Starting phenix.real_space_refine on Thu May 16 11:53:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxi_42765/05_2024/8uxi_42765_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxi_42765/05_2024/8uxi_42765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxi_42765/05_2024/8uxi_42765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxi_42765/05_2024/8uxi_42765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxi_42765/05_2024/8uxi_42765_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxi_42765/05_2024/8uxi_42765_updated.pdb" } resolution = 3.29 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= 0.007 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 876 5.16 5 C 83788 2.51 5 N 22420 2.21 5 O 24540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1028": "NH1" <-> "NH2" Residue "A GLU 1076": "OE1" <-> "OE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1131": "OD1" <-> "OD2" Residue "A ASP 1138": "OD1" <-> "OD2" Residue "A ASP 1167": "OD1" <-> "OD2" Residue "A ASP 1471": "OD1" <-> "OD2" Residue "A TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1960": "NH1" <-> "NH2" Residue "A GLU 2169": "OE1" <-> "OE2" Residue "A GLU 2329": "OE1" <-> "OE2" Residue "A ASP 2379": "OD1" <-> "OD2" Residue "A PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2453": "OE1" <-> "OE2" Residue "A PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2718": "OE1" <-> "OE2" Residue "A GLU 2745": "OE1" <-> "OE2" Residue "A GLU 2765": "OE1" <-> "OE2" Residue "A TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2952": "OE1" <-> "OE2" Residue "A GLU 2959": "OE1" <-> "OE2" Residue "A TYR 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3025": "OD1" <-> "OD2" Residue "A GLU 3051": "OE1" <-> "OE2" Residue "A GLU 3654": "OE1" <-> "OE2" Residue "A ASP 3693": "OD1" <-> "OD2" Residue "A GLU 3783": "OE1" <-> "OE2" Residue "A GLU 3823": "OE1" <-> "OE2" Residue "A ASP 3832": "OD1" <-> "OD2" Residue "A GLU 4146": "OE1" <-> "OE2" Residue "A PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4678": "OD1" <-> "OD2" Residue "A GLU 4882": "OE1" <-> "OE2" Residue "A TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B ARG 913": "NH1" <-> "NH2" Residue "B TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1028": "NH1" <-> "NH2" Residue "B GLU 1076": "OE1" <-> "OE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1131": "OD1" <-> "OD2" Residue "B ASP 1138": "OD1" <-> "OD2" Residue "B ASP 1167": "OD1" <-> "OD2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1960": "NH1" <-> "NH2" Residue "B GLU 2169": "OE1" <-> "OE2" Residue "B GLU 2329": "OE1" <-> "OE2" Residue "B ASP 2379": "OD1" <-> "OD2" Residue "B PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2453": "OE1" <-> "OE2" Residue "B PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2718": "OE1" <-> "OE2" Residue "B GLU 2745": "OE1" <-> "OE2" Residue "B GLU 2765": "OE1" <-> "OE2" Residue "B TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2952": "OE1" <-> "OE2" Residue "B GLU 2959": "OE1" <-> "OE2" Residue "B TYR 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3025": "OD1" <-> "OD2" Residue "B GLU 3051": "OE1" <-> "OE2" Residue "B GLU 3654": "OE1" <-> "OE2" Residue "B ASP 3693": "OD1" <-> "OD2" Residue "B GLU 3783": "OE1" <-> "OE2" Residue "B GLU 3823": "OE1" <-> "OE2" Residue "B ASP 3832": "OD1" <-> "OD2" Residue "B GLU 4146": "OE1" <-> "OE2" Residue "B PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4678": "OD1" <-> "OD2" Residue "B GLU 4882": "OE1" <-> "OE2" Residue "B TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C ARG 913": "NH1" <-> "NH2" Residue "C TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1028": "NH1" <-> "NH2" Residue "C GLU 1076": "OE1" <-> "OE2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1131": "OD1" <-> "OD2" Residue "C ASP 1138": "OD1" <-> "OD2" Residue "C ASP 1167": "OD1" <-> "OD2" Residue "C ASP 1471": "OD1" <-> "OD2" Residue "C TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1960": "NH1" <-> "NH2" Residue "C GLU 2169": "OE1" <-> "OE2" Residue "C GLU 2329": "OE1" <-> "OE2" Residue "C ASP 2379": "OD1" <-> "OD2" Residue "C PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2453": "OE1" <-> "OE2" Residue "C PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2718": "OE1" <-> "OE2" Residue "C GLU 2745": "OE1" <-> "OE2" Residue "C GLU 2765": "OE1" <-> "OE2" Residue "C TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2952": "OE1" <-> "OE2" Residue "C GLU 2959": "OE1" <-> "OE2" Residue "C TYR 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3025": "OD1" <-> "OD2" Residue "C GLU 3051": "OE1" <-> "OE2" Residue "C GLU 3654": "OE1" <-> "OE2" Residue "C ASP 3693": "OD1" <-> "OD2" Residue "C GLU 3783": "OE1" <-> "OE2" Residue "C GLU 3823": "OE1" <-> "OE2" Residue "C ASP 3832": "OD1" <-> "OD2" Residue "C GLU 4146": "OE1" <-> "OE2" Residue "C PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4678": "OD1" <-> "OD2" Residue "C GLU 4882": "OE1" <-> "OE2" Residue "C TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 581": "OE1" <-> "OE2" Residue "D TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D ARG 913": "NH1" <-> "NH2" Residue "D TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1028": "NH1" <-> "NH2" Residue "D GLU 1076": "OE1" <-> "OE2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1131": "OD1" <-> "OD2" Residue "D ASP 1138": "OD1" <-> "OD2" Residue "D ASP 1167": "OD1" <-> "OD2" Residue "D ASP 1471": "OD1" <-> "OD2" Residue "D TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1960": "NH1" <-> "NH2" Residue "D GLU 2169": "OE1" <-> "OE2" Residue "D GLU 2329": "OE1" <-> "OE2" Residue "D ASP 2379": "OD1" <-> "OD2" Residue "D PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2453": "OE1" <-> "OE2" Residue "D PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2718": "OE1" <-> "OE2" Residue "D GLU 2745": "OE1" <-> "OE2" Residue "D GLU 2765": "OE1" <-> "OE2" Residue "D TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2952": "OE1" <-> "OE2" Residue "D GLU 2959": "OE1" <-> "OE2" Residue "D TYR 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3025": "OD1" <-> "OD2" Residue "D GLU 3051": "OE1" <-> "OE2" Residue "D GLU 3654": "OE1" <-> "OE2" Residue "D ASP 3693": "OD1" <-> "OD2" Residue "D GLU 3783": "OE1" <-> "OE2" Residue "D GLU 3823": "OE1" <-> "OE2" Residue "D ASP 3832": "OD1" <-> "OD2" Residue "D GLU 4146": "OE1" <-> "OE2" Residue "D PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4678": "OD1" <-> "OD2" Residue "D GLU 4882": "OE1" <-> "OE2" Residue "D TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.39s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 131656 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "C" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "D" Number of atoms: 32032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4004, 32024 Classifications: {'peptide': 4004} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 145, 'TRANS': 3858} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 32712 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31353 SG CYS A4888 174.017 204.079 85.476 1.00141.24 S ATOM 31378 SG CYS A4891 176.515 203.210 88.241 1.00130.09 S ATOM 66657 SG CYS B4888 175.979 173.384 85.735 1.00147.92 S ATOM 66682 SG CYS B4891 176.828 175.893 88.495 1.00136.77 S ATOM 98689 SG CYS C4888 206.594 175.047 85.298 1.00140.52 S ATOM 98714 SG CYS C4891 204.084 175.909 88.054 1.00129.89 S ATOM A0NPD SG CYS D4888 204.652 205.945 85.659 1.00143.49 S ATOM A0NQ2 SG CYS D4891 203.782 203.453 88.428 1.00134.22 S Time building chain proxies: 90.44, per 1000 atoms: 0.69 Number of scatterers: 131656 At special positions: 0 Unit cell: (380.81, 379.967, 212.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 876 16.00 P 24 15.00 O 24540 8.00 N 22420 7.00 C 83788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.76 Conformation dependent library (CDL) restraints added in 31.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 30776 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 652 helices and 64 sheets defined 58.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 37.83 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 5.406A pdb=" N SER A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.059A 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 260 removed outlier: 4.124A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.883A 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: 3.622A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.970A 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: 3.544A pdb=" N VAL A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 4.974A 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: 4.755A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.699A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.457A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.365A 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: 3.916A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 removed outlier: 4.099A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.729A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.707A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.570A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.516A 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: 4.031A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 900 " --> pdb=" O ASN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 Proline residue: A 925 - end of helix Processing helix chain 'A' and resid 926 through 947 removed outlier: 3.556A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 4.190A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.795A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 4.088A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.403A 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: 5.997A pdb=" N GLN A1233 " --> pdb=" O ILE A1229 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 4.316A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.040A 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: 5.778A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.872A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.100A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.650A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.914A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 3.658A pdb=" N ALA A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.502A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.847A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1937 removed outlier: 4.304A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1939 through 1948 Processing helix chain 'A' and resid 1950 through 1955 removed outlier: 4.516A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1950 through 1955' Processing helix chain 'A' and resid 1956 through 1966 removed outlier: 3.642A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 removed outlier: 4.022A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.528A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.646A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 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: 3.930A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2152 Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2159 through 2166 removed outlier: 3.773A pdb=" N GLY A2166 " --> pdb=" O MET A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 5.326A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 4.100A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A2194 " --> pdb=" O PRO A2190 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.966A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.696A 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: 3.730A 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: 3.934A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.803A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 3.957A pdb=" N THR A2381 " --> pdb=" O GLU A2377 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2377 through 2382' 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: 5.602A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.688A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 4.930A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 5.018A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2510 removed outlier: 3.824A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2510' Processing helix chain 'A' and resid 2511 through 2532 removed outlier: 5.266A 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: 3.534A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.081A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix Processing helix chain 'A' and resid 2634 through 2656 removed outlier: 6.140A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS A2656 " --> pdb=" O LEU A2652 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 3.734A pdb=" N ASP A2696 " --> pdb=" O GLN A2692 " (cutoff:3.500A) Processing helix chain 'A' and resid 2714 through 2740 Processing helix chain 'A' and resid 2767 through 2785 removed outlier: 4.032A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix removed outlier: 3.860A pdb=" N TRP A2785 " --> pdb=" O THR A2781 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 4.315A pdb=" N ASP A2796 " --> pdb=" O THR A2792 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.611A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2881 through 2900 removed outlier: 4.784A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS A2888 " --> pdb=" O LYS A2884 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A2900 " --> pdb=" O LEU A2896 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2948 removed outlier: 3.559A pdb=" N SER A2924 " --> pdb=" O ARG A2920 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 5.346A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 3.583A pdb=" N PHE A3022 " --> pdb=" O ARG A3018 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3018 through 3023' Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.821A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A3040 " --> pdb=" O LEU A3036 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3079 removed outlier: 3.644A pdb=" N GLN A3079 " --> pdb=" O LEU A3075 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.322A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3599 through 3605 removed outlier: 4.495A pdb=" N MET A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 4.010A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.206A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 removed outlier: 3.544A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.779A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.703A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 4.197A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.589A pdb=" N ILE A3744 " --> pdb=" O VAL A3740 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.761A 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 3821 through 3829 removed outlier: 4.229A pdb=" N GLU A3827 " --> pdb=" O GLU A3823 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A3828 " --> pdb=" O GLY A3824 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A3829 " --> pdb=" O SER A3825 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.595A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.562A 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 3962 removed outlier: 3.751A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.506A pdb=" N GLU A3987 " --> pdb=" O LEU A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4027 removed outlier: 4.640A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4029 through 4037 removed outlier: 4.343A pdb=" N TYR A4035 " --> pdb=" O THR A4031 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A4036 " --> pdb=" O PHE A4032 " (cutoff:3.500A) Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.544A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.145A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.790A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 4.180A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A4098 " --> pdb=" O ILE A4094 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 3.737A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 removed outlier: 3.550A pdb=" N ARG A4157 " --> pdb=" O SER A4153 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A4162 " --> pdb=" O THR A4158 " (cutoff:3.500A) Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4181 through 4208 removed outlier: 4.662A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A4205 " --> pdb=" O GLN A4201 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4257 removed outlier: 3.516A pdb=" N LEU A4255 " --> pdb=" O ASN A4251 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4274 Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.799A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 4.611A pdb=" N ILE A4484 " --> pdb=" O PHE A4480 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR A4487 " --> pdb=" O LYS A4483 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 3.685A pdb=" N PHE A4515 " --> pdb=" O PHE A4511 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4569 through 4612 removed outlier: 3.577A pdb=" N ARG A4573 " --> pdb=" O GLU A4569 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.568A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 4.165A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.993A pdb=" N ASP A4702 " --> pdb=" O LEU A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.745A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.721A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.596A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A4761 " --> pdb=" O LEU A4757 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 5.375A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.994A 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: 4.201A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A4823 " --> pdb=" O VAL A4819 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.198A 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 removed outlier: 3.737A pdb=" N ILE A4866 " --> pdb=" O ILE A4862 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.134A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 857 through 862 removed outlier: 3.842A pdb=" N ALA A 860 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 861 " --> pdb=" O THR A 858 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 1497 through 1503 removed outlier: 5.510A pdb=" N ARG A1500 " --> pdb=" O GLY A1497 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A1501 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A1502 " --> pdb=" O GLY A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 4.521A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.844A 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 51 through 56 removed outlier: 5.406A pdb=" N SER B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.058A 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 260 removed outlier: 4.125A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.884A 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: 3.622A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.969A 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: 3.545A pdb=" N VAL B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 4.974A 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: 4.756A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.698A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.458A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.365A 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: 3.916A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 removed outlier: 4.100A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.730A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.707A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.571A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.516A 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: 4.032A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 Proline residue: B 925 - end of helix Processing helix chain 'B' and resid 926 through 947 removed outlier: 3.555A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 4.190A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.796A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 4.086A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.402A 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: 5.996A pdb=" N GLN B1233 " --> pdb=" O ILE B1229 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 4.316A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.040A 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: 5.779A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.872A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.099A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.650A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.914A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 3.657A pdb=" N ALA B1715 " --> pdb=" O LEU B1711 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.503A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1802 Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.847A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1937 removed outlier: 4.304A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1939 through 1948 Processing helix chain 'B' and resid 1950 through 1955 removed outlier: 4.516A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1950 through 1955' Processing helix chain 'B' and resid 1956 through 1966 removed outlier: 3.642A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 removed outlier: 4.023A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.528A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.646A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 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: 3.930A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2152 Processing helix chain 'B' and resid 2153 through 2158 Processing helix chain 'B' and resid 2159 through 2166 removed outlier: 3.773A pdb=" N GLY B2166 " --> pdb=" O MET B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 5.326A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 4.100A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B2194 " --> pdb=" O PRO B2190 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.966A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.697A 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: 3.731A 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: 3.934A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.804A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B2320 " --> pdb=" O ASN B2316 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2377 through 2382 removed outlier: 3.957A pdb=" N THR B2381 " --> pdb=" O GLU B2377 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2377 through 2382' 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: 5.602A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.689A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 4.930A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 5.019A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2510 removed outlier: 3.824A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2510' Processing helix chain 'B' and resid 2511 through 2532 removed outlier: 5.267A 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: 3.534A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.080A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix Processing helix chain 'B' and resid 2634 through 2656 removed outlier: 6.140A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS B2656 " --> pdb=" O LEU B2652 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 3.735A pdb=" N ASP B2696 " --> pdb=" O GLN B2692 " (cutoff:3.500A) Processing helix chain 'B' and resid 2714 through 2740 Processing helix chain 'B' and resid 2767 through 2785 removed outlier: 4.032A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix removed outlier: 3.861A pdb=" N TRP B2785 " --> pdb=" O THR B2781 " (cutoff:3.500A) Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 4.315A pdb=" N ASP B2796 " --> pdb=" O THR B2792 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.611A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2881 through 2900 removed outlier: 4.784A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS B2888 " --> pdb=" O LYS B2884 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B2900 " --> pdb=" O LEU B2896 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2948 removed outlier: 3.559A pdb=" N SER B2924 " --> pdb=" O ARG B2920 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 5.346A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 3.584A pdb=" N PHE B3022 " --> pdb=" O ARG B3018 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3018 through 3023' Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.821A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B3040 " --> pdb=" O LEU B3036 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3079 removed outlier: 3.643A pdb=" N GLN B3079 " --> pdb=" O LEU B3075 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.322A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3599 through 3605 removed outlier: 4.495A pdb=" N MET B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 4.010A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.206A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 removed outlier: 3.544A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.779A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.703A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 4.196A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.588A pdb=" N ILE B3744 " --> pdb=" O VAL B3740 " (cutoff:3.500A) removed outlier: 3.912A 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: 4.761A 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 3821 through 3829 removed outlier: 4.231A pdb=" N GLU B3827 " --> pdb=" O GLU B3823 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B3828 " --> pdb=" O GLY B3824 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B3829 " --> pdb=" O SER B3825 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.594A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.563A 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 3962 removed outlier: 3.751A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.507A pdb=" N GLU B3987 " --> pdb=" O LEU B3983 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4027 removed outlier: 4.640A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4029 through 4037 removed outlier: 4.344A pdb=" N TYR B4035 " --> pdb=" O THR B4031 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B4036 " --> pdb=" O PHE B4032 " (cutoff:3.500A) Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.545A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.144A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.789A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 4.179A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B4098 " --> pdb=" O ILE B4094 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 3.736A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 removed outlier: 3.550A pdb=" N ARG B4157 " --> pdb=" O SER B4153 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B4162 " --> pdb=" O THR B4158 " (cutoff:3.500A) Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4181 through 4208 removed outlier: 4.662A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B4205 " --> pdb=" O GLN B4201 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4257 removed outlier: 3.516A pdb=" N LEU B4255 " --> pdb=" O ASN B4251 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4274 Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.800A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 4.612A pdb=" N ILE B4484 " --> pdb=" O PHE B4480 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR B4487 " --> pdb=" O LYS B4483 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 3.685A pdb=" N PHE B4515 " --> pdb=" O PHE B4511 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4569 through 4612 removed outlier: 3.578A pdb=" N ARG B4573 " --> pdb=" O GLU B4569 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.567A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 4.165A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.993A pdb=" N ASP B4702 " --> pdb=" O LEU B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.744A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.720A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.597A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR B4761 " --> pdb=" O LEU B4757 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 5.374A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.994A 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: 4.201A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B4823 " --> pdb=" O VAL B4819 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.199A 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 removed outlier: 3.738A pdb=" N ILE B4866 " --> pdb=" O ILE B4862 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.133A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 857 through 862 removed outlier: 3.842A pdb=" N ALA B 860 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 861 " --> pdb=" O THR B 858 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B 862 " --> pdb=" O GLN B 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 1497 through 1503 removed outlier: 5.509A pdb=" N ARG B1500 " --> pdb=" O GLY B1497 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B1501 " --> pdb=" O GLN B1498 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B1502 " --> pdb=" O GLY B1499 " (cutoff:3.500A) Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 4.522A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.844A 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 51 through 56 removed outlier: 5.406A pdb=" N SER C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.059A 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 260 removed outlier: 4.125A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.883A 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: 3.622A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.969A 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: 3.544A pdb=" N VAL C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 4.974A 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: 4.755A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.698A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.458A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.366A 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: 3.916A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 removed outlier: 4.100A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.730A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.707A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.570A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.515A 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: 4.031A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 Proline residue: C 925 - end of helix Processing helix chain 'C' and resid 926 through 947 removed outlier: 3.556A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 4.190A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.795A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 4.087A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.403A 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: 5.997A pdb=" N GLN C1233 " --> pdb=" O ILE C1229 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 4.316A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.040A 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: 5.778A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.872A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.099A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.651A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.914A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 3.657A pdb=" N ALA C1715 " --> pdb=" O LEU C1711 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.502A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.848A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1937 removed outlier: 4.303A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1939 through 1948 Processing helix chain 'C' and resid 1950 through 1955 removed outlier: 4.516A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1950 through 1955' Processing helix chain 'C' and resid 1956 through 1966 removed outlier: 3.642A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 removed outlier: 4.023A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.529A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.646A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 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: 3.931A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2152 Processing helix chain 'C' and resid 2153 through 2158 Processing helix chain 'C' and resid 2159 through 2166 removed outlier: 3.774A pdb=" N GLY C2166 " --> pdb=" O MET C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 5.326A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 4.100A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C2194 " --> pdb=" O PRO C2190 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.966A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.697A 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: 3.730A 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: 3.934A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.804A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C2320 " --> pdb=" O ASN C2316 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2377 through 2382 removed outlier: 3.958A pdb=" N THR C2381 " --> pdb=" O GLU C2377 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C2382 " --> pdb=" O GLU C2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2377 through 2382' 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: 5.603A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.688A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 4.930A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 5.019A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2510 removed outlier: 3.824A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2510' Processing helix chain 'C' and resid 2511 through 2532 removed outlier: 5.267A 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: 3.534A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.080A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix Processing helix chain 'C' and resid 2634 through 2656 removed outlier: 6.140A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS C2656 " --> pdb=" O LEU C2652 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 3.735A pdb=" N ASP C2696 " --> pdb=" O GLN C2692 " (cutoff:3.500A) Processing helix chain 'C' and resid 2714 through 2740 Processing helix chain 'C' and resid 2767 through 2785 removed outlier: 4.031A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix removed outlier: 3.860A pdb=" N TRP C2785 " --> pdb=" O THR C2781 " (cutoff:3.500A) Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 4.315A pdb=" N ASP C2796 " --> pdb=" O THR C2792 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.612A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2881 through 2900 removed outlier: 4.784A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS C2888 " --> pdb=" O LYS C2884 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C2900 " --> pdb=" O LEU C2896 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2948 removed outlier: 3.559A pdb=" N SER C2924 " --> pdb=" O ARG C2920 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 5.346A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 3.584A pdb=" N PHE C3022 " --> pdb=" O ARG C3018 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3018 through 3023' Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.821A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C3040 " --> pdb=" O LEU C3036 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3079 removed outlier: 3.644A pdb=" N GLN C3079 " --> pdb=" O LEU C3075 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.323A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3599 through 3605 removed outlier: 4.495A pdb=" N MET C3605 " --> pdb=" O ALA C3601 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 4.009A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.206A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 removed outlier: 3.544A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.779A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.703A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 4.196A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.589A pdb=" N ILE C3744 " --> pdb=" O VAL C3740 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.761A 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 3821 through 3829 removed outlier: 4.229A pdb=" N GLU C3827 " --> pdb=" O GLU C3823 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C3828 " --> pdb=" O GLY C3824 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL C3829 " --> pdb=" O SER C3825 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.595A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.563A 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 3962 removed outlier: 3.750A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.506A pdb=" N GLU C3987 " --> pdb=" O LEU C3983 " (cutoff:3.500A) Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4027 removed outlier: 4.641A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4029 through 4037 removed outlier: 4.344A pdb=" N TYR C4035 " --> pdb=" O THR C4031 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP C4036 " --> pdb=" O PHE C4032 " (cutoff:3.500A) Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.545A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.144A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.790A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 4.181A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C4098 " --> pdb=" O ILE C4094 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 3.736A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 removed outlier: 3.550A pdb=" N ARG C4157 " --> pdb=" O SER C4153 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C4162 " --> pdb=" O THR C4158 " (cutoff:3.500A) Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4181 through 4208 removed outlier: 4.662A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C4205 " --> pdb=" O GLN C4201 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4257 removed outlier: 3.517A pdb=" N LEU C4255 " --> pdb=" O ASN C4251 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4274 Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.799A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 4.611A pdb=" N ILE C4484 " --> pdb=" O PHE C4480 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR C4487 " --> pdb=" O LYS C4483 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 3.685A pdb=" N PHE C4515 " --> pdb=" O PHE C4511 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4569 through 4612 removed outlier: 3.577A pdb=" N ARG C4573 " --> pdb=" O GLU C4569 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.566A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 4.165A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.993A pdb=" N ASP C4702 " --> pdb=" O LEU C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.744A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.720A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.597A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C4761 " --> pdb=" O LEU C4757 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 5.375A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.994A 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: 4.201A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C4823 " --> pdb=" O VAL C4819 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.199A 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 removed outlier: 3.737A pdb=" N ILE C4866 " --> pdb=" O ILE C4862 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.135A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 857 through 862 removed outlier: 3.842A pdb=" N ALA C 860 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 861 " --> pdb=" O THR C 858 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE C 862 " --> pdb=" O GLN C 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 1497 through 1503 removed outlier: 5.509A pdb=" N ARG C1500 " --> pdb=" O GLY C1497 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN C1501 " --> pdb=" O GLN C1498 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN C1502 " --> pdb=" O GLY C1499 " (cutoff:3.500A) Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 4.521A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.844A 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 51 through 56 removed outlier: 5.407A pdb=" N SER D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.059A 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 260 removed outlier: 4.124A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL D 260 " --> pdb=" O GLN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.883A 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: 3.622A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.970A 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: 3.545A pdb=" N VAL D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 4.974A 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: 4.755A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.698A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.457A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.366A 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: 3.916A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 590 removed outlier: 4.100A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.730A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.707A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.571A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.516A 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: 4.032A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 900 " --> pdb=" O ASN D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 925 Proline residue: D 925 - end of helix Processing helix chain 'D' and resid 926 through 947 removed outlier: 3.555A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 4.191A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.796A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 4.088A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.403A 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: 5.997A pdb=" N GLN D1233 " --> pdb=" O ILE D1229 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 4.315A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.040A 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: 5.778A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.872A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.099A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.651A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.914A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 3.657A pdb=" N ALA D1715 " --> pdb=" O LEU D1711 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.503A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1802 Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.847A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1937 removed outlier: 4.304A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1939 through 1948 Processing helix chain 'D' and resid 1950 through 1955 removed outlier: 4.516A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1950 through 1955' Processing helix chain 'D' and resid 1956 through 1966 removed outlier: 3.643A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 removed outlier: 4.022A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.528A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.646A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 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: 3.930A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2152 Processing helix chain 'D' and resid 2153 through 2158 Processing helix chain 'D' and resid 2159 through 2166 removed outlier: 3.773A pdb=" N GLY D2166 " --> pdb=" O MET D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 5.326A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 4.100A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D2194 " --> pdb=" O PRO D2190 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.965A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.696A 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: 3.731A 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: 3.934A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.804A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D2320 " --> pdb=" O ASN D2316 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2377 through 2382 removed outlier: 3.958A pdb=" N THR D2381 " --> pdb=" O GLU D2377 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2377 through 2382' 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: 5.603A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.689A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 4.930A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 5.019A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2510 removed outlier: 3.825A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2510' Processing helix chain 'D' and resid 2511 through 2532 removed outlier: 5.267A 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: 3.534A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.081A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix Processing helix chain 'D' and resid 2634 through 2656 removed outlier: 6.140A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS D2656 " --> pdb=" O LEU D2652 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 3.735A pdb=" N ASP D2696 " --> pdb=" O GLN D2692 " (cutoff:3.500A) Processing helix chain 'D' and resid 2714 through 2740 Processing helix chain 'D' and resid 2767 through 2785 removed outlier: 4.031A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix removed outlier: 3.861A pdb=" N TRP D2785 " --> pdb=" O THR D2781 " (cutoff:3.500A) Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 4.314A pdb=" N ASP D2796 " --> pdb=" O THR D2792 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.611A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2881 through 2900 removed outlier: 4.783A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS D2888 " --> pdb=" O LYS D2884 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D2900 " --> pdb=" O LEU D2896 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2948 removed outlier: 3.559A pdb=" N SER D2924 " --> pdb=" O ARG D2920 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 5.345A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 3.583A pdb=" N PHE D3022 " --> pdb=" O ARG D3018 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3018 through 3023' Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.822A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D3040 " --> pdb=" O LEU D3036 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3079 removed outlier: 3.644A pdb=" N GLN D3079 " --> pdb=" O LEU D3075 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.322A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3599 through 3605 removed outlier: 4.495A pdb=" N MET D3605 " --> pdb=" O ALA D3601 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 4.009A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.207A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 removed outlier: 3.543A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.780A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.702A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 4.197A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.588A pdb=" N ILE D3744 " --> pdb=" O VAL D3740 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.761A 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 3821 through 3829 removed outlier: 4.230A pdb=" N GLU D3827 " --> pdb=" O GLU D3823 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D3828 " --> pdb=" O GLY D3824 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL D3829 " --> pdb=" O SER D3825 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.595A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.563A 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 3962 removed outlier: 3.751A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.507A pdb=" N GLU D3987 " --> pdb=" O LEU D3983 " (cutoff:3.500A) Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4027 removed outlier: 4.641A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4029 through 4037 removed outlier: 4.344A pdb=" N TYR D4035 " --> pdb=" O THR D4031 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP D4036 " --> pdb=" O PHE D4032 " (cutoff:3.500A) Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.544A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.144A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.790A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 4.180A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D4098 " --> pdb=" O ILE D4094 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 3.736A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 removed outlier: 3.550A pdb=" N ARG D4157 " --> pdb=" O SER D4153 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS D4162 " --> pdb=" O THR D4158 " (cutoff:3.500A) Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4181 through 4208 removed outlier: 4.662A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN D4205 " --> pdb=" O GLN D4201 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4257 removed outlier: 3.515A pdb=" N LEU D4255 " --> pdb=" O ASN D4251 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4274 Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.799A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 4.612A pdb=" N ILE D4484 " --> pdb=" O PHE D4480 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR D4487 " --> pdb=" O LYS D4483 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 3.685A pdb=" N PHE D4515 " --> pdb=" O PHE D4511 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4569 through 4612 removed outlier: 3.577A pdb=" N ARG D4573 " --> pdb=" O GLU D4569 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.568A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 4.165A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.992A pdb=" N ASP D4702 " --> pdb=" O LEU D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.745A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.721A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.597A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR D4761 " --> pdb=" O LEU D4757 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 5.374A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.994A 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: 4.201A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D4823 " --> pdb=" O VAL D4819 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.199A 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 removed outlier: 3.737A pdb=" N ILE D4866 " --> pdb=" O ILE D4862 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.134A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 857 through 862 removed outlier: 3.842A pdb=" N ALA D 860 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 861 " --> pdb=" O THR D 858 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE D 862 " --> pdb=" O GLN D 859 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 1497 through 1503 removed outlier: 5.510A pdb=" N ARG D1500 " --> pdb=" O GLY D1497 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN D1501 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN D1502 " --> pdb=" O GLY D1499 " (cutoff:3.500A) Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 4.521A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.844A 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: 3.738A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 4.172A pdb=" N MET E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.720A pdb=" N ALA E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 83' Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.738A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 4.174A pdb=" N MET F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.718A pdb=" N ALA F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 83' Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.738A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 4.174A pdb=" N MET G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.718A pdb=" N ALA G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 78 through 83' Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.739A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 4.174A pdb=" N MET H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.718A pdb=" N ALA H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 78 through 83' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 5.563A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.472A 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: 6.748A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 4, first strand: chain 'A' and resid 274 through 279 removed outlier: 8.338A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 300 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 14.395A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 307 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 329 through 333 removed outlier: 3.512A pdb=" N TYR A 362 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 692 through 697 removed outlier: 5.635A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.808A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP A1617 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.517A pdb=" N GLU A1478 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.178A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE A1105 " --> pdb=" O VAL A1162 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 948 through 952 Processing sheet with id= 11, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 6.953A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A1208 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A1090 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1280 through 1285 removed outlier: 3.971A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1505 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.629A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.884A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 16, first strand: chain 'B' and resid 47 through 50 removed outlier: 5.563A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.747A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 19, first strand: chain 'B' and resid 274 through 279 removed outlier: 8.338A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 300 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 14.396A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 307 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.512A pdb=" N TYR B 362 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 692 through 697 removed outlier: 5.635A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.808A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP B1617 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 777 through 780 removed outlier: 3.518A pdb=" N GLU B1478 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.178A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE B1105 " --> pdb=" O VAL B1162 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 948 through 952 Processing sheet with id= 26, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 6.953A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B1208 " --> pdb=" O ASP B1112 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B1090 " --> pdb=" O PRO B1203 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 1280 through 1285 removed outlier: 3.971A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B1505 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.629A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.884A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 31, first strand: chain 'C' and resid 47 through 50 removed outlier: 5.563A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.748A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 34, first strand: chain 'C' and resid 274 through 279 removed outlier: 8.339A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 300 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 14.396A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 307 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 329 through 333 removed outlier: 3.511A pdb=" N TYR C 362 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 692 through 697 removed outlier: 5.635A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.808A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C1617 " --> pdb=" O PHE C 802 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 777 through 780 removed outlier: 3.517A pdb=" N GLU C1478 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.177A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C1105 " --> pdb=" O VAL C1162 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 948 through 952 Processing sheet with id= 41, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 6.953A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY C1208 " --> pdb=" O ASP C1112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1090 " --> pdb=" O PRO C1203 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 1280 through 1285 removed outlier: 3.971A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C1505 " --> pdb=" O ILE C1432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.628A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.883A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 46, first strand: chain 'D' and resid 47 through 50 removed outlier: 5.563A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.473A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.748A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 49, first strand: chain 'D' and resid 274 through 279 removed outlier: 8.338A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 300 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 14.396A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 307 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'D' and resid 329 through 333 removed outlier: 3.511A pdb=" N TYR D 362 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'D' and resid 692 through 697 removed outlier: 5.636A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.808A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP D1617 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 777 through 780 removed outlier: 3.518A pdb=" N GLU D1478 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.177A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE D1105 " --> pdb=" O VAL D1162 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 948 through 952 Processing sheet with id= 56, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 6.953A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D1208 " --> pdb=" O ASP D1112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D1090 " --> pdb=" O PRO D1203 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 1280 through 1285 removed outlier: 3.971A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D1505 " --> pdb=" O ILE D1432 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.629A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.884A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 61, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.591A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU E 6 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.591A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU F 6 " --> pdb=" O LYS F 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.591A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU G 6 " --> pdb=" O LYS G 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.591A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU H 6 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 6776 hydrogen bonds defined for protein. 20236 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: 99.26 Time building geometry restraints manager: 43.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 37515 1.33 - 1.46: 30221 1.46 - 1.58: 65352 1.58 - 1.71: 32 1.71 - 1.83: 1416 Bond restraints: 134536 Sorted by residual: bond pdb=" CA ILE A 881 " pdb=" C ILE A 881 " ideal model delta sigma weight residual 1.523 1.542 -0.019 9.60e-03 1.09e+04 3.96e+00 bond pdb=" CA ILE B 881 " pdb=" C ILE B 881 " ideal model delta sigma weight residual 1.523 1.541 -0.019 9.60e-03 1.09e+04 3.76e+00 bond pdb=" CA PRO D1968 " pdb=" C PRO D1968 " ideal model delta sigma weight residual 1.514 1.504 0.011 5.50e-03 3.31e+04 3.76e+00 bond pdb=" CA ILE C 881 " pdb=" C ILE C 881 " ideal model delta sigma weight residual 1.523 1.541 -0.019 9.60e-03 1.09e+04 3.72e+00 bond pdb=" CA ILE D 881 " pdb=" C ILE D 881 " ideal model delta sigma weight residual 1.523 1.541 -0.018 9.60e-03 1.09e+04 3.68e+00 ... (remaining 134531 not shown) Histogram of bond angle deviations from ideal: 95.49 - 104.37: 2141 104.37 - 113.25: 72982 113.25 - 122.14: 83663 122.14 - 131.02: 22251 131.02 - 139.90: 715 Bond angle restraints: 181752 Sorted by residual: angle pdb=" C VAL A1563 " pdb=" N MET A1564 " pdb=" CA MET A1564 " ideal model delta sigma weight residual 120.67 132.48 -11.81 1.34e+00 5.57e-01 7.77e+01 angle pdb=" C VAL C1563 " pdb=" N MET C1564 " pdb=" CA MET C1564 " ideal model delta sigma weight residual 120.67 132.48 -11.81 1.34e+00 5.57e-01 7.77e+01 angle pdb=" C VAL D1563 " pdb=" N MET D1564 " pdb=" CA MET D1564 " ideal model delta sigma weight residual 120.67 132.43 -11.76 1.34e+00 5.57e-01 7.71e+01 angle pdb=" C VAL B1563 " pdb=" N MET B1564 " pdb=" CA MET B1564 " ideal model delta sigma weight residual 120.67 132.43 -11.76 1.34e+00 5.57e-01 7.70e+01 angle pdb=" CA ARG F 50 " pdb=" CB ARG F 50 " pdb=" CG ARG F 50 " ideal model delta sigma weight residual 114.10 128.78 -14.68 2.00e+00 2.50e-01 5.39e+01 ... (remaining 181747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 72436 17.97 - 35.93: 6781 35.93 - 53.90: 1235 53.90 - 71.86: 464 71.86 - 89.83: 104 Dihedral angle restraints: 81020 sinusoidal: 33260 harmonic: 47760 Sorted by residual: 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 -128.93 -51.07 0 5.00e+00 4.00e-02 1.04e+02 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 -128.98 -51.02 0 5.00e+00 4.00e-02 1.04e+02 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 -129.00 -51.00 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 81017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 18072 0.073 - 0.146: 1720 0.146 - 0.218: 80 0.218 - 0.291: 4 0.291 - 0.364: 8 Chirality restraints: 19884 Sorted by residual: chirality pdb=" CG LEU B2763 " pdb=" CB LEU B2763 " pdb=" CD1 LEU B2763 " pdb=" CD2 LEU B2763 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU D2763 " pdb=" CB LEU D2763 " pdb=" CD1 LEU D2763 " pdb=" CD2 LEU D2763 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CG LEU C2763 " pdb=" CB LEU C2763 " pdb=" CD1 LEU C2763 " pdb=" CD2 LEU C2763 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 19881 not shown) Planarity restraints: 23364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 880 " -0.810 9.50e-02 1.11e+02 3.64e-01 8.50e+01 pdb=" NE ARG A 880 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 880 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 880 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 880 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 880 " -0.810 9.50e-02 1.11e+02 3.64e-01 8.49e+01 pdb=" NE ARG D 880 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D 880 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG D 880 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 880 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 880 " -0.810 9.50e-02 1.11e+02 3.64e-01 8.49e+01 pdb=" NE ARG B 880 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 880 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG B 880 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 880 " -0.010 2.00e-02 2.50e+03 ... (remaining 23361 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1466 2.62 - 3.19: 120897 3.19 - 3.76: 215624 3.76 - 4.33: 291043 4.33 - 4.90: 469898 Nonbonded interactions: 1098928 Sorted by model distance: nonbonded pdb=" NH2 ARG B3043 " pdb=" O GLN B3116 " model vdw 2.050 2.520 nonbonded pdb=" NH2 ARG C3043 " pdb=" O GLN C3116 " model vdw 2.051 2.520 nonbonded pdb=" NH2 ARG A3043 " pdb=" O GLN A3116 " model vdw 2.051 2.520 nonbonded pdb=" NH2 ARG D3043 " pdb=" O GLN D3116 " model vdw 2.051 2.520 nonbonded pdb=" OD2 ASP A4018 " pdb=" OG SER A4124 " model vdw 2.094 2.440 ... (remaining 1098923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.620 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: 0.160 Extract box with map and model: 30.230 Check model and map are aligned: 0.740 Set scattering table: 0.900 Process input model: 421.620 Find NCS groups from input model: 7.840 Set up NCS constraints: 1.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 472.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 134536 Z= 0.209 Angle : 0.825 21.400 181752 Z= 0.446 Chirality : 0.042 0.364 19884 Planarity : 0.008 0.364 23364 Dihedral : 14.983 89.827 50232 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 1.28 % Allowed : 1.03 % Favored : 97.69 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % 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: 0.82 (0.07), residues: 16332 helix: 1.40 (0.06), residues: 8508 sheet: 0.19 (0.13), residues: 1556 loop : -0.48 (0.08), residues: 6268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.002 TRP A 893 HIS 0.026 0.001 HIS B 890 PHE 0.064 0.001 PHE A4640 TYR 0.037 0.001 TYR A2901 ARG 0.036 0.001 ARG A 880 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 837 time to evaluate : 11.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.7546 (mmm) cc_final: 0.7148 (mmm) REVERT: A 880 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8736 (ttp80) REVERT: A 882 ARG cc_start: 0.9059 (pmt-80) cc_final: 0.8765 (pmt-80) REVERT: A 921 PHE cc_start: 0.9691 (p90) cc_final: 0.9363 (p90) REVERT: A 1249 MET cc_start: 0.8144 (ttm) cc_final: 0.7882 (ttt) REVERT: A 2584 MET cc_start: 0.8822 (mmm) cc_final: 0.8555 (mmm) REVERT: A 2702 ASN cc_start: 0.8738 (t0) cc_final: 0.8422 (t0) REVERT: A 2724 TYR cc_start: 0.8695 (t80) cc_final: 0.8415 (t80) REVERT: A 2895 PHE cc_start: 0.8954 (t80) cc_final: 0.8327 (t80) REVERT: A 2975 PHE cc_start: 0.8779 (m-10) cc_final: 0.8528 (m-10) REVERT: A 2982 PHE cc_start: 0.8650 (m-80) cc_final: 0.8100 (m-80) REVERT: A 3033 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 3072 MET cc_start: 0.7176 (mmt) cc_final: 0.6975 (mmm) REVERT: A 3104 MET cc_start: 0.8802 (tmm) cc_final: 0.8482 (tmm) REVERT: A 4002 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7953 (ttp) REVERT: A 4035 TYR cc_start: 0.8777 (m-80) cc_final: 0.8342 (m-80) REVERT: A 4292 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8272 (mmm) REVERT: A 4748 MET cc_start: 0.7867 (mpp) cc_final: 0.7217 (mpp) REVERT: A 4965 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: E 19 LYS cc_start: 0.8861 (tppp) cc_final: 0.8585 (tppp) REVERT: E 45 LYS cc_start: 0.9114 (ptpp) cc_final: 0.8905 (ptpp) REVERT: E 58 LYS cc_start: 0.8711 (ptpt) cc_final: 0.7782 (ptpp) REVERT: E 103 GLU cc_start: 0.8083 (tt0) cc_final: 0.7845 (tm-30) REVERT: F 45 LYS cc_start: 0.9116 (ptpp) cc_final: 0.8892 (ptpp) REVERT: F 51 ILE cc_start: 0.8947 (mm) cc_final: 0.8732 (mm) REVERT: F 58 LYS cc_start: 0.8542 (ptpt) cc_final: 0.7648 (ptpp) REVERT: F 103 GLU cc_start: 0.8040 (tt0) cc_final: 0.7787 (tm-30) REVERT: G 58 LYS cc_start: 0.8739 (ptpt) cc_final: 0.7684 (ptpp) REVERT: H 58 LYS cc_start: 0.8837 (ptpt) cc_final: 0.7675 (ptpp) REVERT: B 893 TRP cc_start: 0.8506 (m-90) cc_final: 0.8116 (m-90) REVERT: B 1022 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7839 (tp-100) REVERT: B 1057 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9096 (pp) REVERT: B 1202 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8165 (pt) REVERT: B 2580 LEU cc_start: 0.8630 (mt) cc_final: 0.8399 (mt) REVERT: B 2605 MET cc_start: 0.8654 (tmm) cc_final: 0.8369 (tmm) REVERT: B 2609 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8875 (pp) REVERT: B 2702 ASN cc_start: 0.8860 (t0) cc_final: 0.8585 (t0) REVERT: B 2724 TYR cc_start: 0.8735 (t80) cc_final: 0.8482 (t80) REVERT: B 2835 ARG cc_start: 0.8994 (tpm170) cc_final: 0.8595 (tpm170) REVERT: B 2843 MET cc_start: 0.6980 (ppp) cc_final: 0.6552 (ppp) REVERT: B 2884 LYS cc_start: 0.9395 (tmmt) cc_final: 0.9039 (tppt) REVERT: B 3104 MET cc_start: 0.8773 (tmm) cc_final: 0.8567 (tmm) REVERT: B 3719 MET cc_start: 0.8414 (mmp) cc_final: 0.8104 (mmp) REVERT: B 4052 MET cc_start: 0.7812 (mmm) cc_final: 0.7421 (mmp) REVERT: B 4186 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8473 (mmm) REVERT: B 4256 MET cc_start: 0.8305 (mmt) cc_final: 0.8067 (mmm) REVERT: B 4279 MET cc_start: 0.7985 (tpt) cc_final: 0.7715 (tpt) REVERT: B 4748 MET cc_start: 0.7251 (mpp) cc_final: 0.6997 (mpp) REVERT: C 393 MET cc_start: 0.7805 (mmm) cc_final: 0.7552 (mmm) REVERT: C 880 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8742 (ttp80) REVERT: C 882 ARG cc_start: 0.9094 (pmt-80) cc_final: 0.8771 (pmt-80) REVERT: C 921 PHE cc_start: 0.9683 (p90) cc_final: 0.9316 (p90) REVERT: C 1022 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8116 (tp-100) REVERT: C 1064 LEU cc_start: 0.9036 (pp) cc_final: 0.8836 (pp) REVERT: C 2605 MET cc_start: 0.8618 (tmm) cc_final: 0.8392 (tmm) REVERT: C 2724 TYR cc_start: 0.8822 (t80) cc_final: 0.8587 (t80) REVERT: C 2768 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8828 (mmtt) REVERT: C 2779 LEU cc_start: 0.9682 (mt) cc_final: 0.9347 (pp) REVERT: C 2837 LEU cc_start: 0.9436 (tp) cc_final: 0.9226 (tp) REVERT: C 2843 MET cc_start: 0.7221 (ppp) cc_final: 0.6827 (ppp) REVERT: C 2895 PHE cc_start: 0.9074 (t80) cc_final: 0.8763 (t80) REVERT: C 3104 MET cc_start: 0.8818 (tmm) cc_final: 0.8590 (tmm) REVERT: C 4002 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8340 (ttp) REVERT: C 4035 TYR cc_start: 0.8522 (m-80) cc_final: 0.8207 (m-80) REVERT: C 4048 PHE cc_start: 0.8418 (t80) cc_final: 0.7996 (t80) REVERT: C 4052 MET cc_start: 0.8091 (mmm) cc_final: 0.7614 (mmp) REVERT: C 4080 TYR cc_start: 0.8565 (p90) cc_final: 0.8188 (p90) REVERT: C 4748 MET cc_start: 0.7711 (mpp) cc_final: 0.6939 (mpp) REVERT: D 393 MET cc_start: 0.7407 (mmm) cc_final: 0.7020 (mmm) REVERT: D 880 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8544 (tpm170) REVERT: D 893 TRP cc_start: 0.8444 (m-90) cc_final: 0.8114 (m-90) REVERT: D 1165 MET cc_start: 0.7899 (mtm) cc_final: 0.7351 (mpp) REVERT: D 1729 MET cc_start: 0.7695 (tpp) cc_final: 0.7322 (mmt) REVERT: D 2702 ASN cc_start: 0.8573 (t0) cc_final: 0.8312 (t0) REVERT: D 2871 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8855 (tt) REVERT: D 2982 PHE cc_start: 0.8502 (m-80) cc_final: 0.7849 (m-80) REVERT: D 3033 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8443 (tt) REVERT: D 3072 MET cc_start: 0.7725 (mmt) cc_final: 0.7435 (mmm) REVERT: D 3104 MET cc_start: 0.8786 (tmm) cc_final: 0.8505 (tmm) REVERT: D 3600 VAL cc_start: 0.3905 (OUTLIER) cc_final: 0.3518 (t) REVERT: D 4035 TYR cc_start: 0.8666 (m-80) cc_final: 0.8355 (m-80) REVERT: D 4052 MET cc_start: 0.7839 (mmm) cc_final: 0.7418 (mmp) REVERT: D 4186 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8103 (mmm) REVERT: D 4292 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7761 (mmm) REVERT: D 4965 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7832 (pm20) outliers start: 184 outliers final: 40 residues processed: 925 average time/residue: 1.1457 time to fit residues: 1848.5095 Evaluate side-chains 795 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 734 time to evaluate : 10.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 1041 ARG Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2586 GLN Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2836 ASP Chi-restraints excluded: chain A residue 2844 MET Chi-restraints excluded: chain A residue 3033 LEU Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4292 MET Chi-restraints excluded: chain A residue 4965 GLN Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 1022 GLN Chi-restraints excluded: chain B residue 1041 ARG Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 2384 MET Chi-restraints excluded: chain B residue 2609 LEU Chi-restraints excluded: chain B residue 2836 ASP Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 3033 LEU Chi-restraints excluded: chain B residue 4186 MET Chi-restraints excluded: chain B residue 4965 GLN Chi-restraints excluded: chain C residue 655 MET Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 799 LYS Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 998 LYS Chi-restraints excluded: chain C residue 1022 GLN Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 2384 MET Chi-restraints excluded: chain C residue 2768 LYS Chi-restraints excluded: chain C residue 2836 ASP Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 3033 LEU Chi-restraints excluded: chain C residue 4002 MET Chi-restraints excluded: chain C residue 4887 LYS Chi-restraints excluded: chain C residue 4965 GLN Chi-restraints excluded: chain D residue 655 MET Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 998 LYS Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 2384 MET Chi-restraints excluded: chain D residue 2586 GLN Chi-restraints excluded: chain D residue 2836 ASP Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2871 LEU Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3600 VAL Chi-restraints excluded: chain D residue 4186 MET Chi-restraints excluded: chain D residue 4292 MET Chi-restraints excluded: chain D residue 4965 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1384 optimal weight: 0.3980 chunk 1243 optimal weight: 9.9990 chunk 689 optimal weight: 30.0000 chunk 424 optimal weight: 5.9990 chunk 838 optimal weight: 7.9990 chunk 664 optimal weight: 9.9990 chunk 1285 optimal weight: 9.9990 chunk 497 optimal weight: 8.9990 chunk 781 optimal weight: 7.9990 chunk 956 optimal weight: 9.9990 chunk 1489 optimal weight: 20.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 GLN ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2540 HIS A3666 GLN ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1452 GLN ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2977 ASN B3666 GLN ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4579 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1452 GLN ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2540 HIS ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2977 ASN C3666 GLN ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 971 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2540 HIS D3666 GLN ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4579 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 134536 Z= 0.433 Angle : 0.714 14.146 181752 Z= 0.367 Chirality : 0.044 0.235 19884 Planarity : 0.006 0.156 23364 Dihedral : 6.413 81.268 18253 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 96.99 % Rotamer: Outliers : 0.67 % Allowed : 4.78 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.07), residues: 16332 helix: 1.53 (0.06), residues: 8496 sheet: -0.05 (0.13), residues: 1584 loop : -0.47 (0.08), residues: 6252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 893 HIS 0.017 0.002 HIS C 890 PHE 0.044 0.002 PHE D2943 TYR 0.030 0.002 TYR C2901 ARG 0.013 0.001 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 814 time to evaluate : 11.087 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: A 78 LEU cc_start: 0.8980 (tp) cc_final: 0.8689 (pp) REVERT: A 240 HIS cc_start: 0.7816 (m90) cc_final: 0.7580 (m170) REVERT: A 241 MET cc_start: 0.8319 (pmm) cc_final: 0.7627 (ppp) REVERT: A 309 MET cc_start: 0.8163 (mmp) cc_final: 0.7907 (mmm) REVERT: A 494 MET cc_start: 0.8592 (mmm) cc_final: 0.8391 (mmt) REVERT: A 902 TRP cc_start: 0.8282 (t-100) cc_final: 0.7686 (t-100) REVERT: A 1215 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8101 (mtm) REVERT: A 2142 MET cc_start: 0.8347 (mmm) cc_final: 0.8021 (tpp) REVERT: A 2162 MET cc_start: 0.8726 (mmp) cc_final: 0.8465 (mmp) REVERT: A 2584 MET cc_start: 0.8840 (mmm) cc_final: 0.8561 (mmm) REVERT: A 2702 ASN cc_start: 0.8856 (t0) cc_final: 0.8537 (t0) REVERT: A 2719 TYR cc_start: 0.8579 (t80) cc_final: 0.8240 (t80) REVERT: A 2828 MET cc_start: 0.7677 (tpt) cc_final: 0.7399 (tpt) REVERT: A 2840 MET cc_start: 0.4689 (mmt) cc_final: 0.3883 (mmt) REVERT: A 2848 TYR cc_start: 0.6477 (m-10) cc_final: 0.6096 (m-10) REVERT: A 2895 PHE cc_start: 0.9184 (t80) cc_final: 0.7082 (t80) REVERT: A 2975 PHE cc_start: 0.8851 (m-10) cc_final: 0.8624 (m-10) REVERT: A 2982 PHE cc_start: 0.8769 (m-80) cc_final: 0.8273 (m-80) REVERT: A 3008 PHE cc_start: 0.8290 (t80) cc_final: 0.8006 (t80) REVERT: A 3033 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8642 (tt) REVERT: A 3104 MET cc_start: 0.8797 (tmm) cc_final: 0.8535 (tmm) REVERT: A 3954 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8302 (tpp) REVERT: A 4035 TYR cc_start: 0.8785 (m-80) cc_final: 0.8235 (m-80) REVERT: A 4274 MET cc_start: 0.5622 (ppp) cc_final: 0.5117 (pmm) REVERT: A 4504 MET cc_start: 0.8407 (mmm) cc_final: 0.8120 (mpp) REVERT: E 51 ILE cc_start: 0.9325 (mm) cc_final: 0.9094 (mm) REVERT: F 6 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: F 51 ILE cc_start: 0.9298 (mm) cc_final: 0.8157 (mm) REVERT: F 58 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8241 (ptpp) REVERT: G 58 LYS cc_start: 0.8604 (ptpt) cc_final: 0.8372 (ptpp) REVERT: H 51 ILE cc_start: 0.9444 (mm) cc_final: 0.8583 (mm) REVERT: H 58 LYS cc_start: 0.8644 (ptpt) cc_final: 0.8234 (ptpp) REVERT: H 61 GLU cc_start: 0.8813 (tp30) cc_final: 0.8546 (tp30) REVERT: B 241 MET cc_start: 0.8176 (pmm) cc_final: 0.7693 (ppp) REVERT: B 494 MET cc_start: 0.8387 (mmp) cc_final: 0.8119 (mmt) REVERT: B 893 TRP cc_start: 0.8685 (m-90) cc_final: 0.8230 (m-90) REVERT: B 921 PHE cc_start: 0.9769 (p90) cc_final: 0.9544 (p90) REVERT: B 946 LEU cc_start: 0.9265 (mt) cc_final: 0.8990 (pp) REVERT: B 995 MET cc_start: 0.8391 (mtt) cc_final: 0.8030 (ptp) REVERT: B 1168 MET cc_start: 0.8314 (mmm) cc_final: 0.7921 (mmm) REVERT: B 1202 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8231 (pt) REVERT: B 1306 MET cc_start: 0.8878 (mtp) cc_final: 0.8590 (mtp) REVERT: B 2150 MET cc_start: 0.8675 (mmm) cc_final: 0.8450 (mmm) REVERT: B 2172 MET cc_start: 0.8362 (ttp) cc_final: 0.8122 (ttp) REVERT: B 2644 LEU cc_start: 0.9237 (tt) cc_final: 0.9025 (pp) REVERT: B 2681 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8459 (mmp) REVERT: B 2702 ASN cc_start: 0.8989 (t0) cc_final: 0.8701 (t0) REVERT: B 2840 MET cc_start: 0.5430 (mmt) cc_final: 0.4525 (mmt) REVERT: B 2843 MET cc_start: 0.6952 (ppp) cc_final: 0.6655 (ppp) REVERT: B 3985 MET cc_start: 0.9125 (tpp) cc_final: 0.8849 (mmm) REVERT: B 4052 MET cc_start: 0.8013 (mmm) cc_final: 0.7588 (mmp) REVERT: B 4707 MET cc_start: 0.8294 (ttm) cc_final: 0.8069 (ttp) REVERT: C 241 MET cc_start: 0.8328 (pmm) cc_final: 0.7827 (ppp) REVERT: C 878 LEU cc_start: 0.9570 (mt) cc_final: 0.9297 (mt) REVERT: C 902 TRP cc_start: 0.8317 (t-100) cc_final: 0.7826 (t-100) REVERT: C 921 PHE cc_start: 0.9722 (p90) cc_final: 0.9376 (p90) REVERT: C 995 MET cc_start: 0.8265 (mtt) cc_final: 0.7879 (ptp) REVERT: C 2142 MET cc_start: 0.8420 (mmm) cc_final: 0.7888 (mpp) REVERT: C 2644 LEU cc_start: 0.9306 (tt) cc_final: 0.9099 (pp) REVERT: C 2681 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8598 (mmp) REVERT: C 2702 ASN cc_start: 0.9121 (t0) cc_final: 0.8810 (t0) REVERT: C 2719 TYR cc_start: 0.8928 (t80) cc_final: 0.8646 (t80) REVERT: C 2779 LEU cc_start: 0.9688 (mt) cc_final: 0.9384 (pp) REVERT: C 2837 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9297 (tp) REVERT: C 2840 MET cc_start: 0.7538 (mmt) cc_final: 0.6661 (mmt) REVERT: C 2895 PHE cc_start: 0.9247 (t80) cc_final: 0.8847 (t80) REVERT: C 3104 MET cc_start: 0.8838 (tmm) cc_final: 0.8618 (tmm) REVERT: C 3999 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8883 (ttm) REVERT: C 4035 TYR cc_start: 0.8554 (m-80) cc_final: 0.8070 (m-80) REVERT: C 4048 PHE cc_start: 0.8474 (t80) cc_final: 0.8034 (t80) REVERT: C 4052 MET cc_start: 0.8228 (mmm) cc_final: 0.7776 (mmp) REVERT: C 4080 TYR cc_start: 0.8623 (p90) cc_final: 0.8202 (p90) REVERT: C 4274 MET cc_start: 0.5913 (ppp) cc_final: 0.4834 (pmm) REVERT: C 4504 MET cc_start: 0.8345 (mmm) cc_final: 0.8050 (mpp) REVERT: D 78 LEU cc_start: 0.8951 (tp) cc_final: 0.8638 (pp) REVERT: D 241 MET cc_start: 0.8176 (pmm) cc_final: 0.7634 (ppp) REVERT: D 309 MET cc_start: 0.8138 (mmp) cc_final: 0.7909 (mmm) REVERT: D 893 TRP cc_start: 0.8556 (m-90) cc_final: 0.8177 (m-90) REVERT: D 995 MET cc_start: 0.7391 (mtt) cc_final: 0.6917 (ptp) REVERT: D 1419 PHE cc_start: 0.9204 (t80) cc_final: 0.8971 (t80) REVERT: D 1729 MET cc_start: 0.8269 (tpp) cc_final: 0.7939 (mmm) REVERT: D 2585 MET cc_start: 0.7653 (ttm) cc_final: 0.7380 (ttp) REVERT: D 2681 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8130 (mmp) REVERT: D 2702 ASN cc_start: 0.8594 (t0) cc_final: 0.8268 (t0) REVERT: D 2768 LYS cc_start: 0.9073 (mmtm) cc_final: 0.8808 (mmtm) REVERT: D 2828 MET cc_start: 0.7263 (tpt) cc_final: 0.6853 (tpt) REVERT: D 2982 PHE cc_start: 0.8741 (m-80) cc_final: 0.8099 (m-80) REVERT: D 3008 PHE cc_start: 0.8429 (t80) cc_final: 0.7963 (t80) REVERT: D 3033 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8524 (tt) REVERT: D 3104 MET cc_start: 0.8766 (tmm) cc_final: 0.8502 (tmm) REVERT: D 3600 VAL cc_start: 0.3807 (OUTLIER) cc_final: 0.3554 (t) REVERT: D 4035 TYR cc_start: 0.8656 (m-80) cc_final: 0.8116 (m-80) REVERT: D 4052 MET cc_start: 0.8040 (mmm) cc_final: 0.7526 (mmp) REVERT: D 4748 MET cc_start: 0.7947 (mpp) cc_final: 0.7712 (mmm) outliers start: 97 outliers final: 29 residues processed: 851 average time/residue: 1.1256 time to fit residues: 1691.1974 Evaluate side-chains 812 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 771 time to evaluate : 10.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2836 ASP Chi-restraints excluded: chain A residue 3033 LEU Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2609 LEU Chi-restraints excluded: chain B residue 2681 MET Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4302 PHE Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2681 MET Chi-restraints excluded: chain C residue 2837 LEU Chi-restraints excluded: chain C residue 2874 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3600 VAL Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4302 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 827 optimal weight: 2.9990 chunk 462 optimal weight: 9.9990 chunk 1239 optimal weight: 0.3980 chunk 1014 optimal weight: 6.9990 chunk 410 optimal weight: 5.9990 chunk 1491 optimal weight: 20.0000 chunk 1611 optimal weight: 40.0000 chunk 1328 optimal weight: 20.0000 chunk 1479 optimal weight: 20.0000 chunk 508 optimal weight: 7.9990 chunk 1196 optimal weight: 10.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 GLN ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4579 HIS B 198 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2977 ASN ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 GLN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2868 HIS C2977 ASN ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4579 HIS C4933 HIS D 198 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1452 GLN ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 134536 Z= 0.325 Angle : 0.621 14.343 181752 Z= 0.318 Chirality : 0.041 0.194 19884 Planarity : 0.005 0.146 23364 Dihedral : 5.461 85.031 18089 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 0.61 % Allowed : 6.19 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.07), residues: 16332 helix: 1.79 (0.06), residues: 8480 sheet: -0.14 (0.13), residues: 1612 loop : -0.44 (0.08), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 893 HIS 0.014 0.001 HIS C2849 PHE 0.027 0.001 PHE A4640 TYR 0.020 0.001 TYR A2724 ARG 0.011 0.001 ARG A 882 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 795 time to evaluate : 11.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9007 (tp) cc_final: 0.8796 (pp) REVERT: A 309 MET cc_start: 0.8269 (mmp) cc_final: 0.7964 (mmm) REVERT: A 317 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7197 (ptt) REVERT: A 393 MET cc_start: 0.7806 (mmt) cc_final: 0.7540 (mmm) REVERT: A 902 TRP cc_start: 0.7931 (t-100) cc_final: 0.7021 (t-100) REVERT: A 2142 MET cc_start: 0.8320 (mmm) cc_final: 0.7978 (tpp) REVERT: A 2512 MET cc_start: 0.8727 (tmm) cc_final: 0.8361 (tmm) REVERT: A 2584 MET cc_start: 0.8768 (mmm) cc_final: 0.8498 (mmm) REVERT: A 2702 ASN cc_start: 0.8860 (t0) cc_final: 0.8539 (t0) REVERT: A 2719 TYR cc_start: 0.8595 (t80) cc_final: 0.8214 (t80) REVERT: A 2886 ARG cc_start: 0.9090 (mpp80) cc_final: 0.8878 (mpp80) REVERT: A 2895 PHE cc_start: 0.8937 (t80) cc_final: 0.8325 (t80) REVERT: A 2975 PHE cc_start: 0.8835 (m-10) cc_final: 0.8605 (m-10) REVERT: A 2982 PHE cc_start: 0.8765 (m-80) cc_final: 0.8244 (m-80) REVERT: A 3008 PHE cc_start: 0.8302 (t80) cc_final: 0.8096 (t80) REVERT: A 3033 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 3104 MET cc_start: 0.8775 (tmm) cc_final: 0.8543 (tmm) REVERT: A 3954 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8338 (tpp) REVERT: A 4035 TYR cc_start: 0.8711 (m-80) cc_final: 0.8132 (m-80) REVERT: A 4274 MET cc_start: 0.5797 (ppp) cc_final: 0.5208 (pmm) REVERT: A 4504 MET cc_start: 0.8275 (mmm) cc_final: 0.8009 (mpp) REVERT: F 50 ARG cc_start: 0.8565 (ptm-80) cc_final: 0.8260 (ptm-80) REVERT: F 51 ILE cc_start: 0.9391 (mm) cc_final: 0.9012 (mm) REVERT: G 53 LYS cc_start: 0.9525 (mmmt) cc_final: 0.8983 (mmmt) REVERT: H 6 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: B 494 MET cc_start: 0.8329 (mmp) cc_final: 0.8120 (mmt) REVERT: B 921 PHE cc_start: 0.9777 (p90) cc_final: 0.9542 (p90) REVERT: B 946 LEU cc_start: 0.9212 (mt) cc_final: 0.8992 (pp) REVERT: B 1168 MET cc_start: 0.8350 (mmm) cc_final: 0.7943 (mmm) REVERT: B 1202 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8243 (pt) REVERT: B 1306 MET cc_start: 0.8864 (mtp) cc_final: 0.8569 (mtp) REVERT: B 1729 MET cc_start: 0.8540 (mmt) cc_final: 0.8215 (mmt) REVERT: B 2512 MET cc_start: 0.8627 (tmm) cc_final: 0.8425 (tmm) REVERT: B 2644 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9018 (pp) REVERT: B 2681 MET cc_start: 0.8680 (mmp) cc_final: 0.8459 (mmp) REVERT: B 2688 MET cc_start: 0.3093 (ttm) cc_final: 0.2624 (ttt) REVERT: B 2702 ASN cc_start: 0.8978 (t0) cc_final: 0.8694 (t0) REVERT: B 2840 MET cc_start: 0.6024 (mmt) cc_final: 0.4749 (mmt) REVERT: B 2843 MET cc_start: 0.7771 (ppp) cc_final: 0.6999 (ppp) REVERT: B 2939 TYR cc_start: 0.8997 (m-10) cc_final: 0.8715 (m-80) REVERT: B 2982 PHE cc_start: 0.8899 (m-80) cc_final: 0.8413 (m-80) REVERT: B 3104 MET cc_start: 0.8907 (tmm) cc_final: 0.8289 (ppp) REVERT: B 4052 MET cc_start: 0.8196 (mmm) cc_final: 0.7665 (mmp) REVERT: B 4109 MET cc_start: 0.8305 (mmp) cc_final: 0.8042 (mmp) REVERT: B 4707 MET cc_start: 0.8310 (ttm) cc_final: 0.8080 (ttp) REVERT: B 4748 MET cc_start: 0.8176 (mmm) cc_final: 0.7858 (mmp) REVERT: C 902 TRP cc_start: 0.7944 (t-100) cc_final: 0.7421 (t-100) REVERT: C 921 PHE cc_start: 0.9715 (p90) cc_final: 0.9341 (p90) REVERT: C 995 MET cc_start: 0.8212 (mtt) cc_final: 0.7774 (ptp) REVERT: C 1215 MET cc_start: 0.8580 (mtp) cc_final: 0.8242 (mtt) REVERT: C 1729 MET cc_start: 0.8527 (mmt) cc_final: 0.8210 (mmt) REVERT: C 2142 MET cc_start: 0.8429 (mmm) cc_final: 0.7985 (mpp) REVERT: C 2192 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8432 (tpt) REVERT: C 2644 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9073 (pp) REVERT: C 2681 MET cc_start: 0.8762 (mmp) cc_final: 0.8378 (mmp) REVERT: C 2688 MET cc_start: 0.4147 (ttm) cc_final: 0.3809 (ttt) REVERT: C 2702 ASN cc_start: 0.9115 (t0) cc_final: 0.8791 (t0) REVERT: C 2768 LYS cc_start: 0.9033 (mptt) cc_final: 0.8503 (mmtt) REVERT: C 2837 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9301 (tp) REVERT: C 2840 MET cc_start: 0.7071 (mmt) cc_final: 0.6768 (mmt) REVERT: C 2843 MET cc_start: 0.7440 (ppp) cc_final: 0.7220 (ppp) REVERT: C 2895 PHE cc_start: 0.8996 (t80) cc_final: 0.8604 (t80) REVERT: C 3033 LEU cc_start: 0.9245 (mp) cc_final: 0.8976 (pp) REVERT: C 3104 MET cc_start: 0.8808 (tmm) cc_final: 0.8600 (tmm) REVERT: C 4035 TYR cc_start: 0.8529 (m-80) cc_final: 0.7971 (m-80) REVERT: C 4048 PHE cc_start: 0.8560 (t80) cc_final: 0.8282 (t80) REVERT: C 4052 MET cc_start: 0.8322 (mmm) cc_final: 0.7970 (mmm) REVERT: C 4274 MET cc_start: 0.5916 (ppp) cc_final: 0.4830 (pmm) REVERT: C 4809 MET cc_start: 0.7990 (ttm) cc_final: 0.7748 (tpp) REVERT: D 78 LEU cc_start: 0.9007 (tp) cc_final: 0.8763 (pp) REVERT: D 128 MET cc_start: 0.8729 (mtm) cc_final: 0.8477 (mtp) REVERT: D 309 MET cc_start: 0.8229 (mmp) cc_final: 0.7975 (mmm) REVERT: D 393 MET cc_start: 0.7748 (mmt) cc_final: 0.7441 (mmm) REVERT: D 893 TRP cc_start: 0.8530 (m-10) cc_final: 0.8159 (m-90) REVERT: D 895 MET cc_start: 0.8681 (mmm) cc_final: 0.8398 (mmm) REVERT: D 944 LEU cc_start: 0.9194 (mt) cc_final: 0.8992 (mt) REVERT: D 1174 MET cc_start: 0.8111 (pmm) cc_final: 0.7900 (pmm) REVERT: D 1419 PHE cc_start: 0.9194 (t80) cc_final: 0.8953 (t80) REVERT: D 2162 MET cc_start: 0.8741 (mmp) cc_final: 0.8504 (mmm) REVERT: D 2585 MET cc_start: 0.7695 (ttm) cc_final: 0.7360 (ttp) REVERT: D 2702 ASN cc_start: 0.8679 (t0) cc_final: 0.8362 (t0) REVERT: D 2828 MET cc_start: 0.7193 (tpt) cc_final: 0.6565 (tpt) REVERT: D 2840 MET cc_start: 0.3501 (mmt) cc_final: 0.3141 (mmt) REVERT: D 2843 MET cc_start: 0.6649 (ppp) cc_final: 0.6154 (ppp) REVERT: D 2895 PHE cc_start: 0.8950 (t80) cc_final: 0.8676 (t80) REVERT: D 2982 PHE cc_start: 0.8741 (m-80) cc_final: 0.8116 (m-80) REVERT: D 3008 PHE cc_start: 0.8425 (t80) cc_final: 0.7958 (t80) REVERT: D 3033 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8515 (tt) REVERT: D 3046 MET cc_start: 0.8789 (pmm) cc_final: 0.8566 (pmm) REVERT: D 3104 MET cc_start: 0.8805 (tmm) cc_final: 0.8554 (tmm) REVERT: D 3600 VAL cc_start: 0.3845 (OUTLIER) cc_final: 0.3564 (t) REVERT: D 3978 MET cc_start: 0.9057 (ttp) cc_final: 0.8817 (ttp) REVERT: D 4035 TYR cc_start: 0.8602 (m-80) cc_final: 0.8041 (m-80) REVERT: D 4052 MET cc_start: 0.8217 (mmm) cc_final: 0.7779 (mmm) outliers start: 88 outliers final: 42 residues processed: 844 average time/residue: 1.1161 time to fit residues: 1664.1134 Evaluate side-chains 819 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 766 time to evaluate : 10.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 3033 LEU Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2609 LEU Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2724 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2644 LEU Chi-restraints excluded: chain C residue 2837 LEU Chi-restraints excluded: chain C residue 2852 TRP Chi-restraints excluded: chain C residue 2927 GLN Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3600 VAL Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1474 optimal weight: 20.0000 chunk 1121 optimal weight: 50.0000 chunk 774 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 712 optimal weight: 20.0000 chunk 1001 optimal weight: 4.9990 chunk 1497 optimal weight: 5.9990 chunk 1585 optimal weight: 5.9990 chunk 782 optimal weight: 10.0000 chunk 1419 optimal weight: 5.9990 chunk 427 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 ASN ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2309 ASN ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1587 HIS ** B2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2977 ASN ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2309 ASN ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2309 ASN ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 134536 Z= 0.395 Angle : 0.632 13.830 181752 Z= 0.323 Chirality : 0.041 0.194 19884 Planarity : 0.005 0.143 23364 Dihedral : 5.319 74.052 18087 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 0.65 % Allowed : 7.52 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.07), residues: 16332 helix: 1.84 (0.06), residues: 8524 sheet: -0.28 (0.13), residues: 1644 loop : -0.46 (0.08), residues: 6164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 902 HIS 0.020 0.001 HIS A 915 PHE 0.041 0.002 PHE D2943 TYR 0.020 0.002 TYR A2724 ARG 0.008 0.001 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 789 time to evaluate : 13.576 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 78 LEU cc_start: 0.9044 (tp) cc_final: 0.8825 (pp) REVERT: A 241 MET cc_start: 0.8375 (pmm) cc_final: 0.7676 (ppp) REVERT: A 309 MET cc_start: 0.8354 (mmp) cc_final: 0.7972 (mmm) REVERT: A 317 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7217 (ptt) REVERT: A 393 MET cc_start: 0.7895 (mmt) cc_final: 0.7689 (mmm) REVERT: A 778 MET cc_start: 0.8133 (ptp) cc_final: 0.7908 (ptm) REVERT: A 995 MET cc_start: 0.8012 (mtt) cc_final: 0.7544 (ptp) REVERT: A 2192 MET cc_start: 0.8642 (tpt) cc_final: 0.8344 (tpp) REVERT: A 2688 MET cc_start: 0.5728 (ttt) cc_final: 0.4023 (ttt) REVERT: A 2702 ASN cc_start: 0.8854 (t0) cc_final: 0.8538 (t0) REVERT: A 2719 TYR cc_start: 0.8561 (t80) cc_final: 0.8188 (t80) REVERT: A 2840 MET cc_start: 0.5048 (mmt) cc_final: 0.4306 (mmt) REVERT: A 2843 MET cc_start: 0.6569 (ppp) cc_final: 0.5594 (ppp) REVERT: A 2895 PHE cc_start: 0.8809 (t80) cc_final: 0.8353 (t80) REVERT: A 2968 LEU cc_start: 0.8883 (tp) cc_final: 0.8638 (tp) REVERT: A 2975 PHE cc_start: 0.8872 (m-10) cc_final: 0.8575 (m-10) REVERT: A 2982 PHE cc_start: 0.8816 (m-80) cc_final: 0.8311 (m-10) REVERT: A 3104 MET cc_start: 0.8748 (tmm) cc_final: 0.8524 (tmm) REVERT: A 4035 TYR cc_start: 0.8704 (m-80) cc_final: 0.8219 (m-80) REVERT: A 4274 MET cc_start: 0.5859 (ppp) cc_final: 0.5239 (pmm) REVERT: A 4504 MET cc_start: 0.8236 (mmm) cc_final: 0.7976 (mpp) REVERT: A 4809 MET cc_start: 0.8185 (tpp) cc_final: 0.7576 (tpp) REVERT: E 6 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: E 53 LYS cc_start: 0.9505 (mmmt) cc_final: 0.8930 (mmmt) REVERT: F 6 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: F 50 ARG cc_start: 0.8575 (ptm-80) cc_final: 0.8356 (ptm-80) REVERT: F 51 ILE cc_start: 0.9323 (mm) cc_final: 0.8997 (mm) REVERT: G 53 LYS cc_start: 0.9475 (mmmt) cc_final: 0.9257 (mmmt) REVERT: H 6 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: H 50 ARG cc_start: 0.8658 (mtm110) cc_final: 0.8423 (mtm110) REVERT: B 241 MET cc_start: 0.8285 (pmm) cc_final: 0.7815 (ppp) REVERT: B 880 ARG cc_start: 0.9053 (ptt180) cc_final: 0.8782 (ptt-90) REVERT: B 921 PHE cc_start: 0.9787 (p90) cc_final: 0.9551 (p90) REVERT: B 995 MET cc_start: 0.8342 (mtt) cc_final: 0.7989 (ptp) REVERT: B 1064 LEU cc_start: 0.9001 (pt) cc_final: 0.8733 (pt) REVERT: B 1168 MET cc_start: 0.8394 (mmm) cc_final: 0.7986 (mmm) REVERT: B 1202 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8256 (pt) REVERT: B 1306 MET cc_start: 0.8869 (mtp) cc_final: 0.8576 (mtp) REVERT: B 1494 MET cc_start: 0.8080 (mmm) cc_final: 0.7837 (tpt) REVERT: B 1729 MET cc_start: 0.8538 (mmt) cc_final: 0.8226 (mmt) REVERT: B 2384 MET cc_start: 0.9331 (mmm) cc_final: 0.8713 (mmm) REVERT: B 2644 LEU cc_start: 0.9270 (tt) cc_final: 0.9043 (pp) REVERT: B 2681 MET cc_start: 0.8731 (mmp) cc_final: 0.8479 (mmp) REVERT: B 2688 MET cc_start: 0.2987 (ttm) cc_final: 0.2391 (ttt) REVERT: B 2702 ASN cc_start: 0.9034 (t0) cc_final: 0.8752 (t0) REVERT: B 2785 TRP cc_start: 0.4628 (m-10) cc_final: 0.4002 (m-10) REVERT: B 2840 MET cc_start: 0.6128 (mmt) cc_final: 0.5045 (mmt) REVERT: B 2843 MET cc_start: 0.7875 (ppp) cc_final: 0.6833 (ppp) REVERT: B 2939 TYR cc_start: 0.9024 (m-10) cc_final: 0.8734 (m-80) REVERT: B 2982 PHE cc_start: 0.8994 (m-80) cc_final: 0.8420 (m-80) REVERT: B 3104 MET cc_start: 0.8904 (tmm) cc_final: 0.8243 (ppp) REVERT: B 4035 TYR cc_start: 0.7583 (m-10) cc_final: 0.6718 (m-10) REVERT: B 4052 MET cc_start: 0.8238 (mmm) cc_final: 0.7659 (mmp) REVERT: B 4109 MET cc_start: 0.8427 (mmp) cc_final: 0.8085 (mmp) REVERT: B 4707 MET cc_start: 0.8340 (ttm) cc_final: 0.8117 (ttp) REVERT: B 4748 MET cc_start: 0.8211 (mmm) cc_final: 0.7881 (mmt) REVERT: C 240 HIS cc_start: 0.7850 (m90) cc_final: 0.7559 (m-70) REVERT: C 241 MET cc_start: 0.8365 (pmm) cc_final: 0.7639 (ppp) REVERT: C 393 MET cc_start: 0.7910 (mmm) cc_final: 0.7388 (mmm) REVERT: C 893 TRP cc_start: 0.8500 (m-10) cc_final: 0.8028 (m-90) REVERT: C 902 TRP cc_start: 0.8001 (t-100) cc_final: 0.7500 (t-100) REVERT: C 921 PHE cc_start: 0.9715 (p90) cc_final: 0.9348 (p90) REVERT: C 995 MET cc_start: 0.8182 (mtt) cc_final: 0.7882 (ptp) REVERT: C 1113 MET cc_start: 0.8337 (mtt) cc_final: 0.7857 (mtt) REVERT: C 1215 MET cc_start: 0.8571 (mtp) cc_final: 0.8258 (mtt) REVERT: C 2142 MET cc_start: 0.8423 (mmm) cc_final: 0.7947 (mpp) REVERT: C 2192 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8552 (tpt) REVERT: C 2384 MET cc_start: 0.9275 (mmm) cc_final: 0.8899 (mmm) REVERT: C 2605 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8476 (tmm) REVERT: C 2644 LEU cc_start: 0.9309 (tt) cc_final: 0.9088 (pp) REVERT: C 2681 MET cc_start: 0.8844 (mmp) cc_final: 0.8607 (mmp) REVERT: C 2702 ASN cc_start: 0.9125 (t0) cc_final: 0.8778 (t0) REVERT: C 2837 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9328 (tp) REVERT: C 2840 MET cc_start: 0.7299 (mmt) cc_final: 0.6760 (mmt) REVERT: C 2843 MET cc_start: 0.7259 (ppp) cc_final: 0.6827 (ppp) REVERT: C 2975 PHE cc_start: 0.8788 (m-10) cc_final: 0.8551 (m-10) REVERT: C 4035 TYR cc_start: 0.8522 (m-80) cc_final: 0.8086 (m-80) REVERT: C 4048 PHE cc_start: 0.8584 (t80) cc_final: 0.8326 (t80) REVERT: C 4052 MET cc_start: 0.8345 (mmm) cc_final: 0.7931 (mmm) REVERT: C 4080 TYR cc_start: 0.8603 (p90) cc_final: 0.8211 (p90) REVERT: C 4504 MET cc_start: 0.8348 (mmm) cc_final: 0.8003 (mpp) REVERT: D 128 MET cc_start: 0.8756 (mtm) cc_final: 0.8522 (mtp) REVERT: D 241 MET cc_start: 0.8321 (pmm) cc_final: 0.7718 (ppp) REVERT: D 309 MET cc_start: 0.8350 (mmp) cc_final: 0.8032 (mmm) REVERT: D 393 MET cc_start: 0.7891 (mmt) cc_final: 0.7523 (mmm) REVERT: D 944 LEU cc_start: 0.9231 (mt) cc_final: 0.9013 (mt) REVERT: D 995 MET cc_start: 0.7493 (mtt) cc_final: 0.7075 (ptp) REVERT: D 1174 MET cc_start: 0.8032 (pmm) cc_final: 0.7812 (pmm) REVERT: D 1419 PHE cc_start: 0.9221 (t80) cc_final: 0.8975 (t80) REVERT: D 2134 MET cc_start: 0.8821 (mmm) cc_final: 0.8616 (tpt) REVERT: D 2585 MET cc_start: 0.7684 (ttm) cc_final: 0.7355 (ttp) REVERT: D 2702 ASN cc_start: 0.8760 (t0) cc_final: 0.8446 (t0) REVERT: D 2828 MET cc_start: 0.7280 (tpt) cc_final: 0.6889 (tpt) REVERT: D 2840 MET cc_start: 0.4178 (mmt) cc_final: 0.3929 (mmt) REVERT: D 2895 PHE cc_start: 0.9008 (t80) cc_final: 0.8626 (t80) REVERT: D 2943 PHE cc_start: 0.8420 (m-80) cc_final: 0.8188 (m-80) REVERT: D 2968 LEU cc_start: 0.8906 (tp) cc_final: 0.8636 (tp) REVERT: D 2982 PHE cc_start: 0.8822 (m-80) cc_final: 0.8196 (m-80) REVERT: D 3008 PHE cc_start: 0.8476 (t80) cc_final: 0.8027 (t80) REVERT: D 3033 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8545 (tt) REVERT: D 3104 MET cc_start: 0.8803 (tmm) cc_final: 0.8551 (tmm) REVERT: D 3600 VAL cc_start: 0.3746 (OUTLIER) cc_final: 0.3516 (t) REVERT: D 4035 TYR cc_start: 0.8592 (m-80) cc_final: 0.8137 (m-80) REVERT: D 4052 MET cc_start: 0.8300 (mmm) cc_final: 0.7731 (mmp) REVERT: D 4726 MET cc_start: 0.8687 (tpp) cc_final: 0.8432 (tpt) REVERT: D 4748 MET cc_start: 0.8169 (mmm) cc_final: 0.7850 (mmp) REVERT: D 4809 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7739 (tpp) outliers start: 94 outliers final: 53 residues processed: 839 average time/residue: 1.1414 time to fit residues: 1695.2635 Evaluate side-chains 829 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 765 time to evaluate : 10.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 3046 MET Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2609 LEU Chi-restraints excluded: chain B residue 2836 ASP Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2605 MET Chi-restraints excluded: chain C residue 2781 THR Chi-restraints excluded: chain C residue 2837 LEU Chi-restraints excluded: chain C residue 2852 TRP Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 902 TRP Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3600 VAL Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4809 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1320 optimal weight: 10.0000 chunk 899 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 1180 optimal weight: 7.9990 chunk 654 optimal weight: 8.9990 chunk 1352 optimal weight: 9.9990 chunk 1095 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 809 optimal weight: 20.0000 chunk 1422 optimal weight: 0.9990 chunk 400 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 GLN ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2847 ASN B2977 ASN ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2849 HIS ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 134536 Z= 0.277 Angle : 0.593 14.570 181752 Z= 0.300 Chirality : 0.040 0.192 19884 Planarity : 0.005 0.138 23364 Dihedral : 5.199 73.882 18085 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 0.71 % Allowed : 8.46 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.07), residues: 16332 helix: 1.98 (0.06), residues: 8500 sheet: -0.29 (0.13), residues: 1640 loop : -0.41 (0.08), residues: 6192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2785 HIS 0.016 0.001 HIS A4055 PHE 0.039 0.001 PHE D2943 TYR 0.036 0.001 TYR A4035 ARG 0.010 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 779 time to evaluate : 10.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7268 (ptt) REVERT: A 778 MET cc_start: 0.8101 (ptp) cc_final: 0.7867 (ptm) REVERT: A 995 MET cc_start: 0.7991 (mtt) cc_final: 0.7459 (ptp) REVERT: A 2004 MET cc_start: 0.9079 (mmp) cc_final: 0.8781 (mmp) REVERT: A 2192 MET cc_start: 0.8536 (tpt) cc_final: 0.8251 (tpp) REVERT: A 2384 MET cc_start: 0.9388 (mmm) cc_final: 0.8747 (mmm) REVERT: A 2702 ASN cc_start: 0.8864 (t0) cc_final: 0.8539 (t0) REVERT: A 2719 TYR cc_start: 0.8531 (t80) cc_final: 0.8164 (t80) REVERT: A 2840 MET cc_start: 0.5454 (mmt) cc_final: 0.4691 (mmt) REVERT: A 2843 MET cc_start: 0.6475 (ppp) cc_final: 0.5827 (ppp) REVERT: A 2886 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8910 (mpp80) REVERT: A 2895 PHE cc_start: 0.8762 (t80) cc_final: 0.8356 (t80) REVERT: A 2975 PHE cc_start: 0.8831 (m-10) cc_final: 0.8553 (m-10) REVERT: A 2982 PHE cc_start: 0.8777 (m-80) cc_final: 0.8263 (m-10) REVERT: A 3954 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8335 (tpp) REVERT: A 4274 MET cc_start: 0.5889 (ppp) cc_final: 0.5639 (ptp) REVERT: A 4504 MET cc_start: 0.8211 (mmm) cc_final: 0.7954 (mpp) REVERT: A 4809 MET cc_start: 0.8146 (tpp) cc_final: 0.7611 (tpp) REVERT: E 4 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: E 6 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: E 53 LYS cc_start: 0.9392 (mmmt) cc_final: 0.9174 (mmmt) REVERT: F 50 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8363 (ptm-80) REVERT: G 6 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: H 6 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 241 MET cc_start: 0.8268 (pmm) cc_final: 0.7837 (ppp) REVERT: B 921 PHE cc_start: 0.9791 (p90) cc_final: 0.9550 (p90) REVERT: B 995 MET cc_start: 0.8251 (mtt) cc_final: 0.7841 (ptp) REVERT: B 1064 LEU cc_start: 0.8851 (pt) cc_final: 0.8547 (pt) REVERT: B 1168 MET cc_start: 0.8398 (mmm) cc_final: 0.7925 (mmm) REVERT: B 1202 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8263 (pt) REVERT: B 1306 MET cc_start: 0.8845 (mtp) cc_final: 0.8554 (mtp) REVERT: B 1494 MET cc_start: 0.7996 (mmm) cc_final: 0.7703 (tpp) REVERT: B 2644 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9031 (pp) REVERT: B 2681 MET cc_start: 0.8701 (mmp) cc_final: 0.8465 (mmp) REVERT: B 2688 MET cc_start: 0.3198 (ttm) cc_final: 0.2645 (ttt) REVERT: B 2702 ASN cc_start: 0.9036 (t0) cc_final: 0.8752 (t0) REVERT: B 2785 TRP cc_start: 0.4649 (m-10) cc_final: 0.4129 (m-10) REVERT: B 2840 MET cc_start: 0.6122 (mmt) cc_final: 0.4950 (mmt) REVERT: B 2843 MET cc_start: 0.7831 (ppp) cc_final: 0.6764 (ppp) REVERT: B 2939 TYR cc_start: 0.9032 (m-10) cc_final: 0.8732 (m-80) REVERT: B 2982 PHE cc_start: 0.8942 (m-80) cc_final: 0.8339 (m-80) REVERT: B 3104 MET cc_start: 0.8908 (tmm) cc_final: 0.8248 (ppp) REVERT: B 4052 MET cc_start: 0.8278 (mmm) cc_final: 0.7679 (mmp) REVERT: B 4707 MET cc_start: 0.8321 (ttm) cc_final: 0.8085 (ttp) REVERT: B 4748 MET cc_start: 0.8122 (mmm) cc_final: 0.7804 (mmp) REVERT: C 393 MET cc_start: 0.7876 (mmm) cc_final: 0.7466 (mmm) REVERT: C 902 TRP cc_start: 0.7897 (t-100) cc_final: 0.7457 (t-100) REVERT: C 921 PHE cc_start: 0.9714 (p90) cc_final: 0.9349 (p90) REVERT: C 995 MET cc_start: 0.8155 (mtt) cc_final: 0.7839 (ptp) REVERT: C 1215 MET cc_start: 0.8537 (mtp) cc_final: 0.8253 (mtt) REVERT: C 2142 MET cc_start: 0.8376 (mmm) cc_final: 0.7924 (mpp) REVERT: C 2192 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8559 (tpt) REVERT: C 2605 MET cc_start: 0.8634 (tmm) cc_final: 0.8428 (tmm) REVERT: C 2644 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9083 (pp) REVERT: C 2681 MET cc_start: 0.8822 (mmp) cc_final: 0.8583 (mmp) REVERT: C 2702 ASN cc_start: 0.9138 (t0) cc_final: 0.8799 (t0) REVERT: C 2837 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9309 (tp) REVERT: C 2840 MET cc_start: 0.7168 (mmt) cc_final: 0.6624 (mmt) REVERT: C 2843 MET cc_start: 0.7249 (ppp) cc_final: 0.6751 (ppp) REVERT: C 2975 PHE cc_start: 0.8737 (m-10) cc_final: 0.8502 (m-10) REVERT: C 3104 MET cc_start: 0.8860 (tmm) cc_final: 0.8161 (ppp) REVERT: C 4048 PHE cc_start: 0.8613 (t80) cc_final: 0.7987 (t80) REVERT: C 4052 MET cc_start: 0.8353 (mmm) cc_final: 0.7747 (mmp) REVERT: C 4239 LEU cc_start: 0.8740 (pt) cc_final: 0.8135 (tt) REVERT: C 4504 MET cc_start: 0.8316 (mmm) cc_final: 0.7981 (mpp) REVERT: D 309 MET cc_start: 0.8337 (mmp) cc_final: 0.8019 (mmm) REVERT: D 393 MET cc_start: 0.7899 (mmt) cc_final: 0.7602 (mmm) REVERT: D 944 LEU cc_start: 0.9240 (mt) cc_final: 0.9025 (mt) REVERT: D 995 MET cc_start: 0.7410 (mtt) cc_final: 0.7132 (ptp) REVERT: D 1174 MET cc_start: 0.8026 (pmm) cc_final: 0.7769 (pmm) REVERT: D 1419 PHE cc_start: 0.9202 (t80) cc_final: 0.8957 (t80) REVERT: D 2512 MET cc_start: 0.8779 (tmm) cc_final: 0.8401 (tmm) REVERT: D 2585 MET cc_start: 0.7688 (ttm) cc_final: 0.7350 (ttp) REVERT: D 2702 ASN cc_start: 0.8766 (t0) cc_final: 0.8455 (t0) REVERT: D 2840 MET cc_start: 0.4316 (mmt) cc_final: 0.4014 (mmt) REVERT: D 2843 MET cc_start: 0.7032 (ppp) cc_final: 0.6576 (ppp) REVERT: D 2844 MET cc_start: 0.8905 (ppp) cc_final: 0.8353 (ppp) REVERT: D 2895 PHE cc_start: 0.9026 (t80) cc_final: 0.8568 (t80) REVERT: D 2943 PHE cc_start: 0.8404 (m-80) cc_final: 0.8150 (m-80) REVERT: D 2982 PHE cc_start: 0.8790 (m-80) cc_final: 0.8148 (m-80) REVERT: D 3008 PHE cc_start: 0.8453 (t80) cc_final: 0.7990 (t80) REVERT: D 3033 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8506 (tt) REVERT: D 3104 MET cc_start: 0.8775 (tmm) cc_final: 0.8570 (tmm) REVERT: D 4052 MET cc_start: 0.8330 (mmm) cc_final: 0.7651 (mmp) REVERT: D 4726 MET cc_start: 0.8633 (tpp) cc_final: 0.8413 (tpt) REVERT: D 4748 MET cc_start: 0.8136 (mmm) cc_final: 0.7816 (mmp) outliers start: 102 outliers final: 66 residues processed: 834 average time/residue: 1.1319 time to fit residues: 1670.2723 Evaluate side-chains 837 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 757 time to evaluate : 10.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 3046 MET Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1004 HIS Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2724 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1004 HIS Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2644 LEU Chi-restraints excluded: chain C residue 2837 LEU Chi-restraints excluded: chain C residue 2849 HIS Chi-restraints excluded: chain C residue 2852 TRP Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3066 GLU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 533 optimal weight: 8.9990 chunk 1427 optimal weight: 1.9990 chunk 313 optimal weight: 0.7980 chunk 930 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 1586 optimal weight: 9.9990 chunk 1317 optimal weight: 0.0870 chunk 734 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 524 optimal weight: 6.9990 chunk 833 optimal weight: 0.8980 overall best weight: 2.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 GLN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2849 HIS ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3034 HIS ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 134536 Z= 0.187 Angle : 0.578 17.177 181752 Z= 0.289 Chirality : 0.039 0.190 19884 Planarity : 0.004 0.133 23364 Dihedral : 5.081 74.477 18082 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 0.74 % Allowed : 8.88 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.07), residues: 16332 helix: 2.07 (0.06), residues: 8512 sheet: -0.13 (0.13), residues: 1568 loop : -0.40 (0.08), residues: 6252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2785 HIS 0.022 0.001 HIS C2849 PHE 0.036 0.001 PHE D2943 TYR 0.030 0.001 TYR C2848 ARG 0.011 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 775 time to evaluate : 10.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8187 (mmp) cc_final: 0.7833 (mmm) REVERT: A 317 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7300 (ptt) REVERT: A 778 MET cc_start: 0.8071 (ptp) cc_final: 0.7859 (ptm) REVERT: A 921 PHE cc_start: 0.9722 (p90) cc_final: 0.9433 (p90) REVERT: A 995 MET cc_start: 0.7877 (mtt) cc_final: 0.7338 (ptp) REVERT: A 2192 MET cc_start: 0.8439 (tpt) cc_final: 0.8167 (tpp) REVERT: A 2384 MET cc_start: 0.9352 (mmm) cc_final: 0.8759 (mmm) REVERT: A 2702 ASN cc_start: 0.8862 (t0) cc_final: 0.8520 (t0) REVERT: A 2719 TYR cc_start: 0.8454 (t80) cc_final: 0.8104 (t80) REVERT: A 2785 TRP cc_start: 0.4725 (m-90) cc_final: 0.4261 (m-90) REVERT: A 2828 MET cc_start: 0.8649 (mmt) cc_final: 0.8302 (tpt) REVERT: A 2840 MET cc_start: 0.5138 (mmt) cc_final: 0.4670 (mmt) REVERT: A 2843 MET cc_start: 0.6746 (ppp) cc_final: 0.6148 (ppp) REVERT: A 2975 PHE cc_start: 0.8809 (m-10) cc_final: 0.8524 (m-10) REVERT: A 2982 PHE cc_start: 0.8731 (m-80) cc_final: 0.8212 (m-10) REVERT: A 4504 MET cc_start: 0.8184 (mmm) cc_final: 0.7928 (mpp) REVERT: A 4809 MET cc_start: 0.8077 (tpp) cc_final: 0.7655 (tpp) REVERT: E 4 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: E 6 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: E 53 LYS cc_start: 0.9286 (mmmt) cc_final: 0.9060 (mmmt) REVERT: F 6 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: G 6 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: B 241 MET cc_start: 0.8272 (pmm) cc_final: 0.7857 (ppp) REVERT: B 317 MET cc_start: 0.7901 (ppp) cc_final: 0.7656 (ppp) REVERT: B 921 PHE cc_start: 0.9790 (p90) cc_final: 0.9556 (p90) REVERT: B 995 MET cc_start: 0.8308 (mtt) cc_final: 0.7912 (ptp) REVERT: B 1064 LEU cc_start: 0.8889 (pt) cc_final: 0.8571 (pt) REVERT: B 1168 MET cc_start: 0.8379 (mmm) cc_final: 0.7919 (mmm) REVERT: B 1202 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8238 (pt) REVERT: B 1306 MET cc_start: 0.8806 (mtp) cc_final: 0.8523 (mtm) REVERT: B 1494 MET cc_start: 0.8039 (mmm) cc_final: 0.7821 (tpp) REVERT: B 2004 MET cc_start: 0.9090 (mmp) cc_final: 0.8808 (mmp) REVERT: B 2644 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9014 (pp) REVERT: B 2681 MET cc_start: 0.8692 (mmp) cc_final: 0.8439 (mmp) REVERT: B 2688 MET cc_start: 0.3202 (ttm) cc_final: 0.2631 (ttt) REVERT: B 2702 ASN cc_start: 0.9036 (t0) cc_final: 0.8741 (t0) REVERT: B 2785 TRP cc_start: 0.4663 (m-10) cc_final: 0.4246 (m-10) REVERT: B 2840 MET cc_start: 0.6097 (mmt) cc_final: 0.4849 (mmt) REVERT: B 2843 MET cc_start: 0.7730 (ppp) cc_final: 0.6635 (ppp) REVERT: B 2939 TYR cc_start: 0.9038 (m-10) cc_final: 0.8518 (m-80) REVERT: B 2982 PHE cc_start: 0.8896 (m-80) cc_final: 0.8298 (m-80) REVERT: B 4052 MET cc_start: 0.8274 (mmm) cc_final: 0.7899 (mmm) REVERT: B 4256 MET cc_start: 0.8551 (mmt) cc_final: 0.8350 (mmm) REVERT: B 4707 MET cc_start: 0.8300 (ttm) cc_final: 0.8077 (ttp) REVERT: B 4748 MET cc_start: 0.8084 (mmm) cc_final: 0.7770 (mmp) REVERT: C 393 MET cc_start: 0.7890 (mmm) cc_final: 0.7522 (mmm) REVERT: C 902 TRP cc_start: 0.7931 (t-100) cc_final: 0.7532 (t-100) REVERT: C 921 PHE cc_start: 0.9709 (p90) cc_final: 0.9348 (p90) REVERT: C 995 MET cc_start: 0.8139 (mtt) cc_final: 0.7806 (ptp) REVERT: C 1168 MET cc_start: 0.8453 (mmm) cc_final: 0.7955 (mmm) REVERT: C 1215 MET cc_start: 0.8535 (mtp) cc_final: 0.8255 (mtt) REVERT: C 2142 MET cc_start: 0.8368 (mmm) cc_final: 0.7912 (mpp) REVERT: C 2644 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9060 (pp) REVERT: C 2681 MET cc_start: 0.8800 (mmp) cc_final: 0.8411 (mmp) REVERT: C 2840 MET cc_start: 0.7407 (mmt) cc_final: 0.6721 (mmt) REVERT: C 2843 MET cc_start: 0.7297 (ppp) cc_final: 0.6598 (ppp) REVERT: C 2844 MET cc_start: 0.9186 (tmm) cc_final: 0.8933 (ppp) REVERT: C 2849 HIS cc_start: 0.8385 (t70) cc_final: 0.8149 (t-170) REVERT: C 2975 PHE cc_start: 0.8726 (m-10) cc_final: 0.8490 (m-10) REVERT: C 3104 MET cc_start: 0.8844 (tmm) cc_final: 0.8122 (ppp) REVERT: C 4048 PHE cc_start: 0.8599 (t80) cc_final: 0.8002 (t80) REVERT: C 4052 MET cc_start: 0.8361 (mmm) cc_final: 0.7728 (mmp) REVERT: C 4239 LEU cc_start: 0.8739 (pt) cc_final: 0.8123 (tt) REVERT: C 4504 MET cc_start: 0.8296 (mmm) cc_final: 0.8025 (mmm) REVERT: D 241 MET cc_start: 0.8323 (pmm) cc_final: 0.7704 (ppp) REVERT: D 309 MET cc_start: 0.8302 (mmp) cc_final: 0.7989 (mmm) REVERT: D 393 MET cc_start: 0.7848 (mmt) cc_final: 0.7629 (mmm) REVERT: D 778 MET cc_start: 0.8197 (ptp) cc_final: 0.7971 (ptm) REVERT: D 946 LEU cc_start: 0.9095 (mt) cc_final: 0.8869 (pp) REVERT: D 995 MET cc_start: 0.7375 (mtt) cc_final: 0.7057 (ptp) REVERT: D 1174 MET cc_start: 0.8015 (pmm) cc_final: 0.7746 (pmm) REVERT: D 1419 PHE cc_start: 0.9209 (t80) cc_final: 0.8967 (t80) REVERT: D 2162 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8502 (mmp) REVERT: D 2384 MET cc_start: 0.9319 (mmm) cc_final: 0.8731 (mmm) REVERT: D 2585 MET cc_start: 0.7642 (ttm) cc_final: 0.7376 (ttp) REVERT: D 2702 ASN cc_start: 0.8762 (t0) cc_final: 0.8448 (t0) REVERT: D 2840 MET cc_start: 0.4445 (mmt) cc_final: 0.4099 (mmt) REVERT: D 2843 MET cc_start: 0.7103 (ppp) cc_final: 0.6591 (ppp) REVERT: D 2844 MET cc_start: 0.8948 (ppp) cc_final: 0.8458 (ppp) REVERT: D 2895 PHE cc_start: 0.9012 (t80) cc_final: 0.8548 (t80) REVERT: D 2943 PHE cc_start: 0.8381 (m-80) cc_final: 0.8112 (m-80) REVERT: D 2982 PHE cc_start: 0.8772 (m-80) cc_final: 0.8102 (m-80) REVERT: D 3008 PHE cc_start: 0.8447 (t80) cc_final: 0.7967 (t80) REVERT: D 3033 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8477 (tt) REVERT: D 3978 MET cc_start: 0.9061 (ttp) cc_final: 0.8829 (ttp) REVERT: D 4052 MET cc_start: 0.8346 (mmm) cc_final: 0.7769 (mmp) REVERT: D 4748 MET cc_start: 0.8069 (mmm) cc_final: 0.7763 (mmp) outliers start: 107 outliers final: 72 residues processed: 830 average time/residue: 1.1331 time to fit residues: 1667.6781 Evaluate side-chains 844 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 762 time to evaluate : 10.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2781 THR Chi-restraints excluded: chain A residue 3046 MET Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1004 HIS Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1519 THR Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2724 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1004 HIS Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1519 THR Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2644 LEU Chi-restraints excluded: chain C residue 2724 TYR Chi-restraints excluded: chain C residue 2781 THR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3046 MET Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2162 MET Chi-restraints excluded: chain D residue 2886 ARG Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3066 GLU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1529 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 904 optimal weight: 9.9990 chunk 1158 optimal weight: 2.9990 chunk 897 optimal weight: 10.0000 chunk 1335 optimal weight: 9.9990 chunk 886 optimal weight: 9.9990 chunk 1580 optimal weight: 4.9990 chunk 989 optimal weight: 8.9990 chunk 963 optimal weight: 5.9990 chunk 729 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 ASN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2309 ASN ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 ASN ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 134536 Z= 0.246 Angle : 0.590 19.034 181752 Z= 0.294 Chirality : 0.039 0.197 19884 Planarity : 0.004 0.132 23364 Dihedral : 5.037 74.596 18082 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.89 % Rotamer: Outliers : 0.76 % Allowed : 9.21 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.07), residues: 16332 helix: 2.11 (0.06), residues: 8512 sheet: -0.15 (0.13), residues: 1568 loop : -0.41 (0.08), residues: 6252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 902 HIS 0.016 0.001 HIS B2849 PHE 0.032 0.001 PHE D2943 TYR 0.023 0.001 TYR B 931 ARG 0.016 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 772 time to evaluate : 13.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8238 (mmp) cc_final: 0.7839 (mmm) REVERT: A 317 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7294 (ptt) REVERT: A 778 MET cc_start: 0.8071 (ptp) cc_final: 0.7860 (ptm) REVERT: A 921 PHE cc_start: 0.9729 (p90) cc_final: 0.9444 (p90) REVERT: A 935 MET cc_start: 0.9464 (ppp) cc_final: 0.9241 (pmm) REVERT: A 995 MET cc_start: 0.7972 (mtt) cc_final: 0.7423 (ptp) REVERT: A 2192 MET cc_start: 0.8411 (tpt) cc_final: 0.8126 (tpp) REVERT: A 2384 MET cc_start: 0.9325 (mmm) cc_final: 0.8632 (mmm) REVERT: A 2702 ASN cc_start: 0.8861 (t0) cc_final: 0.8516 (t0) REVERT: A 2719 TYR cc_start: 0.8467 (t80) cc_final: 0.8100 (t80) REVERT: A 2785 TRP cc_start: 0.4845 (m-10) cc_final: 0.4271 (m-90) REVERT: A 2828 MET cc_start: 0.8714 (mmt) cc_final: 0.8262 (tpt) REVERT: A 2840 MET cc_start: 0.5207 (mmt) cc_final: 0.4558 (mmt) REVERT: A 2843 MET cc_start: 0.6790 (ppp) cc_final: 0.6012 (ppp) REVERT: A 2975 PHE cc_start: 0.8831 (m-10) cc_final: 0.8530 (m-10) REVERT: A 2982 PHE cc_start: 0.8764 (m-80) cc_final: 0.8247 (m-10) REVERT: A 3104 MET cc_start: 0.8761 (tmm) cc_final: 0.8057 (ppp) REVERT: A 3689 MET cc_start: 0.8533 (mmp) cc_final: 0.8234 (mmt) REVERT: A 3954 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8329 (tpp) REVERT: A 4504 MET cc_start: 0.8193 (mmm) cc_final: 0.7937 (mpp) REVERT: A 4809 MET cc_start: 0.8095 (tpp) cc_final: 0.7598 (tpp) REVERT: A 4884 MET cc_start: 0.8412 (tpt) cc_final: 0.8046 (tpt) REVERT: A 4885 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: E 4 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: E 6 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: E 53 LYS cc_start: 0.9255 (mmmt) cc_final: 0.9043 (mmmt) REVERT: F 6 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: G 6 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: B 241 MET cc_start: 0.8312 (pmm) cc_final: 0.7906 (ppp) REVERT: B 317 MET cc_start: 0.7930 (ppp) cc_final: 0.7695 (ppp) REVERT: B 921 PHE cc_start: 0.9799 (p90) cc_final: 0.9571 (p90) REVERT: B 935 MET cc_start: 0.9572 (ptp) cc_final: 0.9206 (ppp) REVERT: B 995 MET cc_start: 0.8354 (mtt) cc_final: 0.7950 (ptp) REVERT: B 1064 LEU cc_start: 0.8886 (pt) cc_final: 0.8576 (pt) REVERT: B 1168 MET cc_start: 0.8377 (mmm) cc_final: 0.7863 (mmm) REVERT: B 1202 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8233 (pt) REVERT: B 1306 MET cc_start: 0.8814 (mtp) cc_final: 0.8528 (mtm) REVERT: B 1494 MET cc_start: 0.8085 (mmm) cc_final: 0.7872 (tpp) REVERT: B 2644 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9029 (pp) REVERT: B 2681 MET cc_start: 0.8702 (mmp) cc_final: 0.8449 (mmp) REVERT: B 2688 MET cc_start: 0.3406 (ttm) cc_final: 0.2991 (ttt) REVERT: B 2702 ASN cc_start: 0.9059 (t0) cc_final: 0.8757 (t0) REVERT: B 2785 TRP cc_start: 0.4732 (m-10) cc_final: 0.4462 (m-10) REVERT: B 2840 MET cc_start: 0.6114 (mmt) cc_final: 0.5241 (mmt) REVERT: B 2843 MET cc_start: 0.7700 (ppp) cc_final: 0.7056 (ppp) REVERT: B 2982 PHE cc_start: 0.8876 (m-80) cc_final: 0.8286 (m-80) REVERT: B 3104 MET cc_start: 0.8899 (tmm) cc_final: 0.8314 (ppp) REVERT: B 4052 MET cc_start: 0.8270 (mmm) cc_final: 0.7886 (mmm) REVERT: B 4707 MET cc_start: 0.8317 (ttm) cc_final: 0.8093 (ttp) REVERT: B 4748 MET cc_start: 0.8084 (mmm) cc_final: 0.7782 (mmp) REVERT: C 393 MET cc_start: 0.7904 (mmm) cc_final: 0.7492 (mmm) REVERT: C 893 TRP cc_start: 0.8384 (m-10) cc_final: 0.7985 (m-90) REVERT: C 902 TRP cc_start: 0.7920 (t-100) cc_final: 0.7529 (t-100) REVERT: C 921 PHE cc_start: 0.9710 (p90) cc_final: 0.9356 (p90) REVERT: C 935 MET cc_start: 0.9570 (ptp) cc_final: 0.9335 (ppp) REVERT: C 995 MET cc_start: 0.8168 (mtt) cc_final: 0.7815 (ptp) REVERT: C 1215 MET cc_start: 0.8524 (mtp) cc_final: 0.8254 (mtt) REVERT: C 1729 MET cc_start: 0.8683 (mmt) cc_final: 0.8448 (mmt) REVERT: C 2134 MET cc_start: 0.8807 (mmm) cc_final: 0.8571 (tpt) REVERT: C 2142 MET cc_start: 0.8320 (mmm) cc_final: 0.7889 (mpp) REVERT: C 2192 MET cc_start: 0.8814 (mmp) cc_final: 0.8585 (tpt) REVERT: C 2644 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9067 (pp) REVERT: C 2681 MET cc_start: 0.8813 (mmp) cc_final: 0.8569 (mmp) REVERT: C 2840 MET cc_start: 0.7215 (mmt) cc_final: 0.6622 (mmt) REVERT: C 2843 MET cc_start: 0.7267 (ppp) cc_final: 0.6574 (ppp) REVERT: C 2844 MET cc_start: 0.9188 (tmm) cc_final: 0.8944 (ppp) REVERT: C 2975 PHE cc_start: 0.8753 (m-10) cc_final: 0.8525 (m-10) REVERT: C 3033 LEU cc_start: 0.9211 (mp) cc_final: 0.8943 (tt) REVERT: C 3104 MET cc_start: 0.8879 (tmm) cc_final: 0.8216 (ppp) REVERT: C 4048 PHE cc_start: 0.8582 (t80) cc_final: 0.8108 (t80) REVERT: C 4052 MET cc_start: 0.8374 (mmm) cc_final: 0.7965 (mtp) REVERT: C 4239 LEU cc_start: 0.8715 (pt) cc_final: 0.8109 (tt) REVERT: C 4504 MET cc_start: 0.8291 (mmm) cc_final: 0.8024 (mmm) REVERT: D 241 MET cc_start: 0.8361 (pmm) cc_final: 0.7745 (ppp) REVERT: D 309 MET cc_start: 0.8290 (mmp) cc_final: 0.8041 (mmp) REVERT: D 393 MET cc_start: 0.7837 (mmt) cc_final: 0.7615 (mmm) REVERT: D 778 MET cc_start: 0.8222 (ptp) cc_final: 0.7994 (ptm) REVERT: D 893 TRP cc_start: 0.8901 (m-10) cc_final: 0.8293 (m-90) REVERT: D 940 LEU cc_start: 0.9315 (mt) cc_final: 0.8768 (tt) REVERT: D 946 LEU cc_start: 0.9129 (mt) cc_final: 0.8909 (pp) REVERT: D 995 MET cc_start: 0.7404 (mtt) cc_final: 0.6859 (ptp) REVERT: D 1174 MET cc_start: 0.8006 (pmm) cc_final: 0.7751 (pmm) REVERT: D 1419 PHE cc_start: 0.9210 (t80) cc_final: 0.8959 (t80) REVERT: D 2384 MET cc_start: 0.9286 (mmm) cc_final: 0.8705 (mmm) REVERT: D 2585 MET cc_start: 0.7695 (ttm) cc_final: 0.7386 (ttp) REVERT: D 2669 LEU cc_start: 0.9313 (pp) cc_final: 0.8888 (tp) REVERT: D 2689 MET cc_start: 0.8182 (tmm) cc_final: 0.7932 (tmm) REVERT: D 2702 ASN cc_start: 0.8763 (t0) cc_final: 0.8446 (t0) REVERT: D 2734 MET cc_start: 0.8712 (pmm) cc_final: 0.8492 (pmm) REVERT: D 2840 MET cc_start: 0.4798 (mmt) cc_final: 0.4067 (mmt) REVERT: D 2843 MET cc_start: 0.7098 (ppp) cc_final: 0.6559 (ppp) REVERT: D 2895 PHE cc_start: 0.9037 (t80) cc_final: 0.8580 (t80) REVERT: D 2943 PHE cc_start: 0.8404 (m-80) cc_final: 0.8113 (m-80) REVERT: D 2982 PHE cc_start: 0.8795 (m-80) cc_final: 0.8118 (m-80) REVERT: D 3008 PHE cc_start: 0.8463 (t80) cc_final: 0.8040 (t80) REVERT: D 3033 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8498 (tt) REVERT: D 4052 MET cc_start: 0.8334 (mmm) cc_final: 0.7938 (mmm) REVERT: D 4748 MET cc_start: 0.8036 (mmm) cc_final: 0.7746 (mmp) REVERT: D 4885 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7740 (mp0) outliers start: 110 outliers final: 74 residues processed: 832 average time/residue: 1.1466 time to fit residues: 1691.7438 Evaluate side-chains 848 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 762 time to evaluate : 10.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 3046 MET Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4885 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1004 HIS Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1519 THR Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2724 TYR Chi-restraints excluded: chain B residue 2886 ARG Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1004 HIS Chi-restraints excluded: chain C residue 1027 ARG Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1519 THR Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2644 LEU Chi-restraints excluded: chain C residue 2724 TYR Chi-restraints excluded: chain C residue 2781 THR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3046 MET Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2886 ARG Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4885 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 977 optimal weight: 0.2980 chunk 631 optimal weight: 10.0000 chunk 944 optimal weight: 10.0000 chunk 476 optimal weight: 20.0000 chunk 310 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 1004 optimal weight: 0.6980 chunk 1076 optimal weight: 9.9990 chunk 781 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 1242 optimal weight: 7.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3903 GLN D3931 ASN ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 134536 Z= 0.213 Angle : 0.586 17.712 181752 Z= 0.292 Chirality : 0.039 0.312 19884 Planarity : 0.004 0.130 23364 Dihedral : 4.988 74.950 18082 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 0.76 % Allowed : 9.35 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.07), residues: 16332 helix: 2.17 (0.06), residues: 8472 sheet: -0.14 (0.13), residues: 1576 loop : -0.37 (0.08), residues: 6284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D1016 HIS 0.017 0.001 HIS B2849 PHE 0.036 0.001 PHE A2943 TYR 0.026 0.001 TYR A 931 ARG 0.024 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 785 time to evaluate : 11.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8184 (mmp) cc_final: 0.7814 (mmm) REVERT: A 317 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7299 (ptt) REVERT: A 778 MET cc_start: 0.8052 (ptp) cc_final: 0.7841 (ptm) REVERT: A 921 PHE cc_start: 0.9728 (p90) cc_final: 0.9447 (p90) REVERT: A 995 MET cc_start: 0.7990 (mtt) cc_final: 0.7457 (ptp) REVERT: A 2192 MET cc_start: 0.8352 (tpt) cc_final: 0.8076 (tpp) REVERT: A 2702 ASN cc_start: 0.8887 (t0) cc_final: 0.8545 (t0) REVERT: A 2719 TYR cc_start: 0.8421 (t80) cc_final: 0.8061 (t80) REVERT: A 2840 MET cc_start: 0.5186 (mmt) cc_final: 0.4521 (mmt) REVERT: A 2843 MET cc_start: 0.6804 (ppp) cc_final: 0.6296 (ppp) REVERT: A 2886 ARG cc_start: 0.9093 (mtm110) cc_final: 0.8858 (mtm180) REVERT: A 2975 PHE cc_start: 0.8817 (m-10) cc_final: 0.8534 (m-10) REVERT: A 2982 PHE cc_start: 0.8753 (m-80) cc_final: 0.8236 (m-10) REVERT: A 3104 MET cc_start: 0.8765 (tmm) cc_final: 0.8057 (ppp) REVERT: A 3689 MET cc_start: 0.8527 (mmp) cc_final: 0.8227 (mmt) REVERT: A 3954 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8331 (tpp) REVERT: A 4048 PHE cc_start: 0.8347 (t80) cc_final: 0.7986 (t80) REVERT: A 4052 MET cc_start: 0.8237 (mmm) cc_final: 0.7846 (mmp) REVERT: A 4239 LEU cc_start: 0.8755 (pt) cc_final: 0.8203 (tt) REVERT: A 4274 MET cc_start: 0.5595 (ptp) cc_final: 0.4982 (pmm) REVERT: A 4504 MET cc_start: 0.8179 (mmm) cc_final: 0.7930 (mpp) REVERT: A 4809 MET cc_start: 0.8097 (tpp) cc_final: 0.7664 (tpp) REVERT: A 4884 MET cc_start: 0.8421 (tpt) cc_final: 0.8072 (tpt) REVERT: A 4885 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: E 4 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: E 6 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: F 4 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: F 6 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: F 50 ARG cc_start: 0.8544 (ptm-80) cc_final: 0.8221 (ptm-80) REVERT: F 51 ILE cc_start: 0.9212 (mm) cc_final: 0.8873 (tp) REVERT: B 241 MET cc_start: 0.8322 (pmm) cc_final: 0.7922 (ppp) REVERT: B 317 MET cc_start: 0.7933 (ppp) cc_final: 0.7704 (ppp) REVERT: B 921 PHE cc_start: 0.9806 (p90) cc_final: 0.9580 (p90) REVERT: B 935 MET cc_start: 0.9555 (ptp) cc_final: 0.9212 (ppp) REVERT: B 995 MET cc_start: 0.8411 (mtt) cc_final: 0.7942 (ptp) REVERT: B 1064 LEU cc_start: 0.8883 (pt) cc_final: 0.8574 (pt) REVERT: B 1168 MET cc_start: 0.8324 (mmm) cc_final: 0.7856 (mmm) REVERT: B 1202 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8211 (pt) REVERT: B 1306 MET cc_start: 0.8804 (mtp) cc_final: 0.8528 (mtm) REVERT: B 1494 MET cc_start: 0.8060 (mmm) cc_final: 0.7858 (tpp) REVERT: B 2004 MET cc_start: 0.9086 (mmp) cc_final: 0.8819 (mmp) REVERT: B 2384 MET cc_start: 0.9050 (mmm) cc_final: 0.8823 (mmm) REVERT: B 2644 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9016 (pp) REVERT: B 2681 MET cc_start: 0.8676 (mmp) cc_final: 0.8427 (mmp) REVERT: B 2688 MET cc_start: 0.3474 (ttm) cc_final: 0.3060 (ttt) REVERT: B 2702 ASN cc_start: 0.9074 (t0) cc_final: 0.8769 (t0) REVERT: B 2785 TRP cc_start: 0.4757 (m-10) cc_final: 0.4486 (m-10) REVERT: B 2840 MET cc_start: 0.6220 (mmt) cc_final: 0.5252 (mmt) REVERT: B 2843 MET cc_start: 0.7669 (ppp) cc_final: 0.7020 (ppp) REVERT: B 2858 MET cc_start: 0.8310 (mmp) cc_final: 0.8058 (mpp) REVERT: B 2982 PHE cc_start: 0.8851 (m-80) cc_final: 0.8264 (m-80) REVERT: B 3104 MET cc_start: 0.8895 (tmm) cc_final: 0.8282 (ppp) REVERT: B 4052 MET cc_start: 0.8268 (mmm) cc_final: 0.7834 (mmm) REVERT: B 4707 MET cc_start: 0.8285 (ttm) cc_final: 0.8079 (ttp) REVERT: B 4748 MET cc_start: 0.8074 (mmm) cc_final: 0.7806 (mmp) REVERT: C 393 MET cc_start: 0.7921 (mmm) cc_final: 0.7548 (mmm) REVERT: C 902 TRP cc_start: 0.7935 (t-100) cc_final: 0.7570 (t-100) REVERT: C 921 PHE cc_start: 0.9717 (p90) cc_final: 0.9379 (p90) REVERT: C 935 MET cc_start: 0.9547 (ptp) cc_final: 0.9298 (ppp) REVERT: C 995 MET cc_start: 0.8187 (mtt) cc_final: 0.7668 (ptp) REVERT: C 1168 MET cc_start: 0.8429 (mmm) cc_final: 0.7937 (mmm) REVERT: C 1215 MET cc_start: 0.8530 (mtp) cc_final: 0.8283 (mtm) REVERT: C 2134 MET cc_start: 0.8802 (mmm) cc_final: 0.8563 (tpt) REVERT: C 2142 MET cc_start: 0.8308 (mmm) cc_final: 0.7858 (mpp) REVERT: C 2192 MET cc_start: 0.8809 (mmp) cc_final: 0.8579 (tpt) REVERT: C 2644 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9052 (pp) REVERT: C 2681 MET cc_start: 0.8811 (mmp) cc_final: 0.8566 (mmp) REVERT: C 2840 MET cc_start: 0.7301 (mmt) cc_final: 0.6569 (mmt) REVERT: C 2843 MET cc_start: 0.7288 (ppp) cc_final: 0.6582 (ppp) REVERT: C 2844 MET cc_start: 0.9156 (tmm) cc_final: 0.8841 (ppp) REVERT: C 2975 PHE cc_start: 0.8749 (m-10) cc_final: 0.8507 (m-10) REVERT: C 3033 LEU cc_start: 0.9205 (mp) cc_final: 0.8927 (tt) REVERT: C 3104 MET cc_start: 0.8864 (tmm) cc_final: 0.8194 (ppp) REVERT: C 4048 PHE cc_start: 0.8582 (t80) cc_final: 0.8273 (t80) REVERT: C 4052 MET cc_start: 0.8359 (mmm) cc_final: 0.8023 (mtp) REVERT: C 4239 LEU cc_start: 0.8707 (pt) cc_final: 0.8106 (tt) REVERT: C 4504 MET cc_start: 0.8257 (mmm) cc_final: 0.7987 (mmm) REVERT: D 241 MET cc_start: 0.8386 (pmm) cc_final: 0.7762 (ppp) REVERT: D 309 MET cc_start: 0.8290 (mmp) cc_final: 0.8030 (mmp) REVERT: D 393 MET cc_start: 0.7853 (mmt) cc_final: 0.7648 (mmm) REVERT: D 778 MET cc_start: 0.8204 (ptp) cc_final: 0.7934 (ptm) REVERT: D 893 TRP cc_start: 0.8798 (m-10) cc_final: 0.8274 (m-90) REVERT: D 946 LEU cc_start: 0.9095 (mt) cc_final: 0.8874 (pp) REVERT: D 995 MET cc_start: 0.7444 (mtt) cc_final: 0.6910 (ptp) REVERT: D 1174 MET cc_start: 0.7975 (pmm) cc_final: 0.7755 (pmm) REVERT: D 1419 PHE cc_start: 0.9205 (t80) cc_final: 0.8951 (t80) REVERT: D 2162 MET cc_start: 0.8745 (mmp) cc_final: 0.8331 (mmp) REVERT: D 2384 MET cc_start: 0.9252 (mmm) cc_final: 0.8735 (mmm) REVERT: D 2585 MET cc_start: 0.7689 (ttm) cc_final: 0.7377 (ttp) REVERT: D 2669 LEU cc_start: 0.9326 (pp) cc_final: 0.8877 (tp) REVERT: D 2702 ASN cc_start: 0.8769 (t0) cc_final: 0.8461 (t0) REVERT: D 2840 MET cc_start: 0.4772 (mmt) cc_final: 0.4074 (mmt) REVERT: D 2843 MET cc_start: 0.7133 (ppp) cc_final: 0.6595 (ppp) REVERT: D 2849 HIS cc_start: 0.8076 (t70) cc_final: 0.7754 (t-170) REVERT: D 2895 PHE cc_start: 0.9027 (t80) cc_final: 0.8770 (t80) REVERT: D 2943 PHE cc_start: 0.8432 (m-80) cc_final: 0.8103 (m-80) REVERT: D 2982 PHE cc_start: 0.8822 (m-80) cc_final: 0.8132 (m-80) REVERT: D 3008 PHE cc_start: 0.8477 (t80) cc_final: 0.8042 (t80) REVERT: D 3033 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8501 (tt) REVERT: D 3104 MET cc_start: 0.8786 (tmm) cc_final: 0.8051 (ppp) REVERT: D 4048 PHE cc_start: 0.8494 (t80) cc_final: 0.7842 (t80) REVERT: D 4052 MET cc_start: 0.8328 (mmm) cc_final: 0.7734 (mmp) REVERT: D 4748 MET cc_start: 0.8027 (mmm) cc_final: 0.7770 (mmp) outliers start: 109 outliers final: 77 residues processed: 846 average time/residue: 1.1516 time to fit residues: 1719.4561 Evaluate side-chains 855 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 767 time to evaluate : 11.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2781 THR Chi-restraints excluded: chain A residue 3046 MET Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4885 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1004 HIS Chi-restraints excluded: chain B residue 1027 ARG Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1519 THR Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2724 TYR Chi-restraints excluded: chain B residue 2886 ARG Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4885 GLU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1004 HIS Chi-restraints excluded: chain C residue 1027 ARG Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1519 THR Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2644 LEU Chi-restraints excluded: chain C residue 2724 TYR Chi-restraints excluded: chain C residue 2781 THR Chi-restraints excluded: chain C residue 2886 ARG Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3046 MET Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2886 ARG Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4885 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1437 optimal weight: 10.0000 chunk 1514 optimal weight: 6.9990 chunk 1381 optimal weight: 4.9990 chunk 1473 optimal weight: 20.0000 chunk 1513 optimal weight: 0.8980 chunk 886 optimal weight: 10.0000 chunk 641 optimal weight: 0.7980 chunk 1156 optimal weight: 3.9990 chunk 452 optimal weight: 10.0000 chunk 1331 optimal weight: 7.9990 chunk 1393 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3931 ASN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS ** C 544 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3931 ASN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4895 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 134536 Z= 0.255 Angle : 0.602 17.481 181752 Z= 0.299 Chirality : 0.040 0.236 19884 Planarity : 0.004 0.130 23364 Dihedral : 4.978 74.949 18082 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 0.68 % Allowed : 9.51 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.07), residues: 16332 helix: 2.16 (0.06), residues: 8496 sheet: -0.16 (0.13), residues: 1584 loop : -0.39 (0.08), residues: 6252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 902 HIS 0.017 0.001 HIS B2849 PHE 0.034 0.001 PHE D2720 TYR 0.028 0.001 TYR B 931 ARG 0.028 0.000 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 778 time to evaluate : 10.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8195 (mmp) cc_final: 0.7828 (mmp) REVERT: A 317 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7324 (ptt) REVERT: A 778 MET cc_start: 0.8054 (ptp) cc_final: 0.7841 (ptm) REVERT: A 921 PHE cc_start: 0.9736 (p90) cc_final: 0.9462 (p90) REVERT: A 995 MET cc_start: 0.8024 (mtt) cc_final: 0.7503 (ptp) REVERT: A 2192 MET cc_start: 0.8341 (tpt) cc_final: 0.8029 (tpp) REVERT: A 2384 MET cc_start: 0.9170 (mmm) cc_final: 0.8711 (mmm) REVERT: A 2702 ASN cc_start: 0.8893 (t0) cc_final: 0.8552 (t0) REVERT: A 2719 TYR cc_start: 0.8402 (t80) cc_final: 0.8038 (t80) REVERT: A 2840 MET cc_start: 0.5198 (mmt) cc_final: 0.4476 (mmt) REVERT: A 2843 MET cc_start: 0.6808 (ppp) cc_final: 0.6196 (ppp) REVERT: A 2975 PHE cc_start: 0.8852 (m-10) cc_final: 0.8556 (m-10) REVERT: A 2982 PHE cc_start: 0.8776 (m-80) cc_final: 0.8254 (m-10) REVERT: A 3104 MET cc_start: 0.8765 (tmm) cc_final: 0.8055 (ppp) REVERT: A 3689 MET cc_start: 0.8532 (mmp) cc_final: 0.8237 (mmt) REVERT: A 3954 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8325 (tpp) REVERT: A 4052 MET cc_start: 0.8197 (mmm) cc_final: 0.7713 (mmp) REVERT: A 4239 LEU cc_start: 0.8758 (pt) cc_final: 0.8209 (tt) REVERT: A 4274 MET cc_start: 0.5429 (ptp) cc_final: 0.4760 (pmm) REVERT: A 4504 MET cc_start: 0.8185 (mmm) cc_final: 0.7936 (mpp) REVERT: A 4809 MET cc_start: 0.8143 (tpp) cc_final: 0.7616 (tpp) REVERT: A 4884 MET cc_start: 0.8424 (tpt) cc_final: 0.8069 (tpt) REVERT: A 4885 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: E 4 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: E 6 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: F 4 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: F 6 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: F 50 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8265 (ptm-80) REVERT: F 51 ILE cc_start: 0.9224 (mm) cc_final: 0.8960 (tp) REVERT: G 50 ARG cc_start: 0.8448 (ptm-80) cc_final: 0.8173 (ptm-80) REVERT: B 317 MET cc_start: 0.7956 (ppp) cc_final: 0.7721 (ppp) REVERT: B 921 PHE cc_start: 0.9811 (p90) cc_final: 0.9594 (p90) REVERT: B 935 MET cc_start: 0.9549 (ptp) cc_final: 0.9207 (ppp) REVERT: B 1064 LEU cc_start: 0.8868 (pt) cc_final: 0.8570 (pt) REVERT: B 1168 MET cc_start: 0.8321 (mmm) cc_final: 0.7848 (mmm) REVERT: B 1202 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8208 (pt) REVERT: B 1306 MET cc_start: 0.8817 (mtp) cc_final: 0.8540 (mtm) REVERT: B 1494 MET cc_start: 0.8047 (mmm) cc_final: 0.7843 (tpp) REVERT: B 2584 MET cc_start: 0.8784 (mmt) cc_final: 0.8526 (mmm) REVERT: B 2644 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9025 (pp) REVERT: B 2681 MET cc_start: 0.8704 (mmp) cc_final: 0.8465 (mmp) REVERT: B 2688 MET cc_start: 0.3534 (ttm) cc_final: 0.2983 (ttt) REVERT: B 2702 ASN cc_start: 0.9083 (t0) cc_final: 0.8775 (t0) REVERT: B 2785 TRP cc_start: 0.4766 (m-10) cc_final: 0.4357 (m-10) REVERT: B 2840 MET cc_start: 0.6201 (mmt) cc_final: 0.4812 (mmt) REVERT: B 2843 MET cc_start: 0.7596 (ppp) cc_final: 0.6543 (ppp) REVERT: B 2982 PHE cc_start: 0.8850 (m-80) cc_final: 0.8335 (m-80) REVERT: B 3104 MET cc_start: 0.8909 (tmm) cc_final: 0.8306 (ppp) REVERT: B 4052 MET cc_start: 0.8290 (mmm) cc_final: 0.7840 (mtp) REVERT: B 4239 LEU cc_start: 0.8580 (pt) cc_final: 0.8307 (pt) REVERT: B 4707 MET cc_start: 0.8295 (ttm) cc_final: 0.8081 (ttp) REVERT: B 4748 MET cc_start: 0.8093 (mmm) cc_final: 0.7815 (mmp) REVERT: C 393 MET cc_start: 0.7944 (mmm) cc_final: 0.7574 (mmm) REVERT: C 902 TRP cc_start: 0.7944 (t-100) cc_final: 0.7593 (t-100) REVERT: C 921 PHE cc_start: 0.9751 (p90) cc_final: 0.9408 (p90) REVERT: C 935 MET cc_start: 0.9555 (ptp) cc_final: 0.9297 (ppp) REVERT: C 995 MET cc_start: 0.8157 (mtt) cc_final: 0.7842 (ptp) REVERT: C 1168 MET cc_start: 0.8434 (mmm) cc_final: 0.7892 (mmm) REVERT: C 1173 MET cc_start: 0.8508 (mtp) cc_final: 0.8197 (mtm) REVERT: C 1215 MET cc_start: 0.8514 (mtp) cc_final: 0.8268 (mtm) REVERT: C 2134 MET cc_start: 0.8798 (mmm) cc_final: 0.8553 (tpt) REVERT: C 2142 MET cc_start: 0.8318 (mmm) cc_final: 0.7836 (mpp) REVERT: C 2192 MET cc_start: 0.8815 (mmp) cc_final: 0.8589 (tpt) REVERT: C 2644 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9056 (pp) REVERT: C 2681 MET cc_start: 0.8834 (mmp) cc_final: 0.8591 (mmp) REVERT: C 2840 MET cc_start: 0.7209 (mmt) cc_final: 0.6250 (mmt) REVERT: C 2843 MET cc_start: 0.7176 (ppp) cc_final: 0.6530 (ppp) REVERT: C 2844 MET cc_start: 0.9168 (tmm) cc_final: 0.8847 (ppp) REVERT: C 2975 PHE cc_start: 0.8764 (m-10) cc_final: 0.8517 (m-10) REVERT: C 3104 MET cc_start: 0.8880 (tmm) cc_final: 0.8221 (ppp) REVERT: C 4048 PHE cc_start: 0.8604 (t80) cc_final: 0.8296 (t80) REVERT: C 4052 MET cc_start: 0.8372 (mmm) cc_final: 0.8042 (mtp) REVERT: C 4239 LEU cc_start: 0.8733 (pt) cc_final: 0.8151 (tt) REVERT: C 4504 MET cc_start: 0.8261 (mmm) cc_final: 0.7990 (mmm) REVERT: D 241 MET cc_start: 0.8401 (pmm) cc_final: 0.7762 (ppp) REVERT: D 309 MET cc_start: 0.8307 (mmp) cc_final: 0.8024 (mmp) REVERT: D 778 MET cc_start: 0.8219 (ptp) cc_final: 0.7947 (ptm) REVERT: D 893 TRP cc_start: 0.8798 (m-10) cc_final: 0.8273 (m-90) REVERT: D 946 LEU cc_start: 0.9096 (mt) cc_final: 0.8872 (pp) REVERT: D 995 MET cc_start: 0.7548 (mtt) cc_final: 0.6987 (ptp) REVERT: D 1174 MET cc_start: 0.7962 (pmm) cc_final: 0.7737 (pmm) REVERT: D 1419 PHE cc_start: 0.9210 (t80) cc_final: 0.8955 (t80) REVERT: D 2162 MET cc_start: 0.8776 (mmp) cc_final: 0.8414 (mmp) REVERT: D 2384 MET cc_start: 0.9235 (mmm) cc_final: 0.8716 (mmm) REVERT: D 2585 MET cc_start: 0.7680 (ttm) cc_final: 0.7398 (ttp) REVERT: D 2669 LEU cc_start: 0.9332 (pp) cc_final: 0.8884 (tp) REVERT: D 2702 ASN cc_start: 0.8797 (t0) cc_final: 0.8501 (t0) REVERT: D 2840 MET cc_start: 0.4831 (mmt) cc_final: 0.4079 (mmt) REVERT: D 2843 MET cc_start: 0.7137 (ppp) cc_final: 0.6553 (ppp) REVERT: D 2844 MET cc_start: 0.8763 (ppp) cc_final: 0.8552 (ppp) REVERT: D 2849 HIS cc_start: 0.8114 (t70) cc_final: 0.7798 (t-170) REVERT: D 2895 PHE cc_start: 0.9029 (t80) cc_final: 0.8752 (t80) REVERT: D 2943 PHE cc_start: 0.8440 (m-80) cc_final: 0.8094 (m-80) REVERT: D 2982 PHE cc_start: 0.8841 (m-80) cc_final: 0.8167 (m-80) REVERT: D 3008 PHE cc_start: 0.8499 (t80) cc_final: 0.8045 (t80) REVERT: D 3033 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8592 (tt) REVERT: D 3046 MET cc_start: 0.8635 (pmm) cc_final: 0.7407 (mmp) REVERT: D 3104 MET cc_start: 0.8789 (tmm) cc_final: 0.8058 (ppp) REVERT: D 4048 PHE cc_start: 0.8499 (t80) cc_final: 0.8055 (t80) REVERT: D 4052 MET cc_start: 0.8337 (mmm) cc_final: 0.7825 (mmm) REVERT: D 4274 MET cc_start: 0.4558 (tmm) cc_final: 0.3980 (pmm) REVERT: D 4748 MET cc_start: 0.8047 (mmm) cc_final: 0.7782 (mmp) REVERT: D 4895 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7935 (p0) outliers start: 98 outliers final: 79 residues processed: 833 average time/residue: 1.1274 time to fit residues: 1662.8454 Evaluate side-chains 861 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 770 time to evaluate : 10.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2781 THR Chi-restraints excluded: chain A residue 3046 MET Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4885 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1004 HIS Chi-restraints excluded: chain B residue 1027 ARG Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1519 THR Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2724 TYR Chi-restraints excluded: chain B residue 2886 ARG Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4885 GLU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1004 HIS Chi-restraints excluded: chain C residue 1027 ARG Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1519 THR Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2644 LEU Chi-restraints excluded: chain C residue 2724 TYR Chi-restraints excluded: chain C residue 2781 THR Chi-restraints excluded: chain C residue 2886 ARG Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3046 MET Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2886 ARG Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3033 LEU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4885 GLU Chi-restraints excluded: chain D residue 4895 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1467 optimal weight: 9.9990 chunk 967 optimal weight: 0.0030 chunk 1557 optimal weight: 0.9990 chunk 950 optimal weight: 9.9990 chunk 738 optimal weight: 3.9990 chunk 1082 optimal weight: 10.0000 chunk 1633 optimal weight: 7.9990 chunk 1503 optimal weight: 20.0000 chunk 1301 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 1004 optimal weight: 0.6980 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3903 GLN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1546 GLN ** B3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS ** C 544 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2613 HIS ** C2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3903 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 134536 Z= 0.215 Angle : 0.604 17.926 181752 Z= 0.298 Chirality : 0.039 0.243 19884 Planarity : 0.004 0.129 23364 Dihedral : 4.969 75.104 18082 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 0.68 % Allowed : 9.56 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.07), residues: 16332 helix: 2.15 (0.06), residues: 8520 sheet: -0.14 (0.13), residues: 1584 loop : -0.41 (0.08), residues: 6228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 902 HIS 0.019 0.001 HIS B2849 PHE 0.029 0.001 PHE D2720 TYR 0.027 0.001 TYR B 931 ARG 0.015 0.000 ARG A1027 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32664 Ramachandran restraints generated. 16332 Oldfield, 0 Emsley, 16332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 778 time to evaluate : 11.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8181 (mmp) cc_final: 0.7821 (mmp) REVERT: A 317 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7427 (ptt) REVERT: A 778 MET cc_start: 0.8039 (ptp) cc_final: 0.7829 (ptm) REVERT: A 921 PHE cc_start: 0.9750 (p90) cc_final: 0.9477 (p90) REVERT: A 995 MET cc_start: 0.8023 (mtt) cc_final: 0.7493 (ptp) REVERT: A 2162 MET cc_start: 0.8797 (mmm) cc_final: 0.8493 (mmm) REVERT: A 2192 MET cc_start: 0.8302 (tpt) cc_final: 0.7997 (tpp) REVERT: A 2702 ASN cc_start: 0.8904 (t0) cc_final: 0.8563 (t0) REVERT: A 2719 TYR cc_start: 0.8385 (t80) cc_final: 0.8023 (t80) REVERT: A 2840 MET cc_start: 0.5345 (mmt) cc_final: 0.4602 (mmt) REVERT: A 2843 MET cc_start: 0.6805 (ppp) cc_final: 0.6204 (ppp) REVERT: A 2975 PHE cc_start: 0.8844 (m-10) cc_final: 0.8539 (m-10) REVERT: A 2982 PHE cc_start: 0.8767 (m-80) cc_final: 0.8260 (m-10) REVERT: A 3104 MET cc_start: 0.8761 (tmm) cc_final: 0.8047 (ppp) REVERT: A 3689 MET cc_start: 0.8528 (mmp) cc_final: 0.8233 (mmt) REVERT: A 3954 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8330 (tpp) REVERT: A 4048 PHE cc_start: 0.8378 (t80) cc_final: 0.7971 (t80) REVERT: A 4052 MET cc_start: 0.8202 (mmm) cc_final: 0.7775 (mmp) REVERT: A 4239 LEU cc_start: 0.8752 (pt) cc_final: 0.8203 (tt) REVERT: A 4274 MET cc_start: 0.5419 (ptp) cc_final: 0.4758 (pmm) REVERT: A 4504 MET cc_start: 0.8179 (mmm) cc_final: 0.7934 (mpp) REVERT: A 4809 MET cc_start: 0.8099 (tpp) cc_final: 0.7641 (tpp) REVERT: A 4884 MET cc_start: 0.8423 (tpt) cc_final: 0.8075 (tpt) REVERT: A 4885 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: E 4 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: E 6 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: F 4 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: F 6 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: F 50 ARG cc_start: 0.8556 (ptm-80) cc_final: 0.8275 (ptm-80) REVERT: F 51 ILE cc_start: 0.9221 (mm) cc_final: 0.8970 (tp) REVERT: B 317 MET cc_start: 0.7939 (ppp) cc_final: 0.7707 (ppp) REVERT: B 921 PHE cc_start: 0.9809 (p90) cc_final: 0.9591 (p90) REVERT: B 935 MET cc_start: 0.9550 (ptp) cc_final: 0.9202 (ppp) REVERT: B 995 MET cc_start: 0.8340 (mtt) cc_final: 0.8057 (ptp) REVERT: B 1064 LEU cc_start: 0.8865 (pt) cc_final: 0.8576 (pt) REVERT: B 1168 MET cc_start: 0.8344 (mmm) cc_final: 0.7871 (mmm) REVERT: B 1202 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8193 (pt) REVERT: B 1306 MET cc_start: 0.8806 (mtp) cc_final: 0.8532 (mtm) REVERT: B 2384 MET cc_start: 0.9007 (mmm) cc_final: 0.8784 (mmm) REVERT: B 2584 MET cc_start: 0.8781 (mmt) cc_final: 0.8520 (mmm) REVERT: B 2644 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9017 (pp) REVERT: B 2681 MET cc_start: 0.8689 (mmp) cc_final: 0.8441 (mmp) REVERT: B 2688 MET cc_start: 0.3519 (ttm) cc_final: 0.2986 (ttt) REVERT: B 2702 ASN cc_start: 0.9069 (t0) cc_final: 0.8749 (t0) REVERT: B 2785 TRP cc_start: 0.4788 (m-10) cc_final: 0.4342 (m-10) REVERT: B 2840 MET cc_start: 0.6224 (mmt) cc_final: 0.4862 (mmt) REVERT: B 2843 MET cc_start: 0.7668 (ppp) cc_final: 0.6656 (ppp) REVERT: B 2982 PHE cc_start: 0.8862 (m-80) cc_final: 0.8309 (m-80) REVERT: B 3104 MET cc_start: 0.8904 (tmm) cc_final: 0.8289 (ppp) REVERT: B 4052 MET cc_start: 0.8284 (mmm) cc_final: 0.7897 (mtm) REVERT: B 4239 LEU cc_start: 0.8575 (pt) cc_final: 0.7934 (tt) REVERT: B 4707 MET cc_start: 0.8283 (ttm) cc_final: 0.8081 (ttp) REVERT: B 4748 MET cc_start: 0.8089 (mmm) cc_final: 0.7814 (mmp) REVERT: B 4885 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 393 MET cc_start: 0.7950 (mmm) cc_final: 0.7541 (mmm) REVERT: C 902 TRP cc_start: 0.7946 (t-100) cc_final: 0.7561 (t-100) REVERT: C 921 PHE cc_start: 0.9761 (p90) cc_final: 0.9409 (p90) REVERT: C 935 MET cc_start: 0.9549 (ptp) cc_final: 0.9292 (ppp) REVERT: C 995 MET cc_start: 0.8187 (mtt) cc_final: 0.7858 (ptp) REVERT: C 1168 MET cc_start: 0.8427 (mmm) cc_final: 0.7903 (mmm) REVERT: C 1173 MET cc_start: 0.8484 (mtp) cc_final: 0.8170 (mtm) REVERT: C 1215 MET cc_start: 0.8501 (mtp) cc_final: 0.8255 (mtm) REVERT: C 2192 MET cc_start: 0.8806 (mmp) cc_final: 0.8565 (tpt) REVERT: C 2584 MET cc_start: 0.8612 (mmt) cc_final: 0.8386 (mmt) REVERT: C 2644 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9054 (pp) REVERT: C 2681 MET cc_start: 0.8815 (mmp) cc_final: 0.8576 (mmp) REVERT: C 2734 MET cc_start: 0.8907 (pmm) cc_final: 0.8622 (pmm) REVERT: C 2840 MET cc_start: 0.7328 (mmt) cc_final: 0.6360 (mmt) REVERT: C 2843 MET cc_start: 0.7245 (ppp) cc_final: 0.6598 (ppp) REVERT: C 2844 MET cc_start: 0.9146 (tmm) cc_final: 0.8910 (ppp) REVERT: C 2975 PHE cc_start: 0.8759 (m-10) cc_final: 0.8503 (m-10) REVERT: C 3104 MET cc_start: 0.8881 (tmm) cc_final: 0.8228 (ppp) REVERT: C 4048 PHE cc_start: 0.8606 (t80) cc_final: 0.8309 (t80) REVERT: C 4052 MET cc_start: 0.8371 (mmm) cc_final: 0.8052 (mtp) REVERT: C 4239 LEU cc_start: 0.8725 (pt) cc_final: 0.8142 (tt) REVERT: C 4504 MET cc_start: 0.8256 (mmm) cc_final: 0.7984 (mmm) REVERT: D 241 MET cc_start: 0.8411 (pmm) cc_final: 0.7768 (ppp) REVERT: D 309 MET cc_start: 0.8294 (mmp) cc_final: 0.8039 (mmp) REVERT: D 778 MET cc_start: 0.8199 (ptp) cc_final: 0.7959 (ptm) REVERT: D 893 TRP cc_start: 0.8764 (m-10) cc_final: 0.8229 (m-90) REVERT: D 946 LEU cc_start: 0.9089 (mt) cc_final: 0.8855 (pp) REVERT: D 995 MET cc_start: 0.7525 (mtt) cc_final: 0.6992 (ptp) REVERT: D 1174 MET cc_start: 0.7976 (pmm) cc_final: 0.7773 (pmm) REVERT: D 1215 MET cc_start: 0.8273 (ttp) cc_final: 0.8068 (ttt) REVERT: D 1419 PHE cc_start: 0.9206 (t80) cc_final: 0.8953 (t80) REVERT: D 2162 MET cc_start: 0.8767 (mmp) cc_final: 0.8456 (mmp) REVERT: D 2585 MET cc_start: 0.7679 (ttm) cc_final: 0.7370 (ttp) REVERT: D 2669 LEU cc_start: 0.9325 (pp) cc_final: 0.8873 (tp) REVERT: D 2702 ASN cc_start: 0.8801 (t0) cc_final: 0.8506 (t0) REVERT: D 2757 MET cc_start: 0.5302 (tpt) cc_final: 0.5003 (tpt) REVERT: D 2840 MET cc_start: 0.4846 (mmt) cc_final: 0.4208 (mmt) REVERT: D 2843 MET cc_start: 0.7103 (ppp) cc_final: 0.6532 (ppp) REVERT: D 2849 HIS cc_start: 0.8074 (t70) cc_final: 0.7766 (t-170) REVERT: D 2895 PHE cc_start: 0.9020 (t80) cc_final: 0.8742 (t80) REVERT: D 2943 PHE cc_start: 0.8448 (m-80) cc_final: 0.8085 (m-80) REVERT: D 2982 PHE cc_start: 0.8828 (m-80) cc_final: 0.8153 (m-80) REVERT: D 3046 MET cc_start: 0.8630 (pmm) cc_final: 0.7402 (mmp) REVERT: D 3104 MET cc_start: 0.8790 (tmm) cc_final: 0.8054 (ppp) REVERT: D 4048 PHE cc_start: 0.8503 (t80) cc_final: 0.8212 (t80) REVERT: D 4052 MET cc_start: 0.8341 (mmm) cc_final: 0.8042 (mtp) REVERT: D 4748 MET cc_start: 0.8046 (mmm) cc_final: 0.7788 (mmp) outliers start: 98 outliers final: 82 residues processed: 832 average time/residue: 1.1603 time to fit residues: 1704.9875 Evaluate side-chains 864 residues out of total 14408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 771 time to evaluate : 11.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2781 THR Chi-restraints excluded: chain A residue 3046 MET Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4885 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1004 HIS Chi-restraints excluded: chain B residue 1027 ARG Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1519 THR Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2724 TYR Chi-restraints excluded: chain B residue 2886 ARG Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3046 MET Chi-restraints excluded: chain B residue 3700 HIS Chi-restraints excluded: chain B residue 4885 GLU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1004 HIS Chi-restraints excluded: chain C residue 1027 ARG Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1519 THR Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2644 LEU Chi-restraints excluded: chain C residue 2724 TYR Chi-restraints excluded: chain C residue 2781 THR Chi-restraints excluded: chain C residue 2886 ARG Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3046 MET Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2886 ARG Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4885 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 797 optimal weight: 9.9990 chunk 1033 optimal weight: 7.9990 chunk 1385 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 1199 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 1303 optimal weight: 9.9990 chunk 545 optimal weight: 9.9990 chunk 1338 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4251 ASN C 240 HIS ** C 544 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.046075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.033322 restraints weight = 1452755.272| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.38 r_work: 0.2829 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 134536 Z= 0.287 Angle : 0.619 16.900 181752 Z= 0.308 Chirality : 0.040 0.232 19884 Planarity : 0.004 0.129 23364 Dihedral : 4.964 75.005 18080 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 0.69 % Allowed : 9.64 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.01 % 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: 1.43 (0.07), residues: 16332 helix: 2.15 (0.06), residues: 8508 sheet: -0.16 (0.13), residues: 1580 loop : -0.42 (0.08), residues: 6244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 902 HIS 0.018 0.001 HIS B2849 PHE 0.035 0.001 PHE B2943 TYR 0.025 0.001 TYR B 931 ARG 0.017 0.000 ARG C 880 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32136.68 seconds wall clock time: 562 minutes 51.14 seconds (33771.14 seconds total)