cc_final: 0.8918 (tmm) REVERT: L 73 MET cc_start: 0.8810 (mmm) cc_final: 0.8502 (mmm) REVERT: L 77 MET cc_start: 0.7342 (ppp) cc_final: 0.6844 (pmm) REVERT: L 101 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8691 (mt) REVERT: K 14 LYS cc_start: 0.9430 (mmpt) cc_final: 0.9195 (tppt) REVERT: K 50 GLN cc_start: 0.9205 (mt0) cc_final: 0.8755 (mm110) REVERT: K 72 MET cc_start: 0.9349 (tmm) cc_final: 0.9010 (tmm) REVERT: K 73 MET cc_start: 0.8894 (mmp) cc_final: 0.8334 (mmm) REVERT: K 77 MET cc_start: 0.7377 (ppp) cc_final: 0.7137 (pmm) REVERT: K 101 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8753 (mt) REVERT: K 145 MET cc_start: 0.8832 (mmp) cc_final: 0.8422 (mmp) outliers start: 132 outliers final: 65 residues processed: 896 average time/residue: 1.2204 time to fit residues: 1957.1033 Evaluate side-chains 864 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 789 time to evaluate : 12.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2348 GLU Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3252 HIS Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2736 LYS Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3583 LYS Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 1052 GLU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2736 LYS Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3245 TYR Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 3583 LYS Chi-restraints excluded: chain C residue 4067 LEU Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 981 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2348 GLU Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3223 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 101 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 6.9990 chunk 981 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 1286 optimal weight: 3.9990 chunk 713 optimal weight: 7.9990 chunk 1474 optimal weight: 6.9990 chunk 1194 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 882 optimal weight: 3.9990 chunk 1551 optimal weight: 9.9990 chunk 436 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN A1069 GLN ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN B1069 GLN ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3588 HIS ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN C1069 GLN ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3770 ASN ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4514 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 HIS ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN D1069 GLN ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3770 ASN ** D3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4514 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.397 146568 Z= 0.316 Angle : 0.630 23.262 197972 Z= 0.320 Chirality : 0.041 0.409 21688 Planarity : 0.005 0.141 25472 Dihedral : 5.695 89.542 19672 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 0.76 % Allowed : 7.14 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.05 % 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: 1.23 (0.06), residues: 17808 helix: 1.83 (0.05), residues: 9472 sheet: -0.31 (0.12), residues: 1728 loop : -0.29 (0.08), residues: 6608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP C3249 HIS 0.010 0.001 HIS C3034 PHE 0.029 0.001 PHE C3162 TYR 0.050 0.001 TYR C3245 ARG 0.009 0.000 ARG K 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 800 time to evaluate : 12.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8075 (tpt) cc_final: 0.7788 (mmm) REVERT: A 981 MET cc_start: 0.7846 (ppp) cc_final: 0.7208 (ppp) REVERT: A 2840 MET cc_start: 0.9158 (mmm) cc_final: 0.8850 (mmm) REVERT: A 2843 MET cc_start: 0.8536 (ttt) cc_final: 0.8130 (tmm) REVERT: A 2844 MET cc_start: 0.8814 (ppp) cc_final: 0.8423 (tmm) REVERT: A 3138 TYR cc_start: 0.8810 (m-80) cc_final: 0.8482 (m-80) REVERT: A 3162 PHE cc_start: 0.8538 (m-10) cc_final: 0.8167 (m-10) REVERT: A 3215 MET cc_start: 0.9504 (ppp) cc_final: 0.9107 (tpp) REVERT: A 3235 MET cc_start: 0.8368 (pmm) cc_final: 0.7591 (pmm) REVERT: A 3241 MET cc_start: 0.9136 (ttp) cc_final: 0.8856 (tmm) REVERT: A 3243 CYS cc_start: 0.8563 (m) cc_final: 0.8038 (m) REVERT: A 3605 MET cc_start: 0.9203 (ttm) cc_final: 0.8852 (mtm) REVERT: A 3719 MET cc_start: 0.8293 (mmp) cc_final: 0.8062 (mmp) REVERT: A 3819 MET cc_start: 0.6645 (mtt) cc_final: 0.6407 (mmm) REVERT: A 3981 MET cc_start: 0.8988 (tmm) cc_final: 0.8015 (ttp) REVERT: A 4268 MET cc_start: 0.7670 (mmp) cc_final: 0.7177 (ptm) REVERT: E 4 GLU cc_start: 0.8028 (pm20) cc_final: 0.7724 (pm20) REVERT: E 54 GLN cc_start: 0.9159 (mp10) cc_final: 0.8668 (mp10) REVERT: E 108 GLU cc_start: 0.8424 (pp20) cc_final: 0.8032 (pm20) REVERT: F 54 GLN cc_start: 0.9087 (mp10) cc_final: 0.8642 (mp10) REVERT: F 58 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7982 (mtmm) REVERT: F 62 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: G 53 LYS cc_start: 0.9082 (mppt) cc_final: 0.8719 (mptt) REVERT: G 54 GLN cc_start: 0.9171 (mp10) cc_final: 0.8704 (mp10) REVERT: G 58 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: G 62 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: G 108 GLU cc_start: 0.8451 (pp20) cc_final: 0.8168 (pm20) REVERT: H 53 LYS cc_start: 0.9095 (mppt) cc_final: 0.8761 (mptt) REVERT: H 54 GLN cc_start: 0.9216 (mp10) cc_final: 0.8728 (mp10) REVERT: H 108 GLU cc_start: 0.8404 (pp20) cc_final: 0.8086 (pm20) REVERT: I 14 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9134 (tppt) REVERT: I 31 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9198 (mmmt) REVERT: I 73 MET cc_start: 0.8814 (mmm) cc_final: 0.8428 (mmm) REVERT: B 393 MET cc_start: 0.8028 (mmm) cc_final: 0.7281 (mmm) REVERT: B 878 LEU cc_start: 0.9413 (tp) cc_final: 0.9091 (tp) REVERT: B 981 MET cc_start: 0.7672 (ppp) cc_final: 0.7156 (tmm) REVERT: B 995 MET cc_start: 0.8830 (ptp) cc_final: 0.8333 (ptp) REVERT: B 1174 MET cc_start: 0.8386 (ptp) cc_final: 0.8116 (pmm) REVERT: B 1564 MET cc_start: 0.8708 (mmm) cc_final: 0.8478 (mmt) REVERT: B 1953 MET cc_start: 0.9054 (tpt) cc_final: 0.8802 (tpp) REVERT: B 2134 MET cc_start: 0.9084 (tpp) cc_final: 0.8757 (tpt) REVERT: B 2732 TRP cc_start: 0.9072 (t60) cc_final: 0.8710 (t60) REVERT: B 2757 MET cc_start: 0.8475 (mmt) cc_final: 0.8010 (mmm) REVERT: B 2840 MET cc_start: 0.9105 (mmm) cc_final: 0.8755 (mmm) REVERT: B 2843 MET cc_start: 0.8487 (ptp) cc_final: 0.8284 (ptt) REVERT: B 2844 MET cc_start: 0.8927 (ppp) cc_final: 0.8699 (tmm) REVERT: B 3241 MET cc_start: 0.8975 (ttp) cc_final: 0.8693 (tmm) REVERT: B 3243 CYS cc_start: 0.8074 (m) cc_final: 0.7428 (m) REVERT: B 3302 PHE cc_start: 0.8607 (t80) cc_final: 0.8279 (t80) REVERT: B 3719 MET cc_start: 0.8419 (mmp) cc_final: 0.8191 (mmp) REVERT: B 3819 MET cc_start: 0.6944 (mtt) cc_final: 0.6722 (mtt) REVERT: B 4258 MET cc_start: 0.6767 (ttt) cc_final: 0.6322 (ptt) REVERT: B 4268 MET cc_start: 0.8259 (tpp) cc_final: 0.7947 (ptm) REVERT: C 128 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8617 (mtm) REVERT: C 309 MET cc_start: 0.8024 (mmp) cc_final: 0.7743 (mmt) REVERT: C 393 MET cc_start: 0.8128 (mmm) cc_final: 0.7407 (mmm) REVERT: C 878 LEU cc_start: 0.9372 (tp) cc_final: 0.9046 (tp) REVERT: C 981 MET cc_start: 0.7844 (ppp) cc_final: 0.7526 (ppp) REVERT: C 995 MET cc_start: 0.8866 (ptp) cc_final: 0.8383 (ptp) REVERT: C 1165 MET cc_start: 0.8735 (mtt) cc_final: 0.8327 (mtp) REVERT: C 1487 MET cc_start: 0.8587 (mtp) cc_final: 0.8278 (mtp) REVERT: C 1953 MET cc_start: 0.8964 (mmm) cc_final: 0.8740 (mmm) REVERT: C 2732 TRP cc_start: 0.8835 (t60) cc_final: 0.8451 (t60) REVERT: C 2734 MET cc_start: 0.9393 (mtt) cc_final: 0.9168 (mpp) REVERT: C 2737 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9353 (pp) REVERT: C 2757 MET cc_start: 0.8185 (mmp) cc_final: 0.7950 (mmm) REVERT: C 2783 LEU cc_start: 0.9377 (mt) cc_final: 0.9134 (mt) REVERT: C 2843 MET cc_start: 0.8453 (tpp) cc_final: 0.8202 (tpp) REVERT: C 2844 MET cc_start: 0.8710 (tmm) cc_final: 0.8362 (tmm) REVERT: C 2848 TYR cc_start: 0.8108 (m-80) cc_final: 0.7891 (m-80) REVERT: C 2935 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: C 2943 PHE cc_start: 0.8297 (m-80) cc_final: 0.7819 (m-80) REVERT: C 3235 MET cc_start: 0.8769 (pmm) cc_final: 0.8187 (pmm) REVERT: C 3243 CYS cc_start: 0.8505 (m) cc_final: 0.8249 (m) REVERT: C 3263 MET cc_start: 0.9150 (mmp) cc_final: 0.8709 (mpp) REVERT: C 3299 LEU cc_start: 0.9356 (tt) cc_final: 0.9072 (mt) REVERT: C 4268 MET cc_start: 0.8154 (tpp) cc_final: 0.7557 (tpp) REVERT: D 309 MET cc_start: 0.8371 (mmm) cc_final: 0.7778 (mmt) REVERT: D 317 MET cc_start: 0.7788 (ptt) cc_final: 0.7451 (ptt) REVERT: D 393 MET cc_start: 0.8086 (tpt) cc_final: 0.7628 (mmm) REVERT: D 655 MET cc_start: 0.8680 (mmm) cc_final: 0.8408 (mmm) REVERT: D 878 LEU cc_start: 0.9501 (tp) cc_final: 0.9188 (tp) REVERT: D 949 HIS cc_start: 0.8068 (t-90) cc_final: 0.7806 (t-90) REVERT: D 981 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6681 (ppp) REVERT: D 1113 MET cc_start: 0.8852 (mtm) cc_final: 0.8599 (mtp) REVERT: D 1487 MET cc_start: 0.8749 (mtm) cc_final: 0.8499 (mtp) REVERT: D 1953 MET cc_start: 0.8941 (tpt) cc_final: 0.8712 (tpp) REVERT: D 2757 MET cc_start: 0.7564 (mmp) cc_final: 0.7240 (mmm) REVERT: D 2840 MET cc_start: 0.8552 (mmt) cc_final: 0.8121 (mmt) REVERT: D 2939 TYR cc_start: 0.8718 (m-10) cc_final: 0.8281 (m-80) REVERT: D 2943 PHE cc_start: 0.7965 (m-80) cc_final: 0.7466 (m-80) REVERT: D 3263 MET cc_start: 0.8189 (mmp) cc_final: 0.7890 (mpp) REVERT: D 3302 PHE cc_start: 0.8725 (t80) cc_final: 0.8343 (t80) REVERT: D 3719 MET cc_start: 0.8214 (mmp) cc_final: 0.7887 (mmm) REVERT: J 14 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9133 (tppt) REVERT: J 50 GLN cc_start: 0.9079 (mt0) cc_final: 0.8567 (mm110) REVERT: J 53 ILE cc_start: 0.9556 (OUTLIER) cc_final: 0.9343 (pt) REVERT: J 72 MET cc_start: 0.9240 (tmm) cc_final: 0.8507 (tmm) REVERT: J 73 MET cc_start: 0.8886 (mmp) cc_final: 0.8489 (mmm) REVERT: J 101 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8717 (mt) REVERT: L 73 MET cc_start: 0.8857 (mmm) cc_final: 0.8527 (mmm) REVERT: L 101 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8656 (mt) REVERT: K 14 LYS cc_start: 0.9429 (mmpt) cc_final: 0.9217 (tppt) REVERT: K 72 MET cc_start: 0.9324 (tmm) cc_final: 0.8876 (tmm) REVERT: K 73 MET cc_start: 0.8882 (mmp) cc_final: 0.8394 (mmm) REVERT: K 101 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8730 (mt) outliers start: 111 outliers final: 70 residues processed: 872 average time/residue: 1.2207 time to fit residues: 1904.7517 Evaluate side-chains 875 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 791 time to evaluate : 12.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2348 GLU Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3245 TYR Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2736 LYS Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3123 LEU Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3245 TYR Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1052 GLU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2736 LYS Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3245 TYR Chi-restraints excluded: chain C residue 3281 LEU Chi-restraints excluded: chain C residue 3583 LYS Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4067 LEU Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 981 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2348 GLU Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 101 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 8.9990 chunk 1556 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 chunk 1014 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 1729 optimal weight: 8.9990 chunk 1436 optimal weight: 5.9990 chunk 800 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 572 optimal weight: 9.9990 chunk 908 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2118 ASN A2754 GLN ** A3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3588 HIS I 4 GLN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4097 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN C1126 GLN ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3770 ASN C3953 HIS D 32 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.331 146568 Z= 0.438 Angle : 0.671 22.004 197972 Z= 0.340 Chirality : 0.043 0.382 21688 Planarity : 0.005 0.140 25472 Dihedral : 5.696 89.980 19668 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 0.88 % Allowed : 7.56 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.06), residues: 17808 helix: 1.80 (0.05), residues: 9484 sheet: -0.34 (0.12), residues: 1724 loop : -0.28 (0.08), residues: 6600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 893 HIS 0.010 0.001 HIS A3700 PHE 0.042 0.002 PHE C3854 TYR 0.034 0.002 TYR C3245 ARG 0.011 0.001 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 806 time to evaluate : 12.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8093 (tpt) cc_final: 0.7805 (mmm) REVERT: A 878 LEU cc_start: 0.9400 (tp) cc_final: 0.9020 (tp) REVERT: A 1064 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8772 (pp) REVERT: A 2214 MET cc_start: 0.9283 (mmm) cc_final: 0.9064 (mmm) REVERT: A 2754 GLN cc_start: 0.9451 (tt0) cc_final: 0.9156 (tt0) REVERT: A 2757 MET cc_start: 0.7562 (mmm) cc_final: 0.6052 (mmm) REVERT: A 2840 MET cc_start: 0.9183 (mmm) cc_final: 0.8870 (mmm) REVERT: A 2843 MET cc_start: 0.8588 (ttt) cc_final: 0.8227 (tmm) REVERT: A 2844 MET cc_start: 0.8840 (ppp) cc_final: 0.8593 (ppp) REVERT: A 2848 TYR cc_start: 0.8064 (t80) cc_final: 0.7848 (t80) REVERT: A 3138 TYR cc_start: 0.8807 (m-80) cc_final: 0.8445 (m-80) REVERT: A 3162 PHE cc_start: 0.8544 (m-10) cc_final: 0.8279 (m-10) REVERT: A 3215 MET cc_start: 0.9544 (ppp) cc_final: 0.9146 (tpp) REVERT: A 3241 MET cc_start: 0.9196 (ttp) cc_final: 0.8991 (tmm) REVERT: A 3605 MET cc_start: 0.9269 (ttm) cc_final: 0.8897 (mtm) REVERT: A 3981 MET cc_start: 0.8994 (tmm) cc_final: 0.8056 (ttp) REVERT: A 4268 MET cc_start: 0.7674 (mmp) cc_final: 0.7247 (ptt) REVERT: E 4 GLU cc_start: 0.8077 (pm20) cc_final: 0.7746 (pm20) REVERT: E 54 GLN cc_start: 0.9190 (mp10) cc_final: 0.8659 (mp10) REVERT: E 108 GLU cc_start: 0.8414 (pp20) cc_final: 0.8019 (pm20) REVERT: F 54 GLN cc_start: 0.9126 (mp10) cc_final: 0.8673 (mp10) REVERT: F 58 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8129 (ptpp) REVERT: F 62 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: F 108 GLU cc_start: 0.8486 (pp20) cc_final: 0.8028 (pp20) REVERT: G 53 LYS cc_start: 0.9109 (mppt) cc_final: 0.8720 (mptt) REVERT: G 54 GLN cc_start: 0.9194 (mp10) cc_final: 0.8711 (mp10) REVERT: G 58 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8118 (mtmm) REVERT: G 62 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: G 108 GLU cc_start: 0.8453 (pp20) cc_final: 0.8220 (pm20) REVERT: H 53 LYS cc_start: 0.9112 (mppt) cc_final: 0.8732 (mptt) REVERT: H 54 GLN cc_start: 0.9232 (mp10) cc_final: 0.8759 (mp10) REVERT: H 108 GLU cc_start: 0.8400 (pp20) cc_final: 0.8084 (pm20) REVERT: I 14 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9169 (tppt) REVERT: I 31 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9176 (mmmt) REVERT: I 73 MET cc_start: 0.8931 (mmm) cc_final: 0.8485 (mmm) REVERT: B 393 MET cc_start: 0.7976 (mmm) cc_final: 0.7259 (mmm) REVERT: B 878 LEU cc_start: 0.9426 (tp) cc_final: 0.9068 (tp) REVERT: B 995 MET cc_start: 0.8846 (ptp) cc_final: 0.8331 (ptp) REVERT: B 1050 LEU cc_start: 0.9563 (mp) cc_final: 0.9172 (pt) REVERT: B 1174 MET cc_start: 0.8398 (ptp) cc_final: 0.8128 (pmm) REVERT: B 1564 MET cc_start: 0.8699 (mmm) cc_final: 0.8466 (mmt) REVERT: B 1953 MET cc_start: 0.9088 (tpt) cc_final: 0.8838 (tpp) REVERT: B 2134 MET cc_start: 0.9029 (tpp) cc_final: 0.8813 (tpt) REVERT: B 2732 TRP cc_start: 0.9082 (t60) cc_final: 0.8715 (t60) REVERT: B 2757 MET cc_start: 0.8445 (mmt) cc_final: 0.7970 (mmm) REVERT: B 2840 MET cc_start: 0.9150 (mmm) cc_final: 0.8863 (mmm) REVERT: B 2843 MET cc_start: 0.8483 (ptp) cc_final: 0.8199 (ptp) REVERT: B 3241 MET cc_start: 0.8928 (ttp) cc_final: 0.8569 (tmm) REVERT: B 3243 CYS cc_start: 0.8087 (m) cc_final: 0.7132 (m) REVERT: B 3263 MET cc_start: 0.8778 (mmp) cc_final: 0.8445 (mpp) REVERT: B 3302 PHE cc_start: 0.8651 (t80) cc_final: 0.8314 (t80) REVERT: B 3719 MET cc_start: 0.8410 (mmp) cc_final: 0.8134 (mmp) REVERT: B 4258 MET cc_start: 0.6749 (ttt) cc_final: 0.6312 (ptt) REVERT: B 4268 MET cc_start: 0.8293 (tpp) cc_final: 0.7965 (ptm) REVERT: C 128 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (mtm) REVERT: C 309 MET cc_start: 0.8086 (mmp) cc_final: 0.7766 (mmt) REVERT: C 393 MET cc_start: 0.8121 (mmm) cc_final: 0.7622 (mmm) REVERT: C 878 LEU cc_start: 0.9385 (tp) cc_final: 0.8998 (tp) REVERT: C 981 MET cc_start: 0.7855 (ppp) cc_final: 0.7475 (ppp) REVERT: C 995 MET cc_start: 0.8862 (ptp) cc_final: 0.8395 (ptp) REVERT: C 1050 LEU cc_start: 0.9589 (mp) cc_final: 0.9288 (pt) REVERT: C 1165 MET cc_start: 0.8764 (mtt) cc_final: 0.8343 (mtp) REVERT: C 1487 MET cc_start: 0.8645 (mtp) cc_final: 0.8310 (mtp) REVERT: C 1953 MET cc_start: 0.9018 (mmm) cc_final: 0.8759 (mmm) REVERT: C 2732 TRP cc_start: 0.8885 (t60) cc_final: 0.8523 (t60) REVERT: C 2737 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9377 (pp) REVERT: C 2783 LEU cc_start: 0.9416 (mt) cc_final: 0.9196 (mt) REVERT: C 2828 MET cc_start: 0.8923 (tpp) cc_final: 0.8712 (tpp) REVERT: C 2843 MET cc_start: 0.8494 (tpp) cc_final: 0.8159 (tpp) REVERT: C 2844 MET cc_start: 0.8757 (tmm) cc_final: 0.8315 (tmm) REVERT: C 2848 TYR cc_start: 0.8235 (m-80) cc_final: 0.7997 (m-80) REVERT: C 2943 PHE cc_start: 0.8306 (m-80) cc_final: 0.7811 (m-80) REVERT: C 3215 MET cc_start: 0.9497 (ppp) cc_final: 0.9136 (tpp) REVERT: C 3235 MET cc_start: 0.8872 (pmm) cc_final: 0.8388 (pmm) REVERT: C 3243 CYS cc_start: 0.8487 (m) cc_final: 0.8225 (m) REVERT: C 3299 LEU cc_start: 0.9304 (tt) cc_final: 0.9048 (mt) REVERT: D 309 MET cc_start: 0.8412 (mmm) cc_final: 0.7812 (mmt) REVERT: D 317 MET cc_start: 0.7776 (ptt) cc_final: 0.7464 (ptt) REVERT: D 393 MET cc_start: 0.8083 (tpt) cc_final: 0.7632 (mmm) REVERT: D 878 LEU cc_start: 0.9504 (tp) cc_final: 0.9220 (tp) REVERT: D 949 HIS cc_start: 0.8137 (t-90) cc_final: 0.7847 (t-90) REVERT: D 981 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6863 (ppp) REVERT: D 2757 MET cc_start: 0.7695 (mmp) cc_final: 0.7438 (mmm) REVERT: D 2939 TYR cc_start: 0.8727 (m-10) cc_final: 0.8286 (m-80) REVERT: D 2943 PHE cc_start: 0.8055 (m-80) cc_final: 0.7507 (m-80) REVERT: D 3215 MET cc_start: 0.9502 (ppp) cc_final: 0.8874 (tpp) REVERT: D 3263 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7961 (mpp) REVERT: D 3302 PHE cc_start: 0.8746 (t80) cc_final: 0.8369 (t80) REVERT: D 3719 MET cc_start: 0.8245 (mmp) cc_final: 0.7911 (mmm) REVERT: J 14 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9186 (tppt) REVERT: J 50 GLN cc_start: 0.9112 (mt0) cc_final: 0.8818 (mm-40) REVERT: J 72 MET cc_start: 0.9224 (tmm) cc_final: 0.8686 (tmm) REVERT: J 73 MET cc_start: 0.8980 (mmp) cc_final: 0.8485 (mmm) REVERT: J 101 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8746 (mt) REVERT: J 130 ASP cc_start: 0.4089 (OUTLIER) cc_final: 0.3863 (t0) REVERT: L 31 LYS cc_start: 0.9466 (mmmt) cc_final: 0.9200 (mmmt) REVERT: L 73 MET cc_start: 0.9017 (mmm) cc_final: 0.8645 (mmm) REVERT: K 14 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9233 (tppt) REVERT: K 72 MET cc_start: 0.9318 (tmm) cc_final: 0.8829 (tmm) REVERT: K 73 MET cc_start: 0.8982 (mmp) cc_final: 0.8374 (mmm) outliers start: 131 outliers final: 83 residues processed: 895 average time/residue: 1.2415 time to fit residues: 1992.2908 Evaluate side-chains 886 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 789 time to evaluate : 12.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2348 GLU Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3245 TYR Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2736 LYS Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3245 TYR Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3583 LYS Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1979 PHE Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2736 LYS Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3245 TYR Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 981 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2348 GLU Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3263 MET Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 98 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 985 optimal weight: 8.9990 chunk 1263 optimal weight: 10.0000 chunk 978 optimal weight: 1.9990 chunk 1456 optimal weight: 5.9990 chunk 966 optimal weight: 0.8980 chunk 1723 optimal weight: 5.9990 chunk 1078 optimal weight: 20.0000 chunk 1050 optimal weight: 3.9990 chunk 795 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4097 ASN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2754 GLN C3770 ASN ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3949 HIS C4097 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4097 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.335 146568 Z= 0.245 Angle : 0.623 22.312 197972 Z= 0.314 Chirality : 0.040 0.438 21688 Planarity : 0.004 0.136 25472 Dihedral : 5.554 89.915 19664 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 0.85 % Allowed : 7.84 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.06), residues: 17808 helix: 1.94 (0.05), residues: 9452 sheet: -0.31 (0.12), residues: 1728 loop : -0.22 (0.08), residues: 6628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 893 HIS 0.010 0.001 HIS B3700 PHE 0.047 0.001 PHE B2943 TYR 0.024 0.001 TYR C3245 ARG 0.011 0.000 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 805 time to evaluate : 12.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8090 (tpt) cc_final: 0.7808 (mmm) REVERT: A 981 MET cc_start: 0.7714 (ppp) cc_final: 0.7065 (ppp) REVERT: A 1064 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 1215 MET cc_start: 0.8705 (mtp) cc_final: 0.8378 (mtp) REVERT: A 2828 MET cc_start: 0.8761 (ttm) cc_final: 0.8553 (ttt) REVERT: A 2840 MET cc_start: 0.9122 (mmm) cc_final: 0.8823 (mmm) REVERT: A 2843 MET cc_start: 0.8571 (ttt) cc_final: 0.8192 (tmm) REVERT: A 2844 MET cc_start: 0.8816 (ppp) cc_final: 0.8408 (tmm) REVERT: A 2848 TYR cc_start: 0.8010 (t80) cc_final: 0.7792 (t80) REVERT: A 3138 TYR cc_start: 0.8754 (m-80) cc_final: 0.8421 (m-80) REVERT: A 3215 MET cc_start: 0.9516 (ppp) cc_final: 0.9163 (tpp) REVERT: A 3241 MET cc_start: 0.9188 (ttp) cc_final: 0.8932 (tmm) REVERT: A 3243 CYS cc_start: 0.8533 (m) cc_final: 0.8138 (m) REVERT: A 3605 MET cc_start: 0.9133 (ttm) cc_final: 0.8802 (mtm) REVERT: A 3719 MET cc_start: 0.8319 (mmm) cc_final: 0.8102 (mmp) REVERT: A 3981 MET cc_start: 0.8989 (tmm) cc_final: 0.7970 (ttp) REVERT: A 4268 MET cc_start: 0.7624 (mmp) cc_final: 0.7199 (ptt) REVERT: A 4728 MET cc_start: 0.9215 (mmm) cc_final: 0.8978 (mmp) REVERT: E 4 GLU cc_start: 0.8064 (pm20) cc_final: 0.7705 (pm20) REVERT: E 54 GLN cc_start: 0.9185 (mp10) cc_final: 0.8645 (mp10) REVERT: E 108 GLU cc_start: 0.8418 (pp20) cc_final: 0.8033 (pm20) REVERT: F 54 GLN cc_start: 0.9122 (mp10) cc_final: 0.8648 (mp10) REVERT: F 58 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8007 (ptpp) REVERT: F 62 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: F 108 GLU cc_start: 0.8462 (pp20) cc_final: 0.7966 (pp20) REVERT: G 54 GLN cc_start: 0.9188 (mp10) cc_final: 0.8693 (mp10) REVERT: G 58 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8068 (ptpp) REVERT: G 62 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: G 108 GLU cc_start: 0.8459 (pp20) cc_final: 0.8220 (pm20) REVERT: H 30 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7493 (mpp) REVERT: H 53 LYS cc_start: 0.9115 (mppt) cc_final: 0.8746 (mptt) REVERT: H 54 GLN cc_start: 0.9219 (mp10) cc_final: 0.8736 (mp10) REVERT: H 108 GLU cc_start: 0.8397 (pp20) cc_final: 0.8109 (pm20) REVERT: I 14 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9152 (tppt) REVERT: I 31 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9161 (mmmt) REVERT: I 73 MET cc_start: 0.8874 (mmm) cc_final: 0.8452 (mmm) REVERT: B 393 MET cc_start: 0.8030 (mmm) cc_final: 0.7360 (mmm) REVERT: B 878 LEU cc_start: 0.9411 (tp) cc_final: 0.9090 (tp) REVERT: B 981 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6931 (tmm) REVERT: B 995 MET cc_start: 0.8816 (ptp) cc_final: 0.8286 (ptp) REVERT: B 1050 LEU cc_start: 0.9546 (mp) cc_final: 0.9139 (pt) REVERT: B 1174 MET cc_start: 0.8350 (ptp) cc_final: 0.8123 (pmm) REVERT: B 1564 MET cc_start: 0.8674 (mmm) cc_final: 0.8458 (mmt) REVERT: B 1953 MET cc_start: 0.9037 (tpt) cc_final: 0.8789 (tpp) REVERT: B 2134 MET cc_start: 0.9011 (tpp) cc_final: 0.8756 (tpt) REVERT: B 2732 TRP cc_start: 0.9068 (t60) cc_final: 0.8701 (t60) REVERT: B 2757 MET cc_start: 0.8446 (mmt) cc_final: 0.8066 (mmm) REVERT: B 2840 MET cc_start: 0.9134 (mmm) cc_final: 0.8822 (mmm) REVERT: B 2843 MET cc_start: 0.8489 (ptp) cc_final: 0.8213 (ptp) REVERT: B 2943 PHE cc_start: 0.8316 (m-80) cc_final: 0.7865 (m-80) REVERT: B 3105 LEU cc_start: 0.8285 (mt) cc_final: 0.7931 (pp) REVERT: B 3241 MET cc_start: 0.8930 (ttp) cc_final: 0.8674 (tmm) REVERT: B 3243 CYS cc_start: 0.8075 (m) cc_final: 0.7495 (m) REVERT: B 3263 MET cc_start: 0.8847 (mmp) cc_final: 0.8485 (mpp) REVERT: B 3302 PHE cc_start: 0.8640 (t80) cc_final: 0.8344 (t80) REVERT: B 3719 MET cc_start: 0.8400 (mmp) cc_final: 0.8152 (mmp) REVERT: B 4258 MET cc_start: 0.6789 (ttt) cc_final: 0.6392 (ptt) REVERT: B 4268 MET cc_start: 0.8231 (tpp) cc_final: 0.7939 (ptm) REVERT: C 128 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: C 309 MET cc_start: 0.8078 (mmp) cc_final: 0.7777 (mmt) REVERT: C 393 MET cc_start: 0.8115 (mmm) cc_final: 0.7570 (mmm) REVERT: C 878 LEU cc_start: 0.9367 (tp) cc_final: 0.9027 (tp) REVERT: C 981 MET cc_start: 0.7866 (ppp) cc_final: 0.7504 (ppp) REVERT: C 995 MET cc_start: 0.8767 (ptp) cc_final: 0.8251 (ptp) REVERT: C 1487 MET cc_start: 0.8519 (mtp) cc_final: 0.8256 (mtp) REVERT: C 1953 MET cc_start: 0.8969 (mmm) cc_final: 0.8675 (mmm) REVERT: C 2732 TRP cc_start: 0.8857 (t60) cc_final: 0.8321 (t60) REVERT: C 2783 LEU cc_start: 0.9381 (mt) cc_final: 0.9142 (mt) REVERT: C 2828 MET cc_start: 0.8854 (tpp) cc_final: 0.8571 (tpp) REVERT: C 2843 MET cc_start: 0.8454 (tpp) cc_final: 0.8092 (tpp) REVERT: C 2844 MET cc_start: 0.8754 (tmm) cc_final: 0.8377 (tmm) REVERT: C 2848 TYR cc_start: 0.8170 (m-80) cc_final: 0.7905 (m-80) REVERT: C 2943 PHE cc_start: 0.8269 (m-80) cc_final: 0.7798 (m-80) REVERT: C 3215 MET cc_start: 0.9493 (ppp) cc_final: 0.9127 (tpp) REVERT: C 3235 MET cc_start: 0.8820 (pmm) cc_final: 0.8261 (pmm) REVERT: C 3299 LEU cc_start: 0.9257 (tt) cc_final: 0.9005 (mt) REVERT: C 4268 MET cc_start: 0.8096 (tpp) cc_final: 0.7789 (ptm) REVERT: D 317 MET cc_start: 0.7747 (ptt) cc_final: 0.7322 (ptt) REVERT: D 393 MET cc_start: 0.8123 (tpt) cc_final: 0.7662 (mmm) REVERT: D 655 MET cc_start: 0.8638 (mmm) cc_final: 0.8331 (mmm) REVERT: D 878 LEU cc_start: 0.9495 (tp) cc_final: 0.9198 (tp) REVERT: D 949 HIS cc_start: 0.8067 (t-90) cc_final: 0.7808 (t-90) REVERT: D 981 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6727 (ppp) REVERT: D 1421 MET cc_start: 0.9008 (mmp) cc_final: 0.8796 (mmm) REVERT: D 2214 MET cc_start: 0.9174 (mmm) cc_final: 0.8944 (mmm) REVERT: D 2840 MET cc_start: 0.8631 (mmt) cc_final: 0.8220 (mmt) REVERT: D 2939 TYR cc_start: 0.8692 (m-10) cc_final: 0.8279 (m-80) REVERT: D 2943 PHE cc_start: 0.8048 (m-80) cc_final: 0.7608 (m-80) REVERT: D 3215 MET cc_start: 0.9480 (ppp) cc_final: 0.8946 (tpp) REVERT: D 3243 CYS cc_start: 0.7784 (m) cc_final: 0.7229 (m) REVERT: D 3263 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8008 (mpp) REVERT: D 3302 PHE cc_start: 0.8702 (t80) cc_final: 0.8316 (t80) REVERT: D 3719 MET cc_start: 0.8245 (mmp) cc_final: 0.7927 (mmm) REVERT: D 4292 MET cc_start: 0.8975 (mmm) cc_final: 0.8691 (mmm) REVERT: J 14 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9155 (tppt) REVERT: J 50 GLN cc_start: 0.9156 (mt0) cc_final: 0.8781 (mm-40) REVERT: J 72 MET cc_start: 0.9193 (tmm) cc_final: 0.8625 (tmm) REVERT: J 73 MET cc_start: 0.8912 (mmp) cc_final: 0.8445 (mmm) REVERT: J 101 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8707 (mt) REVERT: L 31 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9189 (mmmt) REVERT: L 73 MET cc_start: 0.8990 (mmm) cc_final: 0.8687 (mmm) REVERT: K 14 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9208 (tppt) REVERT: K 31 LYS cc_start: 0.9346 (mmmt) cc_final: 0.9071 (mmmt) REVERT: K 72 MET cc_start: 0.9301 (tmm) cc_final: 0.8801 (tmm) REVERT: K 73 MET cc_start: 0.8877 (mmp) cc_final: 0.8355 (mmm) outliers start: 125 outliers final: 86 residues processed: 889 average time/residue: 1.2291 time to fit residues: 1957.4880 Evaluate side-chains 890 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 790 time to evaluate : 12.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2348 GLU Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3245 TYR Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 981 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2736 LYS Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3245 TYR Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3281 LEU Chi-restraints excluded: chain B residue 3583 LYS Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2348 GLU Chi-restraints excluded: chain C residue 2736 LYS Chi-restraints excluded: chain C residue 2782 MET Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3245 TYR Chi-restraints excluded: chain C residue 4067 LEU Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 981 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1973 ILE Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2348 GLU Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3263 MET Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 98 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 20.0000 chunk 688 optimal weight: 7.9990 chunk 1029 optimal weight: 9.9990 chunk 519 optimal weight: 0.0020 chunk 338 optimal weight: 9.9990 chunk 333 optimal weight: 1.9990 chunk 1095 optimal weight: 5.9990 chunk 1174 optimal weight: 4.9990 chunk 852 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 1354 optimal weight: 0.6980 overall best weight: 2.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4514 ASN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN B1656 HIS ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2754 GLN ** C3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3770 ASN ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3949 HIS ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 971 GLN D1005 ASN D1656 HIS ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2754 GLN ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.308 146568 Z= 0.239 Angle : 0.621 22.559 197972 Z= 0.311 Chirality : 0.040 0.439 21688 Planarity : 0.004 0.134 25472 Dihedral : 5.443 89.803 19664 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 0.81 % Allowed : 8.00 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.06), residues: 17808 helix: 1.97 (0.05), residues: 9484 sheet: -0.18 (0.13), residues: 1696 loop : -0.21 (0.08), residues: 6628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP C 893 HIS 0.009 0.001 HIS D3700 PHE 0.040 0.001 PHE B2943 TYR 0.034 0.001 TYR B3138 ARG 0.018 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 797 time to evaluate : 12.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8088 (tpt) cc_final: 0.7767 (mmm) REVERT: A 878 LEU cc_start: 0.9383 (tp) cc_final: 0.9002 (tp) REVERT: A 981 MET cc_start: 0.7669 (ppp) cc_final: 0.7040 (ppp) REVERT: A 1064 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8674 (pp) REVERT: A 1215 MET cc_start: 0.8714 (mtp) cc_final: 0.8400 (mtp) REVERT: A 2688 MET cc_start: 0.5946 (tmm) cc_final: 0.5600 (tmm) REVERT: A 2828 MET cc_start: 0.8687 (ttm) cc_final: 0.8431 (ttt) REVERT: A 2840 MET cc_start: 0.9131 (mmm) cc_final: 0.8843 (mmm) REVERT: A 2843 MET cc_start: 0.8585 (ttt) cc_final: 0.8160 (tmm) REVERT: A 2844 MET cc_start: 0.8823 (ppp) cc_final: 0.8571 (ppp) REVERT: A 2848 TYR cc_start: 0.8041 (t80) cc_final: 0.7806 (t80) REVERT: A 2943 PHE cc_start: 0.8379 (m-80) cc_final: 0.7970 (m-80) REVERT: A 3138 TYR cc_start: 0.8724 (m-80) cc_final: 0.8441 (m-80) REVERT: A 3215 MET cc_start: 0.9513 (ppp) cc_final: 0.9172 (tpp) REVERT: A 3241 MET cc_start: 0.9188 (ttp) cc_final: 0.8920 (tmm) REVERT: A 3243 CYS cc_start: 0.8546 (m) cc_final: 0.8154 (m) REVERT: A 3605 MET cc_start: 0.9124 (ttm) cc_final: 0.8771 (mtm) REVERT: A 3719 MET cc_start: 0.8333 (mmm) cc_final: 0.8117 (mmp) REVERT: A 4268 MET cc_start: 0.7708 (mmp) cc_final: 0.7154 (ptm) REVERT: A 4728 MET cc_start: 0.9231 (mmm) cc_final: 0.9025 (mmt) REVERT: E 4 GLU cc_start: 0.8078 (pm20) cc_final: 0.7745 (pm20) REVERT: E 54 GLN cc_start: 0.9200 (mp10) cc_final: 0.8640 (mp10) REVERT: E 108 GLU cc_start: 0.8422 (pp20) cc_final: 0.8035 (pm20) REVERT: F 54 GLN cc_start: 0.9147 (mp10) cc_final: 0.8627 (mp10) REVERT: F 58 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7997 (ptpp) REVERT: F 62 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: F 108 GLU cc_start: 0.8471 (pp20) cc_final: 0.7953 (pp20) REVERT: G 54 GLN cc_start: 0.9203 (mp10) cc_final: 0.8699 (mp10) REVERT: G 58 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8065 (ptpp) REVERT: G 62 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: G 108 GLU cc_start: 0.8439 (pp20) cc_final: 0.8187 (pm20) REVERT: H 30 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7431 (mpp) REVERT: H 53 LYS cc_start: 0.9134 (mppt) cc_final: 0.8740 (mptt) REVERT: H 54 GLN cc_start: 0.9215 (mp10) cc_final: 0.8745 (mp10) REVERT: H 108 GLU cc_start: 0.8414 (pp20) cc_final: 0.8129 (pm20) REVERT: I 14 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9140 (tppt) REVERT: I 31 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9155 (mmmt) REVERT: I 50 GLN cc_start: 0.9051 (mt0) cc_final: 0.8716 (mm-40) REVERT: I 73 MET cc_start: 0.8922 (mmm) cc_final: 0.8585 (mmm) REVERT: B 393 MET cc_start: 0.8027 (mmm) cc_final: 0.7384 (mmm) REVERT: B 878 LEU cc_start: 0.9418 (tp) cc_final: 0.9104 (tp) REVERT: B 981 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6910 (tmm) REVERT: B 995 MET cc_start: 0.8819 (ptp) cc_final: 0.8282 (ptp) REVERT: B 1050 LEU cc_start: 0.9543 (mp) cc_final: 0.9138 (pt) REVERT: B 1165 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: B 1174 MET cc_start: 0.8344 (ptp) cc_final: 0.8082 (pmm) REVERT: B 1487 MET cc_start: 0.8553 (mtp) cc_final: 0.8347 (mtp) REVERT: B 1564 MET cc_start: 0.8663 (mmm) cc_final: 0.8444 (mmm) REVERT: B 1953 MET cc_start: 0.9040 (tpt) cc_final: 0.8790 (tpp) REVERT: B 2134 MET cc_start: 0.8948 (tpp) cc_final: 0.8710 (tpt) REVERT: B 2732 TRP cc_start: 0.9055 (t60) cc_final: 0.8721 (t60) REVERT: B 2757 MET cc_start: 0.8413 (mmt) cc_final: 0.8017 (mmm) REVERT: B 3215 MET cc_start: 0.9470 (ppp) cc_final: 0.9151 (tpp) REVERT: B 3243 CYS cc_start: 0.8059 (m) cc_final: 0.7796 (m) REVERT: B 3248 ARG cc_start: 0.9089 (ttm-80) cc_final: 0.8825 (ttm170) REVERT: B 3263 MET cc_start: 0.8898 (mmp) cc_final: 0.8542 (mpp) REVERT: B 3302 PHE cc_start: 0.8685 (t80) cc_final: 0.8444 (t80) REVERT: B 3719 MET cc_start: 0.8388 (mmp) cc_final: 0.8137 (mmp) REVERT: B 4258 MET cc_start: 0.6870 (ttt) cc_final: 0.6484 (ptt) REVERT: B 4268 MET cc_start: 0.8239 (tpp) cc_final: 0.7952 (ptm) REVERT: C 128 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8587 (mtm) REVERT: C 309 MET cc_start: 0.8077 (mmp) cc_final: 0.7793 (mmt) REVERT: C 393 MET cc_start: 0.8076 (mmm) cc_final: 0.7526 (mmm) REVERT: C 878 LEU cc_start: 0.9368 (tp) cc_final: 0.9024 (tp) REVERT: C 981 MET cc_start: 0.7840 (ppp) cc_final: 0.7468 (ppp) REVERT: C 995 MET cc_start: 0.8802 (ptp) cc_final: 0.8269 (ptp) REVERT: C 1487 MET cc_start: 0.8500 (mtp) cc_final: 0.8252 (mtp) REVERT: C 1953 MET cc_start: 0.8981 (mmm) cc_final: 0.8675 (mmm) REVERT: C 2732 TRP cc_start: 0.8941 (t60) cc_final: 0.8726 (t60) REVERT: C 2783 LEU cc_start: 0.9414 (mt) cc_final: 0.9148 (mt) REVERT: C 2828 MET cc_start: 0.8854 (tpp) cc_final: 0.8554 (tpp) REVERT: C 2840 MET cc_start: 0.9027 (mmm) cc_final: 0.8120 (mmt) REVERT: C 2843 MET cc_start: 0.8464 (tpp) cc_final: 0.8100 (tpp) REVERT: C 2844 MET cc_start: 0.8771 (tmm) cc_final: 0.8399 (tmm) REVERT: C 2848 TYR cc_start: 0.8141 (m-80) cc_final: 0.7874 (m-80) REVERT: C 2943 PHE cc_start: 0.8254 (m-80) cc_final: 0.7787 (m-80) REVERT: C 3215 MET cc_start: 0.9493 (ppp) cc_final: 0.9143 (tpp) REVERT: C 3235 MET cc_start: 0.8819 (pmm) cc_final: 0.8236 (pmm) REVERT: C 3299 LEU cc_start: 0.9229 (tt) cc_final: 0.8985 (mt) REVERT: C 3323 MET cc_start: 0.8667 (tpp) cc_final: 0.8128 (mmt) REVERT: C 4268 MET cc_start: 0.8089 (tpp) cc_final: 0.7765 (ptm) REVERT: C 4279 MET cc_start: 0.8576 (ttt) cc_final: 0.8062 (ttp) REVERT: D 309 MET cc_start: 0.8268 (mmp) cc_final: 0.7840 (mmp) REVERT: D 317 MET cc_start: 0.7671 (ptt) cc_final: 0.7432 (ptt) REVERT: D 393 MET cc_start: 0.8095 (tpt) cc_final: 0.7635 (mmm) REVERT: D 878 LEU cc_start: 0.9494 (tp) cc_final: 0.9198 (tp) REVERT: D 949 HIS cc_start: 0.8045 (t-90) cc_final: 0.7793 (t-90) REVERT: D 981 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6734 (ppp) REVERT: D 1421 MET cc_start: 0.9051 (mmp) cc_final: 0.8831 (mmm) REVERT: D 1564 MET cc_start: 0.8759 (mmm) cc_final: 0.8435 (mmm) REVERT: D 2214 MET cc_start: 0.9168 (mmm) cc_final: 0.8840 (mmm) REVERT: D 2585 MET cc_start: 0.8393 (ptp) cc_final: 0.8191 (mtp) REVERT: D 2840 MET cc_start: 0.8617 (mmt) cc_final: 0.8249 (mmt) REVERT: D 2935 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: D 2939 TYR cc_start: 0.8682 (m-10) cc_final: 0.8316 (m-80) REVERT: D 2943 PHE cc_start: 0.8038 (m-80) cc_final: 0.7610 (m-80) REVERT: D 3215 MET cc_start: 0.9498 (ppp) cc_final: 0.9034 (tpp) REVERT: D 3235 MET cc_start: 0.9030 (pmm) cc_final: 0.8825 (pmm) REVERT: D 3243 CYS cc_start: 0.7764 (m) cc_final: 0.7540 (m) REVERT: D 3302 PHE cc_start: 0.8703 (t80) cc_final: 0.8376 (t80) REVERT: D 3719 MET cc_start: 0.8244 (mmp) cc_final: 0.7930 (mmm) REVERT: D 4109 MET cc_start: 0.8388 (mtp) cc_final: 0.8144 (mtt) REVERT: J 14 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9136 (tppt) REVERT: J 50 GLN cc_start: 0.9186 (mt0) cc_final: 0.8850 (mm-40) REVERT: J 72 MET cc_start: 0.9170 (tmm) cc_final: 0.8531 (tmm) REVERT: J 73 MET cc_start: 0.8902 (mmp) cc_final: 0.8429 (mmm) REVERT: J 101 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8688 (mt) REVERT: L 31 LYS cc_start: 0.9443 (mmmt) cc_final: 0.9199 (mmmt) REVERT: L 73 MET cc_start: 0.9117 (mmm) cc_final: 0.8758 (mmm) REVERT: K 14 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9199 (tppt) REVERT: K 31 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9074 (mmmt) REVERT: K 72 MET cc_start: 0.9292 (tmm) cc_final: 0.9004 (tmm) REVERT: K 73 MET cc_start: 0.8892 (mmp) cc_final: 0.8393 (mmm) outliers start: 119 outliers final: 88 residues processed: 872 average time/residue: 1.2340 time to fit residues: 1928.9912 Evaluate side-chains 888 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 786 time to evaluate : 12.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2348 GLU Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3223 GLU Chi-restraints excluded: chain A residue 3245 TYR Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 981 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2736 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3245 TYR Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3281 LEU Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1979 PHE Chi-restraints excluded: chain C residue 2095 ILE Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2736 LYS Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3093 ILE Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3245 TYR Chi-restraints excluded: chain C residue 4067 LEU Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 981 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2348 GLU Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3263 MET Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 98 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 9.9990 chunk 1651 optimal weight: 1.9990 chunk 1506 optimal weight: 9.9990 chunk 1605 optimal weight: 20.0000 chunk 1650 optimal weight: 0.9990 chunk 966 optimal weight: 2.9990 chunk 699 optimal weight: 8.9990 chunk 1261 optimal weight: 9.9990 chunk 492 optimal weight: 7.9990 chunk 1451 optimal weight: 10.0000 chunk 1518 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 79 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4579 HIS ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3770 ASN C3949 HIS ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.288 146568 Z= 0.297 Angle : 0.638 22.603 197972 Z= 0.320 Chirality : 0.041 0.428 21688 Planarity : 0.004 0.134 25472 Dihedral : 5.421 89.871 19664 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 0.81 % Allowed : 8.13 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % 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: 1.37 (0.06), residues: 17808 helix: 1.93 (0.05), residues: 9512 sheet: -0.21 (0.13), residues: 1704 loop : -0.23 (0.08), residues: 6592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 893 HIS 0.015 0.001 HIS J 108 PHE 0.025 0.001 PHE C3854 TYR 0.032 0.001 TYR A3138 ARG 0.014 0.000 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 797 time to evaluate : 12.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8097 (tpt) cc_final: 0.7764 (mmm) REVERT: A 878 LEU cc_start: 0.9398 (tp) cc_final: 0.9020 (tp) REVERT: A 981 MET cc_start: 0.7711 (ppp) cc_final: 0.7088 (ppp) REVERT: A 1215 MET cc_start: 0.8738 (mtp) cc_final: 0.8428 (mtp) REVERT: A 2384 MET cc_start: 0.9093 (mmm) cc_final: 0.8879 (mmm) REVERT: A 2828 MET cc_start: 0.8740 (ttm) cc_final: 0.8449 (ttt) REVERT: A 2840 MET cc_start: 0.9141 (mmm) cc_final: 0.8848 (mmm) REVERT: A 2843 MET cc_start: 0.8617 (ttt) cc_final: 0.8198 (tmm) REVERT: A 2844 MET cc_start: 0.8832 (ppp) cc_final: 0.8576 (ppp) REVERT: A 2848 TYR cc_start: 0.8060 (t80) cc_final: 0.7811 (t80) REVERT: A 2943 PHE cc_start: 0.8402 (m-80) cc_final: 0.7984 (m-80) REVERT: A 3138 TYR cc_start: 0.8665 (m-80) cc_final: 0.8442 (m-80) REVERT: A 3215 MET cc_start: 0.9525 (ppp) cc_final: 0.9184 (tpp) REVERT: A 3241 MET cc_start: 0.9197 (ttp) cc_final: 0.8916 (tmm) REVERT: A 3243 CYS cc_start: 0.8533 (m) cc_final: 0.8108 (m) REVERT: A 3605 MET cc_start: 0.9104 (ttm) cc_final: 0.8697 (mtm) REVERT: A 3719 MET cc_start: 0.8339 (mmm) cc_final: 0.8130 (mmp) REVERT: A 3981 MET cc_start: 0.8914 (tmm) cc_final: 0.8351 (ttp) REVERT: A 4139 MET cc_start: 0.9102 (tpp) cc_final: 0.8889 (tpt) REVERT: A 4268 MET cc_start: 0.7653 (mmp) cc_final: 0.7137 (ptm) REVERT: A 4306 PHE cc_start: 0.7779 (t80) cc_final: 0.7577 (m-10) REVERT: A 4728 MET cc_start: 0.9233 (mmm) cc_final: 0.9031 (mmt) REVERT: E 4 GLU cc_start: 0.8108 (pm20) cc_final: 0.7774 (pm20) REVERT: E 54 GLN cc_start: 0.9214 (mp10) cc_final: 0.8654 (mp10) REVERT: E 108 GLU cc_start: 0.8412 (pp20) cc_final: 0.8028 (pm20) REVERT: F 54 GLN cc_start: 0.9170 (mp10) cc_final: 0.8652 (mp10) REVERT: F 58 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8020 (ptpp) REVERT: F 62 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: F 108 GLU cc_start: 0.8460 (pp20) cc_final: 0.7944 (pp20) REVERT: G 53 LYS cc_start: 0.9133 (mppt) cc_final: 0.8737 (mptt) REVERT: G 54 GLN cc_start: 0.9214 (mp10) cc_final: 0.8716 (mp10) REVERT: G 58 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8106 (ptpp) REVERT: G 62 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: G 108 GLU cc_start: 0.8435 (pp20) cc_final: 0.8183 (pm20) REVERT: H 30 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7440 (mpp) REVERT: H 53 LYS cc_start: 0.9131 (mppt) cc_final: 0.8737 (mptt) REVERT: H 54 GLN cc_start: 0.9222 (mp10) cc_final: 0.8735 (mp10) REVERT: H 108 GLU cc_start: 0.8414 (pp20) cc_final: 0.8123 (pm20) REVERT: I 14 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9147 (tppt) REVERT: I 31 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9163 (mmmt) REVERT: I 72 MET cc_start: 0.9485 (ttt) cc_final: 0.8969 (tmm) REVERT: I 73 MET cc_start: 0.9092 (mmm) cc_final: 0.8059 (mmm) REVERT: B 393 MET cc_start: 0.8005 (mmm) cc_final: 0.7314 (mmm) REVERT: B 878 LEU cc_start: 0.9421 (tp) cc_final: 0.9113 (tp) REVERT: B 981 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6928 (tmm) REVERT: B 995 MET cc_start: 0.8826 (ptp) cc_final: 0.8272 (ptp) REVERT: B 1050 LEU cc_start: 0.9548 (mp) cc_final: 0.9145 (pt) REVERT: B 1165 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8333 (mtt) REVERT: B 1174 MET cc_start: 0.8349 (ptp) cc_final: 0.8087 (pmm) REVERT: B 1953 MET cc_start: 0.9039 (tpt) cc_final: 0.8803 (tpp) REVERT: B 2732 TRP cc_start: 0.9063 (t60) cc_final: 0.8744 (t60) REVERT: B 2757 MET cc_start: 0.8374 (mmt) cc_final: 0.7993 (mmm) REVERT: B 2840 MET cc_start: 0.9185 (mmm) cc_final: 0.8813 (mmm) REVERT: B 2843 MET cc_start: 0.8743 (ptt) cc_final: 0.8313 (ptp) REVERT: B 2943 PHE cc_start: 0.8345 (m-80) cc_final: 0.7788 (m-80) REVERT: B 3138 TYR cc_start: 0.8748 (m-80) cc_final: 0.8438 (m-80) REVERT: B 3215 MET cc_start: 0.9476 (ppp) cc_final: 0.9158 (tpp) REVERT: B 3263 MET cc_start: 0.8929 (mmp) cc_final: 0.8585 (mpp) REVERT: B 3302 PHE cc_start: 0.8763 (t80) cc_final: 0.8519 (t80) REVERT: B 3719 MET cc_start: 0.8399 (mmp) cc_final: 0.8152 (mmp) REVERT: B 4258 MET cc_start: 0.6862 (ttt) cc_final: 0.6481 (ptt) REVERT: B 4268 MET cc_start: 0.8162 (tpp) cc_final: 0.7886 (ptm) REVERT: C 128 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8593 (mtm) REVERT: C 393 MET cc_start: 0.8055 (mmm) cc_final: 0.7541 (mmm) REVERT: C 878 LEU cc_start: 0.9372 (tp) cc_final: 0.8969 (tp) REVERT: C 995 MET cc_start: 0.8804 (ptp) cc_final: 0.8323 (ptp) REVERT: C 1487 MET cc_start: 0.8557 (mtp) cc_final: 0.8250 (mtp) REVERT: C 1953 MET cc_start: 0.8983 (mmm) cc_final: 0.8676 (mmm) REVERT: C 2783 LEU cc_start: 0.9420 (mt) cc_final: 0.9155 (mt) REVERT: C 2828 MET cc_start: 0.8874 (tpp) cc_final: 0.8566 (tpp) REVERT: C 2843 MET cc_start: 0.8491 (tpp) cc_final: 0.8068 (tpp) REVERT: C 2844 MET cc_start: 0.8796 (tmm) cc_final: 0.8588 (tmm) REVERT: C 2943 PHE cc_start: 0.8258 (m-80) cc_final: 0.7760 (m-80) REVERT: C 3235 MET cc_start: 0.8846 (pmm) cc_final: 0.8264 (pmm) REVERT: C 3299 LEU cc_start: 0.9229 (tt) cc_final: 0.8988 (mt) REVERT: C 3605 MET cc_start: 0.9174 (ttm) cc_final: 0.8887 (mtm) REVERT: C 4268 MET cc_start: 0.8118 (tpp) cc_final: 0.7750 (ptm) REVERT: D 309 MET cc_start: 0.8290 (mmp) cc_final: 0.7871 (mmp) REVERT: D 317 MET cc_start: 0.7684 (ptt) cc_final: 0.7459 (ptt) REVERT: D 393 MET cc_start: 0.8086 (tpt) cc_final: 0.7591 (mmm) REVERT: D 878 LEU cc_start: 0.9499 (tp) cc_final: 0.9195 (tp) REVERT: D 949 HIS cc_start: 0.8087 (t-90) cc_final: 0.7832 (t-90) REVERT: D 981 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6693 (ppp) REVERT: D 1564 MET cc_start: 0.8752 (mmm) cc_final: 0.8523 (mmt) REVERT: D 2214 MET cc_start: 0.9178 (mmm) cc_final: 0.8922 (mmm) REVERT: D 2840 MET cc_start: 0.8700 (mmt) cc_final: 0.8112 (mmt) REVERT: D 2843 MET cc_start: 0.8890 (ptp) cc_final: 0.8474 (pmm) REVERT: D 2939 TYR cc_start: 0.8687 (m-10) cc_final: 0.8287 (m-80) REVERT: D 2943 PHE cc_start: 0.8042 (m-80) cc_final: 0.7608 (m-80) REVERT: D 3215 MET cc_start: 0.9512 (ppp) cc_final: 0.9056 (tpp) REVERT: D 3235 MET cc_start: 0.9065 (pmm) cc_final: 0.8846 (pmm) REVERT: D 3243 CYS cc_start: 0.7833 (m) cc_final: 0.7586 (m) REVERT: D 3302 PHE cc_start: 0.8733 (t80) cc_final: 0.8384 (t80) REVERT: D 3719 MET cc_start: 0.8247 (mmp) cc_final: 0.7943 (mmm) REVERT: D 4109 MET cc_start: 0.8439 (mtp) cc_final: 0.8198 (mtt) REVERT: J 14 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9147 (tppt) REVERT: J 50 GLN cc_start: 0.9223 (mt0) cc_final: 0.8700 (mm-40) REVERT: J 52 MET cc_start: 0.9392 (mmm) cc_final: 0.9080 (mtp) REVERT: J 72 MET cc_start: 0.9187 (tmm) cc_final: 0.8525 (tmm) REVERT: J 73 MET cc_start: 0.8982 (mmp) cc_final: 0.8500 (mmm) REVERT: J 101 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8693 (mt) REVERT: L 31 LYS cc_start: 0.9447 (mmmt) cc_final: 0.9207 (mmmt) REVERT: L 73 MET cc_start: 0.9148 (mmm) cc_final: 0.8803 (mmm) REVERT: K 14 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9201 (tppt) REVERT: K 31 LYS cc_start: 0.9365 (mmmt) cc_final: 0.9088 (mmmt) REVERT: K 72 MET cc_start: 0.9297 (tmm) cc_final: 0.8997 (tmm) REVERT: K 73 MET cc_start: 0.8936 (mmp) cc_final: 0.8403 (mmm) outliers start: 119 outliers final: 93 residues processed: 871 average time/residue: 1.2485 time to fit residues: 1942.9806 Evaluate side-chains 899 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 793 time to evaluate : 11.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2348 GLU Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3223 GLU Chi-restraints excluded: chain A residue 3245 TYR Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 981 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2736 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3245 TYR Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3281 LEU Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1979 PHE Chi-restraints excluded: chain C residue 2095 ILE Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2736 LYS Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3093 ILE Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3245 TYR Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 4067 LEU Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 981 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2095 ILE Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2348 GLU Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3263 MET Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 98 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 7.9990 chunk 1054 optimal weight: 6.9990 chunk 1698 optimal weight: 6.9990 chunk 1036 optimal weight: 30.0000 chunk 805 optimal weight: 0.9980 chunk 1180 optimal weight: 6.9990 chunk 1781 optimal weight: 1.9990 chunk 1639 optimal weight: 2.9990 chunk 1418 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 1095 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3770 ASN C3949 HIS ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.350 146568 Z= 0.277 Angle : 0.643 22.761 197972 Z= 0.321 Chirality : 0.041 0.429 21688 Planarity : 0.004 0.133 25472 Dihedral : 5.389 89.945 19664 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 0.74 % Allowed : 8.26 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % 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: 17808 helix: 1.94 (0.05), residues: 9516 sheet: -0.20 (0.13), residues: 1704 loop : -0.22 (0.08), residues: 6588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.002 TRP B3249 HIS 0.014 0.001 HIS J 108 PHE 0.021 0.001 PHE D3854 TYR 0.037 0.001 TYR D3285 ARG 0.014 0.000 ARG H 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35616 Ramachandran restraints generated. 17808 Oldfield, 0 Emsley, 17808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 802 time to evaluate : 11.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8093 (tpt) cc_final: 0.7755 (mmm) REVERT: A 878 LEU cc_start: 0.9398 (tp) cc_final: 0.9014 (tp) REVERT: A 981 MET cc_start: 0.7701 (ppp) cc_final: 0.7080 (ppp) REVERT: A 995 MET cc_start: 0.8811 (ptp) cc_final: 0.8578 (ptp) REVERT: A 1215 MET cc_start: 0.8726 (mtp) cc_final: 0.8421 (mtp) REVERT: A 2757 MET cc_start: 0.8249 (mmm) cc_final: 0.7916 (mmm) REVERT: A 2828 MET cc_start: 0.8704 (ttm) cc_final: 0.8407 (ttt) REVERT: A 2840 MET cc_start: 0.9143 (mmm) cc_final: 0.8857 (mmm) REVERT: A 2843 MET cc_start: 0.8576 (ttt) cc_final: 0.8277 (tmm) REVERT: A 2844 MET cc_start: 0.8827 (ppp) cc_final: 0.8568 (ppp) REVERT: A 2943 PHE cc_start: 0.8390 (m-80) cc_final: 0.7998 (m-80) REVERT: A 3138 TYR cc_start: 0.8678 (m-80) cc_final: 0.8378 (m-80) REVERT: A 3215 MET cc_start: 0.9523 (ppp) cc_final: 0.9186 (tpp) REVERT: A 3241 MET cc_start: 0.9184 (ttp) cc_final: 0.8904 (tmm) REVERT: A 3243 CYS cc_start: 0.8603 (m) cc_final: 0.8195 (m) REVERT: A 3605 MET cc_start: 0.9090 (ttm) cc_final: 0.8691 (mtm) REVERT: A 3719 MET cc_start: 0.8333 (mmm) cc_final: 0.8126 (mmp) REVERT: A 3981 MET cc_start: 0.8941 (tmm) cc_final: 0.8328 (ttp) REVERT: A 4139 MET cc_start: 0.9095 (tpp) cc_final: 0.8881 (tpt) REVERT: A 4268 MET cc_start: 0.7647 (mmp) cc_final: 0.7113 (ptm) REVERT: A 4728 MET cc_start: 0.9238 (mmm) cc_final: 0.9033 (mmt) REVERT: E 4 GLU cc_start: 0.8113 (pm20) cc_final: 0.7772 (pm20) REVERT: E 54 GLN cc_start: 0.9211 (mp10) cc_final: 0.8642 (mp10) REVERT: E 108 GLU cc_start: 0.8401 (pp20) cc_final: 0.8019 (pm20) REVERT: F 54 GLN cc_start: 0.9176 (mp10) cc_final: 0.8649 (mp10) REVERT: F 58 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8021 (ptpp) REVERT: F 62 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: F 108 GLU cc_start: 0.8458 (pp20) cc_final: 0.7954 (pp20) REVERT: G 53 LYS cc_start: 0.9136 (mppt) cc_final: 0.8738 (mptt) REVERT: G 54 GLN cc_start: 0.9219 (mp10) cc_final: 0.8717 (mp10) REVERT: G 58 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8056 (pttm) REVERT: G 62 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: G 108 GLU cc_start: 0.8433 (pp20) cc_final: 0.8182 (pm20) REVERT: H 30 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7394 (mpp) REVERT: H 53 LYS cc_start: 0.9135 (mppt) cc_final: 0.8738 (mptt) REVERT: H 54 GLN cc_start: 0.9219 (mp10) cc_final: 0.8730 (mp10) REVERT: H 108 GLU cc_start: 0.8418 (pp20) cc_final: 0.8125 (pm20) REVERT: I 14 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9145 (tppt) REVERT: I 31 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9148 (mmmt) REVERT: I 73 MET cc_start: 0.9119 (mmm) cc_final: 0.8633 (mmm) REVERT: B 393 MET cc_start: 0.7998 (mmm) cc_final: 0.7338 (mmm) REVERT: B 878 LEU cc_start: 0.9418 (tp) cc_final: 0.9099 (tp) REVERT: B 981 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6944 (tmm) REVERT: B 1050 LEU cc_start: 0.9544 (mp) cc_final: 0.9151 (pt) REVERT: B 1165 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8319 (mtt) REVERT: B 1174 MET cc_start: 0.8321 (ptp) cc_final: 0.8065 (pmm) REVERT: B 1487 MET cc_start: 0.8598 (mtp) cc_final: 0.8367 (mtp) REVERT: B 1953 MET cc_start: 0.9029 (tpt) cc_final: 0.8800 (tpp) REVERT: B 2732 TRP cc_start: 0.9056 (t60) cc_final: 0.8740 (t60) REVERT: B 2757 MET cc_start: 0.8351 (mmt) cc_final: 0.7973 (mmm) REVERT: B 2840 MET cc_start: 0.9129 (mmm) cc_final: 0.8757 (mmm) REVERT: B 2843 MET cc_start: 0.8711 (ptt) cc_final: 0.8272 (ptp) REVERT: B 2943 PHE cc_start: 0.8352 (m-80) cc_final: 0.7803 (m-80) REVERT: B 3138 TYR cc_start: 0.8741 (m-80) cc_final: 0.8443 (m-80) REVERT: B 3215 MET cc_start: 0.9488 (ppp) cc_final: 0.9162 (tpp) REVERT: B 3263 MET cc_start: 0.8956 (mmp) cc_final: 0.8593 (mpp) REVERT: B 3302 PHE cc_start: 0.8710 (t80) cc_final: 0.8436 (t80) REVERT: B 3719 MET cc_start: 0.8401 (mmp) cc_final: 0.8157 (mmp) REVERT: B 4258 MET cc_start: 0.6843 (ttt) cc_final: 0.6472 (ptt) REVERT: B 4268 MET cc_start: 0.8125 (tpp) cc_final: 0.7847 (ptm) REVERT: C 128 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8580 (mtm) REVERT: C 309 MET cc_start: 0.7696 (mmp) cc_final: 0.7402 (mmp) REVERT: C 393 MET cc_start: 0.8065 (mmm) cc_final: 0.7529 (mmm) REVERT: C 878 LEU cc_start: 0.9371 (tp) cc_final: 0.9028 (tp) REVERT: C 995 MET cc_start: 0.8803 (ptp) cc_final: 0.8322 (ptp) REVERT: C 1487 MET cc_start: 0.8537 (mtp) cc_final: 0.8266 (mtp) REVERT: C 1953 MET cc_start: 0.8995 (mmm) cc_final: 0.8675 (mmm) REVERT: C 2783 LEU cc_start: 0.9417 (mt) cc_final: 0.9193 (mt) REVERT: C 2828 MET cc_start: 0.8848 (tpp) cc_final: 0.8541 (tpp) REVERT: C 2843 MET cc_start: 0.8485 (tpp) cc_final: 0.8096 (tpp) REVERT: C 2844 MET cc_start: 0.8800 (tmm) cc_final: 0.8585 (tmm) REVERT: C 2943 PHE cc_start: 0.8227 (m-80) cc_final: 0.7732 (m-80) REVERT: C 3215 MET cc_start: 0.9318 (ppp) cc_final: 0.9043 (tpp) REVERT: C 3299 LEU cc_start: 0.9216 (tt) cc_final: 0.8977 (mt) REVERT: C 4268 MET cc_start: 0.8096 (tpp) cc_final: 0.7737 (ptm) REVERT: C 4279 MET cc_start: 0.8421 (ttt) cc_final: 0.8168 (mtt) REVERT: D 309 MET cc_start: 0.8299 (mmp) cc_final: 0.7888 (mmp) REVERT: D 317 MET cc_start: 0.7687 (ptt) cc_final: 0.7452 (ptt) REVERT: D 393 MET cc_start: 0.8096 (tpt) cc_final: 0.7619 (mmm) REVERT: D 878 LEU cc_start: 0.9500 (tp) cc_final: 0.9195 (tp) REVERT: D 949 HIS cc_start: 0.8105 (t-90) cc_final: 0.7853 (t-90) REVERT: D 981 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6667 (ppp) REVERT: D 1564 MET cc_start: 0.8765 (mmm) cc_final: 0.8541 (mmt) REVERT: D 2214 MET cc_start: 0.9162 (mmm) cc_final: 0.8924 (mmm) REVERT: D 2840 MET cc_start: 0.8640 (mmt) cc_final: 0.8083 (mmt) REVERT: D 2843 MET cc_start: 0.8844 (ptp) cc_final: 0.8420 (pmm) REVERT: D 2939 TYR cc_start: 0.8681 (m-10) cc_final: 0.8282 (m-80) REVERT: D 2943 PHE cc_start: 0.8055 (m-80) cc_final: 0.7624 (m-80) REVERT: D 3215 MET cc_start: 0.9513 (ppp) cc_final: 0.9056 (tpp) REVERT: D 3235 MET cc_start: 0.9071 (pmm) cc_final: 0.8826 (pmm) REVERT: D 3243 CYS cc_start: 0.7896 (m) cc_final: 0.7673 (m) REVERT: D 3302 PHE cc_start: 0.8743 (t80) cc_final: 0.8396 (t80) REVERT: D 3719 MET cc_start: 0.8259 (mmp) cc_final: 0.7956 (mmm) REVERT: D 4109 MET cc_start: 0.8437 (mtp) cc_final: 0.8195 (mtt) REVERT: J 14 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9140 (tppt) REVERT: J 50 GLN cc_start: 0.9222 (mt0) cc_final: 0.8661 (mm-40) REVERT: J 72 MET cc_start: 0.9167 (tmm) cc_final: 0.8506 (tmm) REVERT: J 73 MET cc_start: 0.8979 (mmp) cc_final: 0.8485 (mmm) REVERT: J 101 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8687 (mt) REVERT: L 31 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9205 (mmmt) REVERT: L 52 MET cc_start: 0.9393 (mmm) cc_final: 0.9169 (mtp) REVERT: L 73 MET cc_start: 0.9141 (mmm) cc_final: 0.8790 (mmm) REVERT: K 14 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9200 (tppt) REVERT: K 31 LYS cc_start: 0.9365 (mmmt) cc_final: 0.9092 (mmmt) REVERT: K 52 MET cc_start: 0.9463 (mmm) cc_final: 0.9242 (mtp) outliers start: 109 outliers final: 91 residues processed: 869 average time/residue: 1.1991 time to fit residues: 1857.0560 Evaluate side-chains 898 residues out of total 15712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 794 time to evaluate : 12.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1979 PHE Chi-restraints excluded: chain A residue 2348 GLU Chi-restraints excluded: chain A residue 2736 LYS Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3174 HIS Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3223 GLU Chi-restraints excluded: chain A residue 3245 TYR Chi-restraints excluded: chain A residue 3281 LEU Chi-restraints excluded: chain A residue 3888 PHE Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4753 LEU Chi-restraints excluded: chain A residue 4819 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 981 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1979 PHE Chi-restraints excluded: chain B residue 2348 GLU Chi-restraints excluded: chain B residue 2736 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3126 VAL Chi-restraints excluded: chain B residue 3174 HIS Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3245 TYR Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3281 LEU Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4819 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1979 PHE Chi-restraints excluded: chain C residue 2095 ILE Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2736 LYS Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3093 ILE Chi-restraints excluded: chain C residue 3126 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3245 TYR Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 4067 LEU Chi-restraints excluded: chain C residue 4753 LEU Chi-restraints excluded: chain D residue 981 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1979 PHE Chi-restraints excluded: chain D residue 2095 ILE Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2348 GLU Chi-restraints excluded: chain D residue 2736 LYS Chi-restraints excluded: chain D residue 2777 GLU Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3126 VAL Chi-restraints excluded: chain D residue 3174 HIS Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3263 MET Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 98 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 10.0000 chunk 1126 optimal weight: 9.9990 chunk 1510 optimal weight: 6.9990 chunk 434 optimal weight: 3.9990 chunk 1307 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 394 optimal weight: 50.0000 chunk 1420 optimal weight: 30.0000 chunk 594 optimal weight: 10.0000 chunk 1458 optimal weight: 4.9990 chunk 179 optimal weight: 0.0570 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3770 ASN C3949 HIS D 79 GLN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.036184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.026368 restraints weight = 1994522.841| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.42 r_work: 0.2769 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 146568 Z= 0.288 Angle : 0.649 22.885 197972 Z= 0.324 Chirality : 0.041 0.425 21688 Planarity : 0.004 0.133 25472 Dihedral : 5.352 89.872 19664 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 0.74 % Allowed : 8.35 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % 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: 1.38 (0.06), residues: 17808 helix: 1.93 (0.05), residues: 9520 sheet: -0.19 (0.13), residues: 1704 loop : -0.21 (0.08), residues: 6584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.002 TRP B3249 HIS 0.013 0.001 HIS J 108 PHE 0.024 0.001 PHE C3854 TYR 0.041 0.001 TYR D3285 ARG 0.015 0.000 ARG H 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36339.50 seconds wall clock time: 637 minutes 43.14 seconds (38263.14 seconds total)