Starting phenix.real_space_refine on Thu Mar 21 08:22:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxm_42769/03_2024/8uxm_42769_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxm_42769/03_2024/8uxm_42769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxm_42769/03_2024/8uxm_42769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxm_42769/03_2024/8uxm_42769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxm_42769/03_2024/8uxm_42769_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxm_42769/03_2024/8uxm_42769_updated.pdb" } resolution = 3.56 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= 0.013 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 20 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 972 5.16 5 C 91208 2.51 5 N 24400 2.21 5 O 26836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 7": "OE1" <-> "OE2" Residue "I ASP 119": "OD1" <-> "OD2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1138": "OD1" <-> "OD2" Residue "A ASP 1167": "OD1" <-> "OD2" Residue "A PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1534": "OE1" <-> "OE2" Residue "A ASP 1838": "OD1" <-> "OD2" Residue "A ASP 1982": "OD1" <-> "OD2" Residue "A GLU 2010": "OE1" <-> "OE2" Residue "A ASP 2379": "OD1" <-> "OD2" Residue "A TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2690": "OE1" <-> "OE2" Residue "A GLU 2698": "OE1" <-> "OE2" Residue "A TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2791": "NH1" <-> "NH2" Residue "A ARG 2793": "NH1" <-> "NH2" Residue "A TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3642": "OE1" <-> "OE2" Residue "A GLU 3683": "OE1" <-> "OE2" Residue "A GLU 3716": "OE1" <-> "OE2" Residue "A GLU 3783": "OE1" <-> "OE2" Residue "A GLU 3922": "OE1" <-> "OE2" Residue "A PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4034": "OE1" <-> "OE2" Residue "A TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4107": "OE1" <-> "OE2" Residue "A GLU 4167": "OE1" <-> "OE2" Residue "A PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4624": "OD1" <-> "OD2" Residue "A PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4678": "OD1" <-> "OD2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J ASP 119": "OD1" <-> "OD2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L ASP 119": "OD1" <-> "OD2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K ASP 119": "OD1" <-> "OD2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B ASP 721": "OD1" <-> "OD2" Residue "B GLU 810": "OE1" <-> "OE2" Residue "B PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1138": "OD1" <-> "OD2" Residue "B ASP 1167": "OD1" <-> "OD2" Residue "B PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1199": "OD1" <-> "OD2" Residue "B TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1534": "OE1" <-> "OE2" Residue "B ASP 1838": "OD1" <-> "OD2" Residue "B ASP 1982": "OD1" <-> "OD2" Residue "B GLU 2010": "OE1" <-> "OE2" Residue "B ASP 2379": "OD1" <-> "OD2" Residue "B TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2690": "OE1" <-> "OE2" Residue "B GLU 2698": "OE1" <-> "OE2" Residue "B TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2791": "NH1" <-> "NH2" Residue "B ARG 2793": "NH1" <-> "NH2" Residue "B TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3642": "OE1" <-> "OE2" Residue "B GLU 3683": "OE1" <-> "OE2" Residue "B GLU 3716": "OE1" <-> "OE2" Residue "B GLU 3783": "OE1" <-> "OE2" Residue "B GLU 3922": "OE1" <-> "OE2" Residue "B PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4034": "OE1" <-> "OE2" Residue "B TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4107": "OE1" <-> "OE2" Residue "B GLU 4167": "OE1" <-> "OE2" Residue "B PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4624": "OD1" <-> "OD2" Residue "B PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4678": "OD1" <-> "OD2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C ASP 721": "OD1" <-> "OD2" Residue "C GLU 810": "OE1" <-> "OE2" Residue "C PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1138": "OD1" <-> "OD2" Residue "C ASP 1167": "OD1" <-> "OD2" Residue "C PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1199": "OD1" <-> "OD2" Residue "C TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1534": "OE1" <-> "OE2" Residue "C ASP 1838": "OD1" <-> "OD2" Residue "C ASP 1982": "OD1" <-> "OD2" Residue "C GLU 2010": "OE1" <-> "OE2" Residue "C ASP 2379": "OD1" <-> "OD2" Residue "C TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2690": "OE1" <-> "OE2" Residue "C GLU 2698": "OE1" <-> "OE2" Residue "C TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2791": "NH1" <-> "NH2" Residue "C ARG 2793": "NH1" <-> "NH2" Residue "C TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3642": "OE1" <-> "OE2" Residue "C GLU 3683": "OE1" <-> "OE2" Residue "C GLU 3716": "OE1" <-> "OE2" Residue "C GLU 3783": "OE1" <-> "OE2" Residue "C GLU 3922": "OE1" <-> "OE2" Residue "C PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4034": "OE1" <-> "OE2" Residue "C TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4107": "OE1" <-> "OE2" Residue "C GLU 4167": "OE1" <-> "OE2" Residue "C PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4624": "OD1" <-> "OD2" Residue "C PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4678": "OD1" <-> "OD2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D ASP 721": "OD1" <-> "OD2" Residue "D GLU 810": "OE1" <-> "OE2" Residue "D PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1138": "OD1" <-> "OD2" Residue "D ASP 1167": "OD1" <-> "OD2" Residue "D PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1199": "OD1" <-> "OD2" Residue "D TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1534": "OE1" <-> "OE2" Residue "D ASP 1838": "OD1" <-> "OD2" Residue "D ASP 1982": "OD1" <-> "OD2" Residue "D GLU 2010": "OE1" <-> "OE2" Residue "D ASP 2379": "OD1" <-> "OD2" Residue "D TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2690": "OE1" <-> "OE2" Residue "D GLU 2698": "OE1" <-> "OE2" Residue "D TYR 2743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2791": "NH1" <-> "NH2" Residue "D ARG 2793": "NH1" <-> "NH2" Residue "D TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3642": "OE1" <-> "OE2" Residue "D GLU 3683": "OE1" <-> "OE2" Residue "D GLU 3716": "OE1" <-> "OE2" Residue "D GLU 3783": "OE1" <-> "OE2" Residue "D GLU 3922": "OE1" <-> "OE2" Residue "D PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4034": "OE1" <-> "OE2" Residue "D TYR 4058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4107": "OE1" <-> "OE2" Residue "D GLU 4167": "OE1" <-> "OE2" Residue "D PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4624": "OD1" <-> "OD2" Residue "D PHE 4648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4678": "OD1" <-> "OD2" Time to flip residues: 0.40s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143464 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "A" Number of atoms: 33849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 34568 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: "J" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "L" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "K" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1131 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 33849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 34568 Chain: "C" Number of atoms: 33849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 34568 Chain: "D" Number of atoms: 33849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 4231, 33841 Classifications: {'peptide': 4231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4074} 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: 34568 Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "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: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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 34301 SG CYS A4888 174.422 204.050 84.477 1.00154.49 S ATOM 34326 SG CYS A4891 176.744 203.568 87.412 1.00143.96 S ATOM 74815 SG CYS B4888 175.084 174.483 84.617 1.00154.49 S ATOM 74840 SG CYS B4891 175.562 176.796 87.560 1.00143.96 S ATOM A06OO SG CYS C4888 204.712 174.993 84.542 1.00154.49 S ATOM A06PD SG CYS C4891 202.383 175.474 87.472 1.00143.96 S ATOM A0WSX SG CYS D4888 203.977 204.706 84.652 1.00154.49 S ATOM A0WTM SG CYS D4891 203.502 202.381 87.586 1.00143.96 S Time building chain proxies: 96.16, per 1000 atoms: 0.67 Number of scatterers: 143464 At special positions: 0 Unit cell: (379.967, 379.967, 210.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 20 19.99 S 972 16.00 P 24 15.00 O 26836 8.00 N 24400 7.00 C 91208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.83 Conformation dependent library (CDL) restraints added in 34.7 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 C4888 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " Number of angles added : 4 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33576 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: 736 helices and 64 sheets defined 60.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 42.08 Creating SS restraints... Processing helix chain 'I' and resid 6 through 22 removed outlier: 3.571A pdb=" N PHE I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS I 22 " --> pdb=" O SER I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 41 removed outlier: 3.954A pdb=" N VAL I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 58 removed outlier: 3.523A pdb=" N ASN I 54 " --> pdb=" O GLN I 50 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL I 56 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 removed outlier: 3.907A pdb=" N LYS I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N MET I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 95 removed outlier: 4.969A pdb=" N LYS I 95 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 114 removed outlier: 3.981A pdb=" N LEU I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN I 112 " --> pdb=" O HIS I 108 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU I 113 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY I 114 " --> pdb=" O MET I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 131 removed outlier: 3.661A pdb=" N VAL I 122 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 Processing helix chain 'J' and resid 6 through 22 removed outlier: 3.571A pdb=" N PHE J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.954A pdb=" N VAL J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 58 removed outlier: 3.523A pdb=" N ASN J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL J 56 " --> pdb=" O MET J 52 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA J 58 " --> pdb=" O ASN J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 77 removed outlier: 3.907A pdb=" N LYS J 76 " --> pdb=" O MET J 72 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N MET J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 95 removed outlier: 4.970A pdb=" N LYS J 95 " --> pdb=" O ARG J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 114 removed outlier: 3.981A pdb=" N LEU J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG J 107 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN J 112 " --> pdb=" O HIS J 108 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU J 113 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY J 114 " --> pdb=" O MET J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 131 removed outlier: 3.660A pdb=" N VAL J 122 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP J 123 " --> pdb=" O ASP J 119 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 146 Processing helix chain 'L' and resid 6 through 22 removed outlier: 3.571A pdb=" N PHE L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS L 22 " --> pdb=" O SER L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 41 removed outlier: 3.954A pdb=" N VAL L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 58 removed outlier: 3.523A pdb=" N ASN L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.907A pdb=" N LYS L 76 " --> pdb=" O MET L 72 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N MET L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 95 removed outlier: 4.969A pdb=" N LYS L 95 " --> pdb=" O ARG L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 114 removed outlier: 3.982A pdb=" N LEU L 106 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG L 107 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN L 112 " --> pdb=" O HIS L 108 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU L 113 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY L 114 " --> pdb=" O MET L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 131 removed outlier: 3.661A pdb=" N VAL L 122 " --> pdb=" O THR L 118 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE L 131 " --> pdb=" O ARG L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 146 Processing helix chain 'K' and resid 6 through 22 removed outlier: 3.572A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 41 removed outlier: 3.953A pdb=" N VAL K 36 " --> pdb=" O GLU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 58 removed outlier: 3.524A pdb=" N ASN K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU K 55 " --> pdb=" O ASP K 51 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL K 56 " --> pdb=" O MET K 52 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 77 removed outlier: 3.906A pdb=" N LYS K 76 " --> pdb=" O MET K 72 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N MET K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 95 removed outlier: 4.970A pdb=" N LYS K 95 " --> pdb=" O ARG K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 114 removed outlier: 3.980A pdb=" N LEU K 106 " --> pdb=" O SER K 102 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN K 112 " --> pdb=" O HIS K 108 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU K 113 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY K 114 " --> pdb=" O MET K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 131 removed outlier: 3.661A pdb=" N VAL K 122 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE K 131 " --> pdb=" O ARG K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 146 Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.820A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.730A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TRP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 219 through 224 removed outlier: 5.597A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.132A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.691A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.256A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.554A pdb=" N GLY A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.623A pdb=" N VAL A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 4.988A 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: 3.502A pdb=" N SER A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 3.926A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.631A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 563' Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.640A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.989A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 590' Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.814A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.907A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.695A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.658A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.139A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.962A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 4.165A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 4.864A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.833A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.889A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.036A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 removed outlier: 3.709A pdb=" N MET A1421 " --> pdb=" O TYR A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.661A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 4.755A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1503 removed outlier: 3.595A pdb=" N ASN A1502 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1498 through 1503' Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.991A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.152A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.803A 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: 3.614A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.831A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.824A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 4.405A pdb=" N GLN A1777 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYR A1778 " --> pdb=" O GLU A1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1773 through 1778' Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 4.506A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A1805 " --> pdb=" O GLU A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1899 through 1948 removed outlier: 4.256A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1957 removed outlier: 3.893A pdb=" N LEU A1957 " --> pdb=" O MET A1953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1967 removed outlier: 4.102A pdb=" N LYS A1963 " --> pdb=" O ALA A1959 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 removed outlier: 4.312A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 4.051A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.600A 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: 3.799A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.519A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 5.171A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.623A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.675A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.209A 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: 3.630A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A2265 " --> pdb=" O ASP A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.615A pdb=" N GLY A2295 " --> pdb=" O ASN A2291 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A2300 " --> pdb=" O GLU A2296 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.587A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 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: 5.735A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.805A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 3.702A pdb=" N PHE A2492 " --> pdb=" O LEU A2488 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 5.230A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 4.592A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.225A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 4.412A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 5.284A 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: 4.188A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2603 through 2618 removed outlier: 3.562A pdb=" N LEU A2607 " --> pdb=" O ALA A2603 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.292A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 3.630A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.832A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.776A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2784 Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2793 through 2802 Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.162A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.452A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2921 removed outlier: 4.440A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE A2921 " --> pdb=" O ILE A2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2916 through 2921' Processing helix chain 'A' and resid 2922 through 2948 removed outlier: 3.700A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.428A 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 3017 removed outlier: 5.423A pdb=" N HIS A3017 " --> pdb=" O VAL A3013 " (cutoff:3.500A) Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 3.974A pdb=" N PHE A3022 " --> pdb=" O ARG A3018 " (cutoff:3.500A) removed outlier: 5.262A 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 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3048 removed outlier: 4.843A pdb=" N VAL A3045 " --> pdb=" O ASP A3041 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3075 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.477A pdb=" N LEU A3101 " --> pdb=" O THR A3097 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3117 through 3122 Processing helix chain 'A' and resid 3124 through 3144 removed outlier: 6.635A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS A3144 " --> pdb=" O LEU A3140 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 Processing helix chain 'A' and resid 3153 through 3166 removed outlier: 3.645A pdb=" N GLU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 4.219A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3183 through 3188 Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.056A pdb=" N ALA A3193 " --> pdb=" O SER A3189 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 4.285A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 Proline residue: A3232 - end of helix Processing helix chain 'A' and resid 3233 through 3253 removed outlier: 4.084A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 4.916A pdb=" N SER A3247 " --> pdb=" O CYS A3243 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG A3248 " --> pdb=" O SER A3244 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP A3249 " --> pdb=" O TYR A3245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3291 removed outlier: 4.250A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE A3290 " --> pdb=" O ASN A3286 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP A3291 " --> pdb=" O ASN A3287 " (cutoff:3.500A) Processing helix chain 'A' and resid 3298 through 3304 removed outlier: 4.640A pdb=" N PHE A3302 " --> pdb=" O ARG A3298 " (cutoff:3.500A) Processing helix chain 'A' and resid 3311 through 3318 removed outlier: 4.722A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3329 Processing helix chain 'A' and resid 3584 through 3606 removed outlier: 3.880A pdb=" N GLN A3594 " --> pdb=" O LEU A3590 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A3597 " --> pdb=" O LYS A3593 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3612 through 3632 removed outlier: 4.423A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 removed outlier: 3.619A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.299A 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: 3.545A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.805A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.666A pdb=" N ILE A3744 " --> pdb=" O VAL A3740 " (cutoff:3.500A) removed outlier: 3.842A 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: 4.608A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.530A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.562A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.622A 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: 3.996A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4027 removed outlier: 4.649A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4029 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.053A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.765A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.736A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.945A pdb=" N GLN A4116 " --> pdb=" O ASP A4112 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A4117 " --> pdb=" O THR A4113 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4131 Proline residue: A4131 - end of helix Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4184 through 4208 Processing helix chain 'A' and resid 4237 through 4261 removed outlier: 3.654A pdb=" N LEU A4255 " --> pdb=" O ASN A4251 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4275 removed outlier: 3.698A pdb=" N GLN A4267 " --> pdb=" O SER A4263 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS A4273 " --> pdb=" O LYS A4269 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET A4274 " --> pdb=" O LYS A4270 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THR A4275 " --> pdb=" O VAL A4271 " (cutoff:3.500A) Processing helix chain 'A' and resid 4276 through 4310 removed outlier: 3.732A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 5.124A pdb=" N ILE A4484 " --> pdb=" O PHE A4480 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.558A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 4.139A 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: 3.644A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4662 removed outlier: 5.720A pdb=" N GLU A4659 " --> pdb=" O ASP A4655 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A4660 " --> pdb=" O LYS A4656 " (cutoff:3.500A) Processing helix chain 'A' and resid 4663 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 4.952A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 3.653A pdb=" N ILE A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) removed outlier: 5.478A 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: 3.952A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.842A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.965A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) removed outlier: 3.839A 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: 5.472A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 3.605A pdb=" N GLY A4820 " --> pdb=" O HIS A4816 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.134A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.912A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A4900 " --> pdb=" O ASP A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.821A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.730A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TRP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 219 through 224 removed outlier: 5.597A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 4.131A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.691A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.255A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 removed outlier: 3.553A pdb=" N GLY B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.623A pdb=" N VAL B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 4.988A 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: 3.502A pdb=" N SER B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 3.926A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 563 removed outlier: 3.631A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 563' Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.640A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.989A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 583 through 590' Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.815A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.907A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.695A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.658A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 875 through 901 removed outlier: 4.138A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.963A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 4.165A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 4.864A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.834A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.889A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.035A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1423 removed outlier: 3.709A pdb=" N MET B1421 " --> pdb=" O TYR B1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.661A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 4.756A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1503 removed outlier: 3.595A pdb=" N ASN B1502 " --> pdb=" O GLN B1498 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1498 through 1503' Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.991A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.152A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.803A 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: 3.614A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.831A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.823A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 Processing helix chain 'B' and resid 1773 through 1778 removed outlier: 4.405A pdb=" N GLN B1777 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TYR B1778 " --> pdb=" O GLU B1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1773 through 1778' Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 4.506A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS B1805 " --> pdb=" O GLU B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1899 through 1948 removed outlier: 4.257A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1957 removed outlier: 3.894A pdb=" N LEU B1957 " --> pdb=" O MET B1953 " (cutoff:3.500A) Processing helix chain 'B' and resid 1959 through 1967 removed outlier: 4.101A pdb=" N LYS B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 removed outlier: 4.312A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 4.051A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.600A 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: 3.799A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.519A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 5.171A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.623A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.675A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.209A 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: 3.631A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B2265 " --> pdb=" O ASP B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.614A pdb=" N GLY B2295 " --> pdb=" O ASN B2291 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.586A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 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: 5.735A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.805A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 3.702A pdb=" N PHE B2492 " --> pdb=" O LEU B2488 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 5.230A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 4.592A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.225A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 4.411A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 5.283A 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: 4.187A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2603 through 2618 removed outlier: 3.562A pdb=" N LEU B2607 " --> pdb=" O ALA B2603 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.292A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 3.631A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.832A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.777A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2766 through 2784 Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2793 through 2802 Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.163A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.451A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2921 removed outlier: 4.439A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE B2921 " --> pdb=" O ILE B2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2916 through 2921' Processing helix chain 'B' and resid 2922 through 2948 removed outlier: 3.700A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.428A 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 3017 removed outlier: 5.424A pdb=" N HIS B3017 " --> pdb=" O VAL B3013 " (cutoff:3.500A) Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 3.974A pdb=" N PHE B3022 " --> pdb=" O ARG B3018 " (cutoff:3.500A) removed outlier: 5.261A 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 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3048 removed outlier: 4.843A pdb=" N VAL B3045 " --> pdb=" O ASP B3041 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3075 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.478A pdb=" N LEU B3101 " --> pdb=" O THR B3097 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3117 through 3122 Processing helix chain 'B' and resid 3124 through 3144 removed outlier: 6.635A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS B3144 " --> pdb=" O LEU B3140 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 Processing helix chain 'B' and resid 3153 through 3166 removed outlier: 3.645A pdb=" N GLU B3157 " --> pdb=" O SER B3153 " (cutoff:3.500A) Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 4.219A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3183 through 3188 Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.056A pdb=" N ALA B3193 " --> pdb=" O SER B3189 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 4.285A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 Proline residue: B3232 - end of helix Processing helix chain 'B' and resid 3233 through 3253 removed outlier: 4.085A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 4.916A pdb=" N SER B3247 " --> pdb=" O CYS B3243 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG B3248 " --> pdb=" O SER B3244 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP B3249 " --> pdb=" O TYR B3245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) Processing helix chain 'B' and resid 3269 through 3291 removed outlier: 4.250A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B3290 " --> pdb=" O ASN B3286 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP B3291 " --> pdb=" O ASN B3287 " (cutoff:3.500A) Processing helix chain 'B' and resid 3298 through 3304 removed outlier: 4.640A pdb=" N PHE B3302 " --> pdb=" O ARG B3298 " (cutoff:3.500A) Processing helix chain 'B' and resid 3311 through 3318 removed outlier: 4.722A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) Processing helix chain 'B' and resid 3319 through 3329 Processing helix chain 'B' and resid 3584 through 3606 removed outlier: 3.879A pdb=" N GLN B3594 " --> pdb=" O LEU B3590 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B3597 " --> pdb=" O LYS B3593 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3612 through 3632 removed outlier: 4.424A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 removed outlier: 3.619A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.299A 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: 3.545A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.805A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.666A pdb=" N ILE B3744 " --> pdb=" O VAL B3740 " (cutoff:3.500A) removed outlier: 3.842A 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: 4.608A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.530A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.562A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.621A 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: 3.996A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4027 removed outlier: 4.649A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4029 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.054A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.764A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.736A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.945A pdb=" N GLN B4116 " --> pdb=" O ASP B4112 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B4117 " --> pdb=" O THR B4113 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4131 Proline residue: B4131 - end of helix Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4184 through 4208 Processing helix chain 'B' and resid 4237 through 4261 removed outlier: 3.655A pdb=" N LEU B4255 " --> pdb=" O ASN B4251 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4275 removed outlier: 3.698A pdb=" N GLN B4267 " --> pdb=" O SER B4263 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS B4273 " --> pdb=" O LYS B4269 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B4274 " --> pdb=" O LYS B4270 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THR B4275 " --> pdb=" O VAL B4271 " (cutoff:3.500A) Processing helix chain 'B' and resid 4276 through 4310 removed outlier: 3.732A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 5.125A pdb=" N ILE B4484 " --> pdb=" O PHE B4480 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.558A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 4.139A 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: 3.645A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4662 removed outlier: 5.721A pdb=" N GLU B4659 " --> pdb=" O ASP B4655 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B4660 " --> pdb=" O LYS B4656 " (cutoff:3.500A) Processing helix chain 'B' and resid 4663 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 4.952A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 3.652A pdb=" N ILE B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) removed outlier: 5.478A 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: 3.953A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.842A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.965A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) removed outlier: 3.838A 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: 5.473A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 3.605A pdb=" N GLY B4820 " --> pdb=" O HIS B4816 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.135A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.911A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B4900 " --> pdb=" O ASP B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 54 through 59 Proline residue: B 59 - end of helix No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.821A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.730A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TRP C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 219 through 224 removed outlier: 5.597A pdb=" N ALA C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 4.132A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.691A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.255A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 removed outlier: 3.555A pdb=" N GLY C 461 " --> pdb=" O GLN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.622A pdb=" N VAL C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 4.989A 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: 3.502A pdb=" N SER C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 555 removed outlier: 3.927A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 removed outlier: 3.631A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 556 through 563' Processing helix chain 'C' and resid 567 through 582 removed outlier: 3.639A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.988A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 590' Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.814A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.907A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.695A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.658A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.139A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.962A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 4.164A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 4.864A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.833A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.890A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.036A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1423 removed outlier: 3.709A pdb=" N MET C1421 " --> pdb=" O TYR C1417 " (cutoff:3.500A) Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.660A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 4.755A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1498 through 1503 removed outlier: 3.596A pdb=" N ASN C1502 " --> pdb=" O GLN C1498 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1498 through 1503' Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.991A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.152A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.804A 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: 3.614A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.832A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.823A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 Processing helix chain 'C' and resid 1773 through 1778 removed outlier: 4.405A pdb=" N GLN C1777 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYR C1778 " --> pdb=" O GLU C1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1773 through 1778' Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 4.506A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS C1805 " --> pdb=" O GLU C1801 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1899 through 1948 removed outlier: 4.256A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1957 removed outlier: 3.893A pdb=" N LEU C1957 " --> pdb=" O MET C1953 " (cutoff:3.500A) Processing helix chain 'C' and resid 1959 through 1967 removed outlier: 4.101A pdb=" N LYS C1963 " --> pdb=" O ALA C1959 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 removed outlier: 4.312A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 4.052A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.600A 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: 3.799A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.519A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 5.170A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.624A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.676A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.209A 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: 3.630A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C2265 " --> pdb=" O ASP C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.615A pdb=" N GLY C2295 " --> pdb=" O ASN C2291 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP C2300 " --> pdb=" O GLU C2296 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.586A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 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: 5.734A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.805A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 3.702A pdb=" N PHE C2492 " --> pdb=" O LEU C2488 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 5.230A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 4.592A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.225A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 4.411A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 5.283A 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: 4.188A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2603 through 2618 removed outlier: 3.562A pdb=" N LEU C2607 " --> pdb=" O ALA C2603 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.292A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 3.631A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.833A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.776A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2766 through 2784 Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2793 through 2802 Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.163A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.452A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2921 removed outlier: 4.440A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE C2921 " --> pdb=" O ILE C2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2916 through 2921' Processing helix chain 'C' and resid 2922 through 2948 removed outlier: 3.700A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.428A 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 3017 removed outlier: 5.423A pdb=" N HIS C3017 " --> pdb=" O VAL C3013 " (cutoff:3.500A) Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 3.974A pdb=" N PHE C3022 " --> pdb=" O ARG C3018 " (cutoff:3.500A) removed outlier: 5.262A 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 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3048 removed outlier: 4.843A pdb=" N VAL C3045 " --> pdb=" O ASP C3041 " (cutoff:3.500A) Processing helix chain 'C' and resid 3050 through 3075 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.478A pdb=" N LEU C3101 " --> pdb=" O THR C3097 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3117 through 3122 Processing helix chain 'C' and resid 3124 through 3144 removed outlier: 6.636A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS C3144 " --> pdb=" O LEU C3140 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 Processing helix chain 'C' and resid 3153 through 3166 removed outlier: 3.645A pdb=" N GLU C3157 " --> pdb=" O SER C3153 " (cutoff:3.500A) Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 4.219A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3183 through 3188 Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.056A pdb=" N ALA C3193 " --> pdb=" O SER C3189 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 4.285A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 Proline residue: C3232 - end of helix Processing helix chain 'C' and resid 3233 through 3253 removed outlier: 4.085A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 4.917A pdb=" N SER C3247 " --> pdb=" O CYS C3243 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG C3248 " --> pdb=" O SER C3244 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP C3249 " --> pdb=" O TYR C3245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) Processing helix chain 'C' and resid 3269 through 3291 removed outlier: 4.249A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE C3290 " --> pdb=" O ASN C3286 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP C3291 " --> pdb=" O ASN C3287 " (cutoff:3.500A) Processing helix chain 'C' and resid 3298 through 3304 removed outlier: 4.639A pdb=" N PHE C3302 " --> pdb=" O ARG C3298 " (cutoff:3.500A) Processing helix chain 'C' and resid 3311 through 3318 removed outlier: 4.723A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) Processing helix chain 'C' and resid 3319 through 3329 Processing helix chain 'C' and resid 3584 through 3606 removed outlier: 3.880A pdb=" N GLN C3594 " --> pdb=" O LEU C3590 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C3597 " --> pdb=" O LYS C3593 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3612 through 3632 removed outlier: 4.423A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 removed outlier: 3.619A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.299A 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: 3.545A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.806A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.666A pdb=" N ILE C3744 " --> pdb=" O VAL C3740 " (cutoff:3.500A) removed outlier: 3.842A 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: 4.608A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.530A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.562A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.622A 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: 3.997A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4027 removed outlier: 4.650A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4029 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.053A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.766A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.737A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.945A pdb=" N GLN C4116 " --> pdb=" O ASP C4112 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR C4117 " --> pdb=" O THR C4113 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4131 Proline residue: C4131 - end of helix Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4184 through 4208 Processing helix chain 'C' and resid 4237 through 4261 removed outlier: 3.653A pdb=" N LEU C4255 " --> pdb=" O ASN C4251 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4275 removed outlier: 3.698A pdb=" N GLN C4267 " --> pdb=" O SER C4263 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS C4273 " --> pdb=" O LYS C4269 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET C4274 " --> pdb=" O LYS C4270 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THR C4275 " --> pdb=" O VAL C4271 " (cutoff:3.500A) Processing helix chain 'C' and resid 4276 through 4310 removed outlier: 3.731A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 5.124A pdb=" N ILE C4484 " --> pdb=" O PHE C4480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.558A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 4.139A 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: 3.645A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4662 removed outlier: 5.720A pdb=" N GLU C4659 " --> pdb=" O ASP C4655 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C4660 " --> pdb=" O LYS C4656 " (cutoff:3.500A) Processing helix chain 'C' and resid 4663 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 4.952A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 3.654A pdb=" N ILE C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) removed outlier: 5.478A 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: 3.952A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.842A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.965A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) removed outlier: 3.839A 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: 5.472A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 3.605A pdb=" N GLY C4820 " --> pdb=" O HIS C4816 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.134A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.912A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C4900 " --> pdb=" O ASP C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 54 through 59 Proline residue: C 59 - end of helix No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.821A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 155 through 160 removed outlier: 4.731A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TRP D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing helix chain 'D' and resid 219 through 224 removed outlier: 5.597A pdb=" N ALA D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 4.131A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.691A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.256A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 removed outlier: 3.554A pdb=" N GLY D 461 " --> pdb=" O GLN D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.622A pdb=" N VAL D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 4.989A 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: 3.501A pdb=" N SER D 525 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 555 removed outlier: 3.926A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 563 removed outlier: 3.631A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 556 through 563' Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.639A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.988A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 590' Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.814A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.907A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.695A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.658A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.139A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 3.962A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 4.165A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 4.865A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.833A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.889A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.037A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 removed outlier: 3.709A pdb=" N MET D1421 " --> pdb=" O TYR D1417 " (cutoff:3.500A) Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.661A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 4.756A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1498 through 1503 removed outlier: 3.595A pdb=" N ASN D1502 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1498 through 1503' Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.991A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.152A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.803A 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: 3.614A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.831A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.824A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 Processing helix chain 'D' and resid 1773 through 1778 removed outlier: 4.405A pdb=" N GLN D1777 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYR D1778 " --> pdb=" O GLU D1774 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1773 through 1778' Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 4.506A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS D1805 " --> pdb=" O GLU D1801 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1899 through 1948 removed outlier: 4.257A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1957 removed outlier: 3.893A pdb=" N LEU D1957 " --> pdb=" O MET D1953 " (cutoff:3.500A) Processing helix chain 'D' and resid 1959 through 1967 removed outlier: 4.102A pdb=" N LYS D1963 " --> pdb=" O ALA D1959 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 removed outlier: 4.312A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 4.051A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.600A 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: 3.800A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.519A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 5.171A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.623A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.675A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.209A 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: 3.630A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D2265 " --> pdb=" O ASP D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.615A pdb=" N GLY D2295 " --> pdb=" O ASN D2291 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP D2300 " --> pdb=" O GLU D2296 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.587A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 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: 5.734A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.805A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 3.703A pdb=" N PHE D2492 " --> pdb=" O LEU D2488 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 5.230A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 4.592A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.226A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 4.411A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 5.284A 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: 4.188A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2603 through 2618 removed outlier: 3.563A pdb=" N LEU D2607 " --> pdb=" O ALA D2603 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.291A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 3.630A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.833A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.777A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2766 through 2784 Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2793 through 2802 Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.162A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.452A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2921 removed outlier: 4.440A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE D2921 " --> pdb=" O ILE D2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2916 through 2921' Processing helix chain 'D' and resid 2922 through 2948 removed outlier: 3.700A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.428A 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 3017 removed outlier: 5.424A pdb=" N HIS D3017 " --> pdb=" O VAL D3013 " (cutoff:3.500A) Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 3.975A pdb=" N PHE D3022 " --> pdb=" O ARG D3018 " (cutoff:3.500A) removed outlier: 5.262A 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 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3048 removed outlier: 4.843A pdb=" N VAL D3045 " --> pdb=" O ASP D3041 " (cutoff:3.500A) Processing helix chain 'D' and resid 3050 through 3075 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.477A pdb=" N LEU D3101 " --> pdb=" O THR D3097 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3117 through 3122 Processing helix chain 'D' and resid 3124 through 3144 removed outlier: 6.635A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS D3144 " --> pdb=" O LEU D3140 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 Processing helix chain 'D' and resid 3153 through 3166 removed outlier: 3.644A pdb=" N GLU D3157 " --> pdb=" O SER D3153 " (cutoff:3.500A) Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 4.220A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3183 through 3188 Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.056A pdb=" N ALA D3193 " --> pdb=" O SER D3189 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 4.286A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 Proline residue: D3232 - end of helix Processing helix chain 'D' and resid 3233 through 3253 removed outlier: 4.085A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 4.917A pdb=" N SER D3247 " --> pdb=" O CYS D3243 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG D3248 " --> pdb=" O SER D3244 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP D3249 " --> pdb=" O TYR D3245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) Processing helix chain 'D' and resid 3269 through 3291 removed outlier: 4.251A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE D3290 " --> pdb=" O ASN D3286 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP D3291 " --> pdb=" O ASN D3287 " (cutoff:3.500A) Processing helix chain 'D' and resid 3298 through 3304 removed outlier: 4.640A pdb=" N PHE D3302 " --> pdb=" O ARG D3298 " (cutoff:3.500A) Processing helix chain 'D' and resid 3311 through 3318 removed outlier: 4.722A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) Processing helix chain 'D' and resid 3319 through 3329 Processing helix chain 'D' and resid 3584 through 3606 removed outlier: 3.879A pdb=" N GLN D3594 " --> pdb=" O LEU D3590 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D3597 " --> pdb=" O LYS D3593 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3612 through 3632 removed outlier: 4.423A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 removed outlier: 3.619A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.299A 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: 3.545A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.804A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.665A pdb=" N ILE D3744 " --> pdb=" O VAL D3740 " (cutoff:3.500A) removed outlier: 3.841A 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: 4.607A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.529A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.562A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.622A 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: 3.996A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4027 removed outlier: 4.650A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4029 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.054A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.764A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.736A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.945A pdb=" N GLN D4116 " --> pdb=" O ASP D4112 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR D4117 " --> pdb=" O THR D4113 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4131 Proline residue: D4131 - end of helix Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4184 through 4208 Processing helix chain 'D' and resid 4237 through 4261 removed outlier: 3.653A pdb=" N LEU D4255 " --> pdb=" O ASN D4251 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4275 removed outlier: 3.699A pdb=" N GLN D4267 " --> pdb=" O SER D4263 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS D4273 " --> pdb=" O LYS D4269 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET D4274 " --> pdb=" O LYS D4270 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THR D4275 " --> pdb=" O VAL D4271 " (cutoff:3.500A) Processing helix chain 'D' and resid 4276 through 4310 removed outlier: 3.731A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 5.124A pdb=" N ILE D4484 " --> pdb=" O PHE D4480 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.558A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 4.139A 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: 3.645A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4662 removed outlier: 5.720A pdb=" N GLU D4659 " --> pdb=" O ASP D4655 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE D4660 " --> pdb=" O LYS D4656 " (cutoff:3.500A) Processing helix chain 'D' and resid 4663 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 4.952A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 3.653A pdb=" N ILE D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) removed outlier: 5.479A 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: 3.952A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.842A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.965A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) removed outlier: 3.839A 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: 5.472A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 3.604A pdb=" N GLY D4820 " --> pdb=" O HIS D4816 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.134A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.912A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR D4900 " --> pdb=" O ASP D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.774A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 4.806A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.109A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.774A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 4.807A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.108A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.774A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 4.806A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.109A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.774A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 4.807A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.108A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.553A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.535A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.091A 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: 6.692A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 161 through 165 removed outlier: 3.513A pdb=" N ALA A 165 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP A 180 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 260 through 264 removed outlier: 5.494A pdb=" N LEU A 236 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N VAL A 247 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 15.053A pdb=" N LEU A 234 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 14.520A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.670A 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: 3.515A pdb=" N TYR A 362 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.977A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.636A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 9, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.607A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 3.509A pdb=" N VAL A1115 " --> pdb=" O PHE A1137 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.608A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 5.037A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.752A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 15, first strand: chain 'A' and resid 233 through 238 removed outlier: 5.970A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.553A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.534A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.091A 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: 6.692A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.512A pdb=" N ALA B 165 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP B 180 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 260 through 264 removed outlier: 5.494A pdb=" N LEU B 236 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N VAL B 247 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 15.053A pdb=" N LEU B 234 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 14.521A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.670A 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: 3.516A pdb=" N TYR B 362 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.978A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.636A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 24, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.608A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 3.509A pdb=" N VAL B1115 " --> pdb=" O PHE B1137 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.609A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 5.037A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.751A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 30, first strand: chain 'B' and resid 233 through 238 removed outlier: 5.970A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.553A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.535A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.090A 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: 6.692A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 161 through 165 removed outlier: 3.513A pdb=" N ALA C 165 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP C 180 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 260 through 264 removed outlier: 5.493A pdb=" N LEU C 236 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N VAL C 247 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 15.053A pdb=" N LEU C 234 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 14.520A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 3.670A 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: 3.515A pdb=" N TYR C 362 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.977A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.636A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 39, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.607A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 3.509A pdb=" N VAL C1115 " --> pdb=" O PHE C1137 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.609A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 5.037A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.752A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 45, first strand: chain 'C' and resid 233 through 238 removed outlier: 5.970A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.553A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.535A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.092A 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: 6.693A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 161 through 165 removed outlier: 3.513A pdb=" N ALA D 165 " --> pdb=" O ASP D 180 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP D 180 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'D' and resid 260 through 264 removed outlier: 5.493A pdb=" N LEU D 236 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N VAL D 247 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 15.053A pdb=" N LEU D 234 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 14.520A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.515A pdb=" N TYR D 362 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.978A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.636A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 54, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.608A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 3.508A pdb=" N VAL D1115 " --> pdb=" O PHE D1137 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.608A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 5.037A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.752A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 60, first strand: chain 'D' and resid 233 through 238 removed outlier: 5.969A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.328A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.105A 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: 6.328A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.105A 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: 6.328A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.105A 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: 6.328A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 7476 hydrogen bonds defined for protein. 22324 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: 111.37 Time building geometry restraints manager: 47.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.69: 144940 1.69 - 2.17: 1588 2.17 - 2.65: 0 2.65 - 3.13: 0 3.13 - 3.61: 4 Bond restraints: 146532 Sorted by residual: bond pdb=" CB CYS D3205 " pdb=" SG CYS D3205 " ideal model delta sigma weight residual 1.808 3.608 -1.800 3.30e-02 9.18e+02 2.98e+03 bond pdb=" CB CYS B3205 " pdb=" SG CYS B3205 " ideal model delta sigma weight residual 1.808 3.608 -1.800 3.30e-02 9.18e+02 2.97e+03 bond pdb=" CB CYS A3205 " pdb=" SG CYS A3205 " ideal model delta sigma weight residual 1.808 3.608 -1.800 3.30e-02 9.18e+02 2.97e+03 bond pdb=" CB CYS C3205 " pdb=" SG CYS C3205 " ideal model delta sigma weight residual 1.808 3.607 -1.799 3.30e-02 9.18e+02 2.97e+03 bond pdb=" CD2 TYR B3131 " pdb=" CE2 TYR B3131 " ideal model delta sigma weight residual 1.382 1.834 -0.452 3.00e-02 1.11e+03 2.27e+02 ... (remaining 146527 not shown) Histogram of bond angle deviations from ideal: 95.65 - 104.50: 2411 104.50 - 113.35: 79842 113.35 - 122.20: 92832 122.20 - 131.05: 22110 131.05 - 139.90: 733 Bond angle restraints: 197928 Sorted by residual: angle pdb=" CA CYS C3205 " pdb=" CB CYS C3205 " pdb=" SG CYS C3205 " ideal model delta sigma weight residual 114.40 135.73 -21.33 2.30e+00 1.89e-01 8.60e+01 angle pdb=" CA CYS A3205 " pdb=" CB CYS A3205 " pdb=" SG CYS A3205 " ideal model delta sigma weight residual 114.40 135.71 -21.31 2.30e+00 1.89e-01 8.59e+01 angle pdb=" CA CYS D3205 " pdb=" CB CYS D3205 " pdb=" SG CYS D3205 " ideal model delta sigma weight residual 114.40 135.68 -21.28 2.30e+00 1.89e-01 8.56e+01 angle pdb=" CA CYS B3205 " pdb=" CB CYS B3205 " pdb=" SG CYS B3205 " ideal model delta sigma weight residual 114.40 135.68 -21.28 2.30e+00 1.89e-01 8.56e+01 angle pdb=" N GLU K 124 " pdb=" CA GLU K 124 " pdb=" C GLU K 124 " ideal model delta sigma weight residual 111.40 102.52 8.88 1.22e+00 6.72e-01 5.30e+01 ... (remaining 197923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 78956 17.88 - 35.77: 7497 35.77 - 53.65: 1387 53.65 - 71.53: 412 71.53 - 89.42: 156 Dihedral angle restraints: 88408 sinusoidal: 36332 harmonic: 52076 Sorted by residual: dihedral pdb=" CA PHE D4640 " pdb=" C PHE D4640 " pdb=" N PRO D4641 " pdb=" CA PRO D4641 " ideal model delta harmonic sigma weight residual 180.00 -133.75 -46.25 0 5.00e+00 4.00e-02 8.56e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual -180.00 -133.75 -46.25 0 5.00e+00 4.00e-02 8.56e+01 dihedral pdb=" CA PHE B4640 " pdb=" C PHE B4640 " pdb=" N PRO B4641 " pdb=" CA PRO B4641 " ideal model delta harmonic sigma weight residual 180.00 -133.77 -46.23 0 5.00e+00 4.00e-02 8.55e+01 ... (remaining 88405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 20880 0.097 - 0.194: 767 0.194 - 0.291: 33 0.291 - 0.388: 0 0.388 - 0.485: 4 Chirality restraints: 21684 Sorted by residual: chirality pdb=" CB ILE D3183 " pdb=" CA ILE D3183 " pdb=" CG1 ILE D3183 " pdb=" CG2 ILE D3183 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CB ILE A3183 " pdb=" CA ILE A3183 " pdb=" CG1 ILE A3183 " pdb=" CG2 ILE A3183 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE B3183 " pdb=" CA ILE B3183 " pdb=" CG1 ILE B3183 " pdb=" CG2 ILE B3183 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 21681 not shown) Planarity restraints: 25468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C4640 " 0.105 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO C4641 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO C4641 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO C4641 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " -0.105 5.00e-02 4.00e+02 1.64e-01 4.28e+01 pdb=" N PRO A4641 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D4640 " 0.105 5.00e-02 4.00e+02 1.64e-01 4.28e+01 pdb=" N PRO D4641 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO D4641 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO D4641 " 0.083 5.00e-02 4.00e+02 ... (remaining 25465 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 28 1.89 - 2.64: 1832 2.64 - 3.40: 206784 3.40 - 4.15: 355946 4.15 - 4.90: 637809 Nonbonded interactions: 1202399 Sorted by model distance: nonbonded pdb=" OE2 GLU D3922 " pdb="CA CA D5003 " model vdw 1.138 2.510 nonbonded pdb=" OE2 GLU B3922 " pdb="CA CA B5003 " model vdw 1.138 2.510 nonbonded pdb=" OE2 GLU A3922 " pdb="CA CA A5003 " model vdw 1.138 2.510 nonbonded pdb=" OE2 GLU C3922 " pdb="CA CA C5003 " model vdw 1.138 2.510 nonbonded pdb=" OD1 ASP K 21 " pdb="CA CA K 201 " model vdw 1.511 2.510 ... (remaining 1202394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 30.780 Check model and map are aligned: 1.530 Set scattering table: 0.970 Process input model: 465.590 Find NCS groups from input model: 8.670 Set up NCS constraints: 1.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 517.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.011 1.800 146532 Z= 0.622 Angle : 0.769 21.334 197928 Z= 0.441 Chirality : 0.042 0.485 21684 Planarity : 0.005 0.164 25468 Dihedral : 14.994 89.416 54820 Min Nonbonded Distance : 1.138 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.12 % Rotamer: Outliers : 1.07 % Allowed : 0.77 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.06), residues: 17804 helix: 1.24 (0.05), residues: 9268 sheet: 0.09 (0.14), residues: 1524 loop : -0.51 (0.07), residues: 7012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 893 HIS 0.020 0.001 HIS A1146 PHE 0.048 0.001 PHE B2943 TYR 0.047 0.001 TYR D2801 ARG 0.016 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 798 time to evaluate : 12.171 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: I 14 LYS cc_start: 0.9210 (mmtm) cc_final: 0.8951 (mmmt) REVERT: I 31 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9104 (mmtp) REVERT: I 72 MET cc_start: 0.8254 (tmm) cc_final: 0.7997 (ttt) REVERT: I 73 MET cc_start: 0.8247 (mmm) cc_final: 0.7777 (mmm) REVERT: I 130 ASP cc_start: 0.6081 (OUTLIER) cc_final: 0.5305 (t0) REVERT: A 393 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7360 (mmp) REVERT: A 893 TRP cc_start: 0.8829 (m-90) cc_final: 0.8513 (m-90) REVERT: A 944 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9012 (mt) REVERT: A 981 MET cc_start: 0.8050 (ppp) cc_final: 0.7628 (ppp) REVERT: A 1953 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: A 2406 MET cc_start: 0.8160 (mmm) cc_final: 0.7851 (tpp) REVERT: A 2468 MET cc_start: 0.8956 (mmt) cc_final: 0.8664 (mmm) REVERT: A 2844 MET cc_start: 0.8938 (tmm) cc_final: 0.8526 (tmm) REVERT: A 2848 TYR cc_start: 0.8324 (t80) cc_final: 0.8118 (t80) REVERT: A 2943 PHE cc_start: 0.8625 (m-10) cc_final: 0.8398 (t80) REVERT: A 3104 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8503 (tmm) REVERT: A 3241 MET cc_start: 0.9227 (ttm) cc_final: 0.8746 (tmm) REVERT: A 3318 HIS cc_start: 0.7826 (m-70) cc_final: 0.7485 (m-70) REVERT: A 4292 MET cc_start: 0.7929 (mmm) cc_final: 0.7458 (mmm) REVERT: A 4707 MET cc_start: 0.8250 (tmm) cc_final: 0.7864 (tmm) REVERT: A 4804 MET cc_start: 0.8598 (mmm) cc_final: 0.8248 (mmm) REVERT: A 4809 MET cc_start: 0.8602 (tpt) cc_final: 0.8381 (tpp) REVERT: A 4814 MET cc_start: 0.7966 (tpt) cc_final: 0.7722 (tpt) REVERT: H 54 GLN cc_start: 0.8769 (mp10) cc_final: 0.8563 (mp10) REVERT: J 14 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8938 (mmmt) REVERT: J 31 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9109 (mmtp) REVERT: J 72 MET cc_start: 0.8442 (tmm) cc_final: 0.8215 (tmm) REVERT: J 73 MET cc_start: 0.8368 (mmm) cc_final: 0.7855 (mmm) REVERT: J 130 ASP cc_start: 0.5703 (OUTLIER) cc_final: 0.5009 (t0) REVERT: L 14 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8961 (mmmt) REVERT: L 37 MET cc_start: 0.8852 (ttm) cc_final: 0.8606 (ttm) REVERT: L 73 MET cc_start: 0.8424 (mmm) cc_final: 0.7839 (mmm) REVERT: L 130 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5642 (t0) REVERT: K 14 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8877 (mmmt) REVERT: K 37 MET cc_start: 0.8859 (ttm) cc_final: 0.8597 (ttm) REVERT: K 72 MET cc_start: 0.8476 (tmm) cc_final: 0.8240 (tmm) REVERT: K 73 MET cc_start: 0.8208 (mmm) cc_final: 0.7689 (mmm) REVERT: K 130 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.5733 (t0) REVERT: B 893 TRP cc_start: 0.8758 (m-90) cc_final: 0.8449 (m-90) REVERT: B 944 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8991 (mt) REVERT: B 981 MET cc_start: 0.8014 (ppp) cc_final: 0.7535 (ppp) REVERT: B 1953 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8323 (tpp) REVERT: B 1975 MET cc_start: 0.8212 (mtm) cc_final: 0.7767 (mtp) REVERT: B 2347 MET cc_start: 0.9352 (mmt) cc_final: 0.9112 (mmm) REVERT: B 2843 MET cc_start: 0.8628 (ttp) cc_final: 0.8293 (tmm) REVERT: B 2844 MET cc_start: 0.9018 (tmm) cc_final: 0.8495 (tmm) REVERT: B 3072 MET cc_start: 0.6230 (mpp) cc_final: 0.5957 (mpp) REVERT: B 3104 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8724 (tmm) REVERT: B 3241 MET cc_start: 0.9225 (ttm) cc_final: 0.8708 (tmm) REVERT: B 3296 MET cc_start: 0.8576 (mpp) cc_final: 0.8170 (ppp) REVERT: B 3318 HIS cc_start: 0.8093 (m-70) cc_final: 0.7749 (m-70) REVERT: B 3985 MET cc_start: 0.8792 (mmm) cc_final: 0.8466 (mmm) REVERT: B 4707 MET cc_start: 0.8203 (tmm) cc_final: 0.7736 (tmm) REVERT: C 944 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9010 (mt) REVERT: C 981 MET cc_start: 0.7951 (ppp) cc_final: 0.7508 (ppp) REVERT: C 1564 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8213 (tpt) REVERT: C 2848 TYR cc_start: 0.8282 (t80) cc_final: 0.8021 (t80) REVERT: C 2943 PHE cc_start: 0.8560 (m-10) cc_final: 0.8338 (t80) REVERT: C 3104 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8116 (tmm) REVERT: C 3105 LEU cc_start: 0.8969 (mt) cc_final: 0.8606 (mt) REVERT: C 3231 MET cc_start: 0.9432 (mmp) cc_final: 0.8691 (mmm) REVERT: C 3241 MET cc_start: 0.9229 (ttm) cc_final: 0.8805 (tmm) REVERT: C 3318 HIS cc_start: 0.7486 (m-70) cc_final: 0.7183 (m-70) REVERT: C 3985 MET cc_start: 0.8737 (mmm) cc_final: 0.8434 (mmm) REVERT: C 4012 MET cc_start: 0.8431 (mtp) cc_final: 0.8221 (ttm) REVERT: C 4707 MET cc_start: 0.8381 (tmm) cc_final: 0.7964 (tmm) REVERT: C 4726 MET cc_start: 0.8308 (tpt) cc_final: 0.7936 (tpp) REVERT: C 4814 MET cc_start: 0.7788 (tpt) cc_final: 0.7446 (tpp) REVERT: D 893 TRP cc_start: 0.8950 (m-90) cc_final: 0.8665 (m-90) REVERT: D 944 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9007 (mt) REVERT: D 1953 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8269 (tpp) REVERT: D 2689 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6764 (pmm) REVERT: D 2843 MET cc_start: 0.8470 (ttp) cc_final: 0.8187 (tmm) REVERT: D 2844 MET cc_start: 0.8892 (tmm) cc_final: 0.8429 (ppp) REVERT: D 2943 PHE cc_start: 0.8648 (m-10) cc_final: 0.8429 (t80) REVERT: D 3104 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8297 (tmm) REVERT: D 3105 LEU cc_start: 0.8940 (mt) cc_final: 0.8411 (mt) REVERT: D 3241 MET cc_start: 0.9234 (ttm) cc_final: 0.8754 (tmm) REVERT: D 3318 HIS cc_start: 0.7535 (m-70) cc_final: 0.7207 (m-70) REVERT: D 4707 MET cc_start: 0.8303 (tmm) cc_final: 0.7870 (tmm) REVERT: D 4814 MET cc_start: 0.7950 (tpt) cc_final: 0.7720 (tpp) REVERT: D 4817 MET cc_start: 0.8679 (mmm) cc_final: 0.8441 (mmm) outliers start: 168 outliers final: 36 residues processed: 857 average time/residue: 1.2178 time to fit residues: 1854.5160 Evaluate side-chains 795 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 741 time to evaluate : 11.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 ARG Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1953 MET Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2772 ARG Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3584 LYS Chi-restraints excluded: chain A residue 3847 CYS Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 127 ARG Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1953 MET Chi-restraints excluded: chain B residue 2134 MET Chi-restraints excluded: chain B residue 2737 LEU Chi-restraints excluded: chain B residue 2772 ARG Chi-restraints excluded: chain B residue 3104 MET Chi-restraints excluded: chain B residue 3847 CYS Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1564 MET Chi-restraints excluded: chain C residue 2134 MET Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2772 ARG Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3847 CYS Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1953 MET Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 2772 ARG Chi-restraints excluded: chain D residue 3104 MET Chi-restraints excluded: chain D residue 3847 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 5.9990 chunk 1355 optimal weight: 4.9990 chunk 751 optimal weight: 5.9990 chunk 462 optimal weight: 0.0020 chunk 914 optimal weight: 0.0670 chunk 724 optimal weight: 2.9990 chunk 1401 optimal weight: 10.0000 chunk 542 optimal weight: 9.9990 chunk 852 optimal weight: 4.9990 chunk 1043 optimal weight: 7.9990 chunk 1623 optimal weight: 30.0000 overall best weight: 2.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS A1452 GLN ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 HIS B1452 GLN B2464 HIS ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 HIS C1452 GLN ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1146 HIS D1452 GLN D2464 HIS ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.796 146532 Z= 0.621 Angle : 0.606 21.227 197928 Z= 0.310 Chirality : 0.040 0.301 21684 Planarity : 0.005 0.137 25468 Dihedral : 6.623 80.044 19807 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 0.53 % Allowed : 3.38 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.93 (0.06), residues: 17804 helix: 1.55 (0.05), residues: 9336 sheet: 0.18 (0.14), residues: 1476 loop : -0.51 (0.07), residues: 6992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D2773 HIS 0.015 0.001 HIS C3111 PHE 0.023 0.001 PHE B4306 TYR 0.020 0.001 TYR C 931 ARG 0.008 0.001 ARG A 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 767 time to evaluate : 10.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 72 MET cc_start: 0.8567 (tmm) cc_final: 0.8179 (ttt) REVERT: I 73 MET cc_start: 0.8438 (mmm) cc_final: 0.7883 (mmm) REVERT: I 125 MET cc_start: 0.8329 (tmm) cc_final: 0.8110 (tmm) REVERT: A 393 MET cc_start: 0.7933 (mmt) cc_final: 0.7335 (mmm) REVERT: A 893 TRP cc_start: 0.8858 (m-90) cc_final: 0.8630 (t60) REVERT: A 944 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8970 (mt) REVERT: A 981 MET cc_start: 0.7960 (ppp) cc_final: 0.7442 (ppp) REVERT: A 995 MET cc_start: 0.9087 (ttp) cc_final: 0.8852 (ttp) REVERT: A 1729 MET cc_start: 0.7713 (mtm) cc_final: 0.7423 (mtt) REVERT: A 2234 MET cc_start: 0.8624 (mmm) cc_final: 0.8160 (mtp) REVERT: A 2689 MET cc_start: 0.5890 (pmm) cc_final: 0.5497 (pmm) REVERT: A 2848 TYR cc_start: 0.8352 (t80) cc_final: 0.8098 (t80) REVERT: A 3104 MET cc_start: 0.8870 (tmm) cc_final: 0.8553 (tmm) REVERT: A 3105 LEU cc_start: 0.8981 (mt) cc_final: 0.8743 (mt) REVERT: A 3235 MET cc_start: 0.8485 (ppp) cc_final: 0.7954 (ppp) REVERT: A 3241 MET cc_start: 0.9230 (ttm) cc_final: 0.8817 (tmm) REVERT: A 3318 HIS cc_start: 0.7676 (m-70) cc_final: 0.7217 (m-70) REVERT: A 4292 MET cc_start: 0.7937 (mmm) cc_final: 0.7389 (mmm) REVERT: A 4707 MET cc_start: 0.8260 (tmm) cc_final: 0.7818 (tmm) REVERT: A 4804 MET cc_start: 0.8679 (mmm) cc_final: 0.8293 (mmm) REVERT: A 4814 MET cc_start: 0.7997 (tpt) cc_final: 0.7663 (tpp) REVERT: J 31 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9068 (mmtp) REVERT: J 72 MET cc_start: 0.8575 (tmm) cc_final: 0.8247 (tmm) REVERT: J 73 MET cc_start: 0.8483 (mmm) cc_final: 0.8158 (mmm) REVERT: J 125 MET cc_start: 0.8374 (tmm) cc_final: 0.8114 (tmm) REVERT: J 126 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7772 (pt) REVERT: L 31 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9088 (ptpp) REVERT: L 37 MET cc_start: 0.8985 (ttm) cc_final: 0.8678 (ttm) REVERT: L 73 MET cc_start: 0.8585 (mmm) cc_final: 0.8363 (mmm) REVERT: L 126 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7915 (pt) REVERT: K 31 LYS cc_start: 0.9352 (mmtt) cc_final: 0.9056 (mmtp) REVERT: K 37 MET cc_start: 0.9004 (ttm) cc_final: 0.8685 (ttm) REVERT: K 73 MET cc_start: 0.8357 (mmm) cc_final: 0.8119 (mmm) REVERT: K 125 MET cc_start: 0.8673 (tmm) cc_final: 0.8435 (tmm) REVERT: B 893 TRP cc_start: 0.8797 (m-90) cc_final: 0.8566 (t60) REVERT: B 944 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8964 (mt) REVERT: B 981 MET cc_start: 0.8073 (ppp) cc_final: 0.7453 (ppp) REVERT: B 1729 MET cc_start: 0.7762 (mtm) cc_final: 0.7500 (mtt) REVERT: B 1975 MET cc_start: 0.8214 (mtm) cc_final: 0.7823 (mtp) REVERT: B 2828 MET cc_start: 0.7207 (mmp) cc_final: 0.6421 (mmm) REVERT: B 2843 MET cc_start: 0.8694 (ttp) cc_final: 0.8388 (tmm) REVERT: B 3104 MET cc_start: 0.9062 (tmm) cc_final: 0.8708 (tmm) REVERT: B 3235 MET cc_start: 0.8467 (ppp) cc_final: 0.7940 (ppp) REVERT: B 3241 MET cc_start: 0.9217 (ttm) cc_final: 0.8757 (tmm) REVERT: B 3318 HIS cc_start: 0.8001 (m-70) cc_final: 0.7608 (m-70) REVERT: B 4707 MET cc_start: 0.8214 (tmm) cc_final: 0.7770 (tmm) REVERT: C 893 TRP cc_start: 0.8801 (m100) cc_final: 0.8567 (t60) REVERT: C 944 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8982 (mt) REVERT: C 981 MET cc_start: 0.7879 (ppp) cc_final: 0.7302 (ppp) REVERT: C 2757 MET cc_start: 0.7460 (mmt) cc_final: 0.7242 (mmt) REVERT: C 2848 TYR cc_start: 0.8277 (t80) cc_final: 0.7998 (t80) REVERT: C 3104 MET cc_start: 0.8482 (tmm) cc_final: 0.8070 (tmm) REVERT: C 3105 LEU cc_start: 0.8967 (mt) cc_final: 0.8722 (mt) REVERT: C 3220 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: C 3235 MET cc_start: 0.8556 (ppp) cc_final: 0.7922 (ppp) REVERT: C 3241 MET cc_start: 0.9214 (ttm) cc_final: 0.8840 (tmm) REVERT: C 3318 HIS cc_start: 0.7294 (m-70) cc_final: 0.6851 (m-70) REVERT: C 4279 MET cc_start: 0.6571 (ptm) cc_final: 0.6346 (ptm) REVERT: C 4707 MET cc_start: 0.8375 (tmm) cc_final: 0.7962 (tmm) REVERT: C 4726 MET cc_start: 0.8344 (tpt) cc_final: 0.8016 (tpp) REVERT: C 4804 MET cc_start: 0.8661 (mmm) cc_final: 0.8149 (mmm) REVERT: C 4814 MET cc_start: 0.7862 (tpt) cc_final: 0.7502 (tpp) REVERT: D 655 MET cc_start: 0.8788 (mmp) cc_final: 0.8460 (mmm) REVERT: D 944 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8987 (mt) REVERT: D 981 MET cc_start: 0.7671 (ppp) cc_final: 0.7430 (ppp) REVERT: D 2468 MET cc_start: 0.8878 (mmt) cc_final: 0.8623 (mmm) REVERT: D 2843 MET cc_start: 0.8582 (ttp) cc_final: 0.8262 (tmm) REVERT: D 3104 MET cc_start: 0.8643 (tmm) cc_final: 0.8291 (tmm) REVERT: D 3105 LEU cc_start: 0.8938 (mt) cc_final: 0.8677 (mt) REVERT: D 3235 MET cc_start: 0.8516 (ppp) cc_final: 0.7994 (ppp) REVERT: D 3241 MET cc_start: 0.9228 (ttm) cc_final: 0.8803 (tmm) REVERT: D 3318 HIS cc_start: 0.7498 (m-70) cc_final: 0.7054 (m-70) REVERT: D 4292 MET cc_start: 0.8153 (mmm) cc_final: 0.7721 (mmm) REVERT: D 4707 MET cc_start: 0.8289 (tmm) cc_final: 0.7876 (tmm) REVERT: D 4814 MET cc_start: 0.7997 (tpt) cc_final: 0.7731 (tpp) outliers start: 76 outliers final: 26 residues processed: 812 average time/residue: 1.2162 time to fit residues: 1767.9293 Evaluate side-chains 766 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 733 time to evaluate : 11.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 127 ARG Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 3584 LYS Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain A residue 4306 PHE Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 127 ARG Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 2737 LEU Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4306 PHE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 2737 LEU Chi-restraints excluded: chain D residue 3815 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 8.9990 chunk 503 optimal weight: 8.9990 chunk 1351 optimal weight: 5.9990 chunk 1105 optimal weight: 0.0040 chunk 447 optimal weight: 6.9990 chunk 1626 optimal weight: 5.9990 chunk 1757 optimal weight: 6.9990 chunk 1448 optimal weight: 6.9990 chunk 1613 optimal weight: 40.0000 chunk 554 optimal weight: 50.0000 chunk 1304 optimal weight: 20.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN A 888 ASN A1143 GLN A2217 HIS ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3318 HIS ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN B 261 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN B1143 GLN ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3318 HIS ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 ASN C1296 ASN ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3318 HIS ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN D1143 GLN ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3318 HIS ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.793 146532 Z= 0.660 Angle : 0.611 21.009 197928 Z= 0.311 Chirality : 0.041 0.325 21684 Planarity : 0.005 0.126 25468 Dihedral : 6.020 82.563 19699 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Rotamer: Outliers : 0.67 % Allowed : 5.22 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.06), residues: 17804 helix: 1.71 (0.05), residues: 9320 sheet: 0.04 (0.13), residues: 1524 loop : -0.44 (0.07), residues: 6960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A3587 HIS 0.013 0.001 HIS B3111 PHE 0.022 0.002 PHE D3854 TYR 0.016 0.001 TYR B3131 ARG 0.010 0.001 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 759 time to evaluate : 12.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 31 LYS cc_start: 0.9441 (mmtt) cc_final: 0.9176 (mmtp) REVERT: I 73 MET cc_start: 0.8616 (mmm) cc_final: 0.8337 (mmm) REVERT: A 393 MET cc_start: 0.8055 (mmt) cc_final: 0.7472 (mmm) REVERT: A 944 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9013 (mt) REVERT: A 981 MET cc_start: 0.7962 (ppp) cc_final: 0.7385 (ppp) REVERT: A 995 MET cc_start: 0.9082 (ttp) cc_final: 0.8869 (ttp) REVERT: A 1729 MET cc_start: 0.7752 (mtm) cc_final: 0.7530 (mtm) REVERT: A 1975 MET cc_start: 0.8224 (ttm) cc_final: 0.7967 (ttm) REVERT: A 2689 MET cc_start: 0.5882 (pmm) cc_final: 0.5568 (pmm) REVERT: A 2843 MET cc_start: 0.8800 (ptt) cc_final: 0.8597 (tmm) REVERT: A 2848 TYR cc_start: 0.8371 (t80) cc_final: 0.8076 (t80) REVERT: A 2943 PHE cc_start: 0.8753 (t80) cc_final: 0.8510 (m-10) REVERT: A 3104 MET cc_start: 0.8852 (tmm) cc_final: 0.8524 (tmm) REVERT: A 3105 LEU cc_start: 0.8974 (mt) cc_final: 0.8700 (mt) REVERT: A 3215 MET cc_start: 0.9137 (mmm) cc_final: 0.8737 (ptp) REVERT: A 3235 MET cc_start: 0.8641 (ppp) cc_final: 0.8418 (ppp) REVERT: A 3241 MET cc_start: 0.9211 (ttm) cc_final: 0.8832 (tmm) REVERT: A 3296 MET cc_start: 0.8362 (mmm) cc_final: 0.7975 (ppp) REVERT: A 3318 HIS cc_start: 0.7321 (m90) cc_final: 0.7065 (m-70) REVERT: A 4707 MET cc_start: 0.8280 (tmm) cc_final: 0.7842 (tmm) REVERT: A 4804 MET cc_start: 0.8717 (mmm) cc_final: 0.8293 (mmm) REVERT: A 4809 MET cc_start: 0.8672 (tpt) cc_final: 0.8332 (tpp) REVERT: A 4943 MET cc_start: 0.8696 (mmm) cc_final: 0.7737 (mmm) REVERT: H 62 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: J 31 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9085 (mmtp) REVERT: J 73 MET cc_start: 0.8590 (mmm) cc_final: 0.8346 (mmm) REVERT: J 126 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7979 (pt) REVERT: L 37 MET cc_start: 0.9018 (ttm) cc_final: 0.8679 (ttm) REVERT: L 126 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8123 (pt) REVERT: K 14 LYS cc_start: 0.9265 (mmtm) cc_final: 0.9054 (tppt) REVERT: K 37 MET cc_start: 0.9018 (ttm) cc_final: 0.8690 (ttm) REVERT: K 73 MET cc_start: 0.8468 (mmm) cc_final: 0.8190 (mmm) REVERT: B 944 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9012 (mt) REVERT: B 981 MET cc_start: 0.8056 (ppp) cc_final: 0.7378 (ppp) REVERT: B 1001 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8716 (pp20) REVERT: B 1174 MET cc_start: 0.7814 (ptp) cc_final: 0.7565 (ptp) REVERT: B 1729 MET cc_start: 0.7821 (mtm) cc_final: 0.7585 (mtt) REVERT: B 1975 MET cc_start: 0.8336 (mtm) cc_final: 0.7886 (mtp) REVERT: B 2843 MET cc_start: 0.8751 (ttp) cc_final: 0.8390 (tmm) REVERT: B 2844 MET cc_start: 0.9045 (tmm) cc_final: 0.8734 (tmm) REVERT: B 3104 MET cc_start: 0.9089 (tmm) cc_final: 0.8728 (tmm) REVERT: B 3241 MET cc_start: 0.9211 (ttm) cc_final: 0.8798 (tmm) REVERT: B 3296 MET cc_start: 0.8412 (mpp) cc_final: 0.8186 (ppp) REVERT: B 3318 HIS cc_start: 0.7450 (m90) cc_final: 0.7135 (m90) REVERT: B 3985 MET cc_start: 0.8754 (mmm) cc_final: 0.8503 (mmm) REVERT: B 4707 MET cc_start: 0.8233 (tmm) cc_final: 0.7772 (tmm) REVERT: B 4817 MET cc_start: 0.8644 (mmm) cc_final: 0.8383 (tpp) REVERT: C 393 MET cc_start: 0.8379 (mmm) cc_final: 0.7993 (mmm) REVERT: C 944 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9015 (mt) REVERT: C 981 MET cc_start: 0.7936 (ppp) cc_final: 0.7327 (ppp) REVERT: C 2234 MET cc_start: 0.8623 (mmm) cc_final: 0.8223 (mtp) REVERT: C 2689 MET cc_start: 0.5847 (pmm) cc_final: 0.5460 (pmm) REVERT: C 2848 TYR cc_start: 0.8364 (t80) cc_final: 0.8033 (t80) REVERT: C 3104 MET cc_start: 0.8476 (tmm) cc_final: 0.8061 (tmm) REVERT: C 3105 LEU cc_start: 0.8974 (mt) cc_final: 0.8725 (mt) REVERT: C 3220 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7927 (pp20) REVERT: C 3241 MET cc_start: 0.9190 (ttm) cc_final: 0.8846 (tmm) REVERT: C 3287 ASN cc_start: 0.9030 (t0) cc_final: 0.8782 (t0) REVERT: C 3318 HIS cc_start: 0.6672 (m90) cc_final: 0.6435 (m-70) REVERT: C 4292 MET cc_start: 0.8203 (mmm) cc_final: 0.7754 (mmm) REVERT: C 4707 MET cc_start: 0.8371 (tmm) cc_final: 0.7941 (tmm) REVERT: C 4726 MET cc_start: 0.8434 (tpt) cc_final: 0.8007 (tpp) REVERT: C 4804 MET cc_start: 0.8759 (mmm) cc_final: 0.8286 (mmm) REVERT: D 944 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9018 (mt) REVERT: D 981 MET cc_start: 0.7684 (ppp) cc_final: 0.7364 (ppp) REVERT: D 1729 MET cc_start: 0.7772 (mtm) cc_final: 0.7538 (mtt) REVERT: D 2468 MET cc_start: 0.8881 (mmt) cc_final: 0.8525 (mmm) REVERT: D 2843 MET cc_start: 0.8633 (ttp) cc_final: 0.8277 (tmm) REVERT: D 2844 MET cc_start: 0.9064 (tmm) cc_final: 0.8805 (tmm) REVERT: D 2943 PHE cc_start: 0.8805 (t80) cc_final: 0.8515 (m-10) REVERT: D 3104 MET cc_start: 0.8656 (tmm) cc_final: 0.8276 (tmm) REVERT: D 3105 LEU cc_start: 0.8962 (mt) cc_final: 0.8662 (mt) REVERT: D 3241 MET cc_start: 0.9210 (ttm) cc_final: 0.8826 (tmm) REVERT: D 3296 MET cc_start: 0.8291 (mmm) cc_final: 0.7887 (ppp) REVERT: D 3318 HIS cc_start: 0.6851 (m90) cc_final: 0.6566 (m-70) REVERT: D 4707 MET cc_start: 0.8295 (tmm) cc_final: 0.7830 (tmm) REVERT: D 4814 MET cc_start: 0.7968 (tpt) cc_final: 0.7699 (tpp) outliers start: 97 outliers final: 41 residues processed: 826 average time/residue: 1.2003 time to fit residues: 1769.7802 Evaluate side-chains 785 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 735 time to evaluate : 11.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 3181 TYR Chi-restraints excluded: chain A residue 3587 TRP Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain A residue 4306 PHE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 127 ARG Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain B residue 3587 TRP Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3587 TRP Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4306 PHE Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 3815 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 7.9990 chunk 1222 optimal weight: 40.0000 chunk 844 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 776 optimal weight: 8.9990 chunk 1092 optimal weight: 6.9990 chunk 1632 optimal weight: 9.9990 chunk 1728 optimal weight: 6.9990 chunk 852 optimal weight: 2.9990 chunk 1547 optimal weight: 9.9990 chunk 465 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 54 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4057 HIS ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN J 54 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4057 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1143 GLN ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4057 HIS ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4967 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.792 146532 Z= 0.660 Angle : 0.594 20.960 197928 Z= 0.304 Chirality : 0.040 0.295 21684 Planarity : 0.005 0.122 25468 Dihedral : 5.781 80.191 19684 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 0.60 % Allowed : 6.36 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 1.14 (0.06), residues: 17804 helix: 1.77 (0.05), residues: 9316 sheet: 0.13 (0.14), residues: 1476 loop : -0.44 (0.07), residues: 7012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D2773 HIS 0.012 0.001 HIS B3111 PHE 0.021 0.001 PHE B3854 TYR 0.018 0.001 TYR B2848 ARG 0.010 0.001 ARG B2824 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 747 time to evaluate : 12.201 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: I 31 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9185 (mmtp) REVERT: I 73 MET cc_start: 0.8703 (mmm) cc_final: 0.8396 (mmm) REVERT: I 145 MET cc_start: 0.7994 (ppp) cc_final: 0.7427 (ppp) REVERT: A 944 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9023 (mt) REVERT: A 981 MET cc_start: 0.7998 (ppp) cc_final: 0.7398 (ppp) REVERT: A 1174 MET cc_start: 0.7794 (ptp) cc_final: 0.7585 (ptp) REVERT: A 1953 MET cc_start: 0.8834 (tpp) cc_final: 0.8514 (tpp) REVERT: A 1975 MET cc_start: 0.8215 (ttm) cc_final: 0.7992 (ttm) REVERT: A 2689 MET cc_start: 0.5929 (pmm) cc_final: 0.5622 (pmm) REVERT: A 2843 MET cc_start: 0.8833 (ptt) cc_final: 0.8587 (tmm) REVERT: A 2943 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8547 (m-10) REVERT: A 3104 MET cc_start: 0.8842 (tmm) cc_final: 0.8518 (tmm) REVERT: A 3105 LEU cc_start: 0.8955 (mt) cc_final: 0.8677 (mt) REVERT: A 3241 MET cc_start: 0.9184 (ttm) cc_final: 0.8782 (tmm) REVERT: A 3296 MET cc_start: 0.8319 (mmm) cc_final: 0.8064 (ppp) REVERT: A 3318 HIS cc_start: 0.7308 (m90) cc_final: 0.7044 (m-70) REVERT: A 4707 MET cc_start: 0.8289 (tmm) cc_final: 0.7818 (tmm) REVERT: J 31 LYS cc_start: 0.9392 (mmtt) cc_final: 0.9078 (mmtp) REVERT: J 72 MET cc_start: 0.8675 (tmm) cc_final: 0.8401 (ttt) REVERT: J 126 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8109 (pt) REVERT: L 31 LYS cc_start: 0.9411 (mmtt) cc_final: 0.9192 (mmtp) REVERT: L 37 MET cc_start: 0.9026 (ttm) cc_final: 0.8640 (ttm) REVERT: L 73 MET cc_start: 0.9145 (mmp) cc_final: 0.7292 (mmm) REVERT: L 126 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8061 (pt) REVERT: L 145 MET cc_start: 0.8308 (ppp) cc_final: 0.7306 (ppp) REVERT: K 14 LYS cc_start: 0.9282 (mmtm) cc_final: 0.9077 (tppt) REVERT: K 37 MET cc_start: 0.9024 (ttm) cc_final: 0.8651 (ttm) REVERT: K 73 MET cc_start: 0.8551 (mmm) cc_final: 0.8250 (mmm) REVERT: B 944 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8983 (mt) REVERT: B 981 MET cc_start: 0.8098 (ppp) cc_final: 0.7418 (ppp) REVERT: B 1001 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8751 (pp20) REVERT: B 1975 MET cc_start: 0.8372 (mtm) cc_final: 0.7802 (mtp) REVERT: B 2234 MET cc_start: 0.8725 (mmm) cc_final: 0.8505 (mtp) REVERT: B 2843 MET cc_start: 0.8765 (ttp) cc_final: 0.8389 (tmm) REVERT: B 2844 MET cc_start: 0.9027 (tmm) cc_final: 0.8735 (tmm) REVERT: B 3104 MET cc_start: 0.9029 (tmm) cc_final: 0.8668 (tmm) REVERT: B 3241 MET cc_start: 0.9189 (ttm) cc_final: 0.8770 (tmm) REVERT: B 3296 MET cc_start: 0.8480 (mpp) cc_final: 0.8262 (ppp) REVERT: B 3318 HIS cc_start: 0.7389 (m90) cc_final: 0.7046 (m-70) REVERT: B 3719 MET cc_start: 0.8689 (mmm) cc_final: 0.8327 (mmm) REVERT: B 4258 MET cc_start: 0.5649 (ttp) cc_final: 0.5347 (ttp) REVERT: B 4274 MET cc_start: 0.5070 (ptt) cc_final: 0.4668 (ptt) REVERT: B 4707 MET cc_start: 0.8237 (tmm) cc_final: 0.7794 (tmm) REVERT: C 393 MET cc_start: 0.8407 (mmm) cc_final: 0.7998 (mmm) REVERT: C 944 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8996 (mt) REVERT: C 981 MET cc_start: 0.7987 (ppp) cc_final: 0.7352 (ppp) REVERT: C 1174 MET cc_start: 0.7853 (ptp) cc_final: 0.7606 (ptp) REVERT: C 2234 MET cc_start: 0.8636 (mmm) cc_final: 0.8242 (mtp) REVERT: C 2456 MET cc_start: 0.8732 (mmp) cc_final: 0.8512 (mmp) REVERT: C 2689 MET cc_start: 0.6044 (pmm) cc_final: 0.5695 (pmm) REVERT: C 3104 MET cc_start: 0.8464 (tmm) cc_final: 0.8040 (tmm) REVERT: C 3105 LEU cc_start: 0.8971 (mt) cc_final: 0.8717 (mt) REVERT: C 3220 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7923 (pp20) REVERT: C 3241 MET cc_start: 0.9170 (ttm) cc_final: 0.8757 (tmm) REVERT: C 3296 MET cc_start: 0.8091 (mmm) cc_final: 0.7775 (ppp) REVERT: C 3318 HIS cc_start: 0.6688 (m90) cc_final: 0.6445 (m-70) REVERT: C 4292 MET cc_start: 0.8205 (mmm) cc_final: 0.7765 (mmm) REVERT: C 4707 MET cc_start: 0.8366 (tmm) cc_final: 0.7921 (tmm) REVERT: C 4804 MET cc_start: 0.8733 (mmm) cc_final: 0.8264 (mmm) REVERT: C 4809 MET cc_start: 0.8504 (tpt) cc_final: 0.8167 (tpp) REVERT: D 393 MET cc_start: 0.8355 (mmm) cc_final: 0.8097 (mmm) REVERT: D 944 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9004 (mt) REVERT: D 964 MET cc_start: 0.2818 (ppp) cc_final: 0.2568 (ppp) REVERT: D 981 MET cc_start: 0.7784 (ppp) cc_final: 0.7438 (ppp) REVERT: D 1487 MET cc_start: 0.8647 (mtp) cc_final: 0.8338 (mtp) REVERT: D 2004 MET cc_start: 0.9297 (mmp) cc_final: 0.9097 (mmm) REVERT: D 2234 MET cc_start: 0.8674 (mmm) cc_final: 0.8294 (mtp) REVERT: D 2757 MET cc_start: 0.7476 (mmt) cc_final: 0.6988 (mmt) REVERT: D 2843 MET cc_start: 0.8623 (ttp) cc_final: 0.8281 (tmm) REVERT: D 2844 MET cc_start: 0.9052 (tmm) cc_final: 0.8819 (tmm) REVERT: D 2943 PHE cc_start: 0.8790 (t80) cc_final: 0.8562 (m-10) REVERT: D 3104 MET cc_start: 0.8648 (tmm) cc_final: 0.8262 (tmm) REVERT: D 3105 LEU cc_start: 0.8954 (mt) cc_final: 0.8655 (mt) REVERT: D 3241 MET cc_start: 0.9190 (ttm) cc_final: 0.8801 (tmm) REVERT: D 3296 MET cc_start: 0.8345 (mmm) cc_final: 0.7961 (ppp) REVERT: D 3318 HIS cc_start: 0.6833 (m90) cc_final: 0.6537 (m-70) REVERT: D 3719 MET cc_start: 0.8703 (mmm) cc_final: 0.8286 (mmm) REVERT: D 4274 MET cc_start: 0.5263 (ptt) cc_final: 0.4914 (ptm) REVERT: D 4707 MET cc_start: 0.8283 (tmm) cc_final: 0.7785 (tmm) outliers start: 87 outliers final: 53 residues processed: 794 average time/residue: 1.2505 time to fit residues: 1778.8181 Evaluate side-chains 795 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 733 time to evaluate : 12.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 127 ARG Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3181 TYR Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3587 TRP Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain A residue 4306 PHE Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3587 TRP Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4306 PHE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 3181 TYR Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3815 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 6.9990 chunk 981 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 1286 optimal weight: 4.9990 chunk 713 optimal weight: 5.9990 chunk 1474 optimal weight: 7.9990 chunk 1194 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 882 optimal weight: 7.9990 chunk 1551 optimal weight: 1.9990 chunk 436 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 84 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 ASN C2217 HIS ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4057 HIS ** C4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 84 ASN ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D1296 ASN D2217 HIS ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.792 146532 Z= 0.629 Angle : 0.574 20.927 197928 Z= 0.291 Chirality : 0.039 0.286 21684 Planarity : 0.004 0.118 25468 Dihedral : 5.624 81.082 19672 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 0.71 % Allowed : 6.95 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.06), residues: 17804 helix: 1.88 (0.06), residues: 9292 sheet: 0.17 (0.14), residues: 1472 loop : -0.42 (0.07), residues: 7040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D2773 HIS 0.012 0.001 HIS C3111 PHE 0.026 0.001 PHE C3117 TYR 0.035 0.001 TYR D4567 ARG 0.016 0.000 ARG C 913 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 743 time to evaluate : 12.347 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: I 31 LYS cc_start: 0.9431 (mmtt) cc_final: 0.9164 (mmtp) REVERT: I 53 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9189 (tt) REVERT: I 72 MET cc_start: 0.8624 (tmm) cc_final: 0.8373 (ttt) REVERT: A 393 MET cc_start: 0.8424 (mmm) cc_final: 0.7340 (mmm) REVERT: A 944 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8974 (mt) REVERT: A 981 MET cc_start: 0.8021 (ppp) cc_final: 0.7410 (ppp) REVERT: A 1953 MET cc_start: 0.8822 (tpp) cc_final: 0.8522 (tpp) REVERT: A 1975 MET cc_start: 0.8228 (ttm) cc_final: 0.8001 (ttm) REVERT: A 2843 MET cc_start: 0.8852 (ptt) cc_final: 0.8543 (tmm) REVERT: A 2943 PHE cc_start: 0.8758 (t80) cc_final: 0.8535 (m-10) REVERT: A 3104 MET cc_start: 0.8796 (tmm) cc_final: 0.8459 (tmm) REVERT: A 3105 LEU cc_start: 0.8959 (mt) cc_final: 0.8679 (mt) REVERT: A 3241 MET cc_start: 0.9156 (ttm) cc_final: 0.8755 (tmm) REVERT: A 3296 MET cc_start: 0.8337 (mmm) cc_final: 0.8129 (ppp) REVERT: A 3318 HIS cc_start: 0.7223 (m90) cc_final: 0.6978 (m-70) REVERT: A 3719 MET cc_start: 0.8690 (mmm) cc_final: 0.8318 (mmm) REVERT: A 4707 MET cc_start: 0.8246 (tmm) cc_final: 0.7784 (tmm) REVERT: A 4726 MET cc_start: 0.8462 (tpt) cc_final: 0.8177 (tpp) REVERT: A 4804 MET cc_start: 0.8637 (mmm) cc_final: 0.8342 (mmm) REVERT: A 4943 MET cc_start: 0.8576 (mmm) cc_final: 0.7460 (mmm) REVERT: H 62 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: J 31 LYS cc_start: 0.9390 (mmtt) cc_final: 0.9078 (mmtp) REVERT: J 73 MET cc_start: 0.8995 (mmp) cc_final: 0.8245 (mmm) REVERT: J 126 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8189 (pt) REVERT: J 130 ASP cc_start: 0.5305 (OUTLIER) cc_final: 0.4676 (t0) REVERT: L 31 LYS cc_start: 0.9392 (mmtt) cc_final: 0.9184 (mmtp) REVERT: L 37 MET cc_start: 0.9029 (ttm) cc_final: 0.8630 (ttm) REVERT: L 72 MET cc_start: 0.8801 (tmm) cc_final: 0.8419 (tmm) REVERT: L 73 MET cc_start: 0.8922 (mmp) cc_final: 0.8531 (mmm) REVERT: L 126 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7911 (pt) REVERT: L 130 ASP cc_start: 0.5433 (OUTLIER) cc_final: 0.4676 (t0) REVERT: K 14 LYS cc_start: 0.9302 (mmtm) cc_final: 0.9089 (tppt) REVERT: K 37 MET cc_start: 0.9025 (ttm) cc_final: 0.8604 (ttm) REVERT: K 73 MET cc_start: 0.8552 (mmm) cc_final: 0.8012 (mmm) REVERT: B 393 MET cc_start: 0.8523 (mmm) cc_final: 0.7969 (mmm) REVERT: B 944 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8979 (mt) REVERT: B 981 MET cc_start: 0.8145 (ppp) cc_final: 0.7458 (ppp) REVERT: B 1842 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8539 (pt) REVERT: B 1975 MET cc_start: 0.8348 (mtm) cc_final: 0.7767 (mtp) REVERT: B 2234 MET cc_start: 0.8683 (mmm) cc_final: 0.8471 (mtp) REVERT: B 2828 MET cc_start: 0.7419 (mmp) cc_final: 0.6709 (mmp) REVERT: B 2843 MET cc_start: 0.8750 (ttp) cc_final: 0.8352 (tmm) REVERT: B 2844 MET cc_start: 0.9016 (tmm) cc_final: 0.8761 (tmm) REVERT: B 3104 MET cc_start: 0.9001 (tmm) cc_final: 0.8628 (tmm) REVERT: B 3241 MET cc_start: 0.9158 (ttm) cc_final: 0.8744 (tmm) REVERT: B 3318 HIS cc_start: 0.7353 (m90) cc_final: 0.7032 (m-70) REVERT: B 3719 MET cc_start: 0.8654 (mmm) cc_final: 0.8266 (mmm) REVERT: B 4707 MET cc_start: 0.8234 (tmm) cc_final: 0.7772 (tmm) REVERT: B 4943 MET cc_start: 0.8357 (mtp) cc_final: 0.8128 (ttp) REVERT: C 393 MET cc_start: 0.8406 (mmm) cc_final: 0.7974 (mmm) REVERT: C 944 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8996 (mt) REVERT: C 981 MET cc_start: 0.8021 (ppp) cc_final: 0.7374 (ppp) REVERT: C 1842 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8526 (pt) REVERT: C 2214 MET cc_start: 0.8959 (mmp) cc_final: 0.8754 (mmm) REVERT: C 2234 MET cc_start: 0.8625 (mmm) cc_final: 0.8208 (mtp) REVERT: C 2689 MET cc_start: 0.6155 (pmm) cc_final: 0.5699 (pmm) REVERT: C 2848 TYR cc_start: 0.8297 (t80) cc_final: 0.8012 (t80) REVERT: C 3104 MET cc_start: 0.8448 (tmm) cc_final: 0.8013 (tmm) REVERT: C 3105 LEU cc_start: 0.8948 (mt) cc_final: 0.8691 (mt) REVERT: C 3220 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7994 (pp20) REVERT: C 3241 MET cc_start: 0.9158 (ttm) cc_final: 0.8802 (tmm) REVERT: C 3318 HIS cc_start: 0.6637 (m90) cc_final: 0.6402 (m-70) REVERT: C 4274 MET cc_start: 0.5106 (ptt) cc_final: 0.4847 (mtt) REVERT: C 4615 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8363 (tt) REVERT: C 4707 MET cc_start: 0.8325 (tmm) cc_final: 0.7877 (tmm) REVERT: C 4726 MET cc_start: 0.8374 (tpt) cc_final: 0.8171 (tpp) REVERT: C 4804 MET cc_start: 0.8754 (mmm) cc_final: 0.8253 (mmm) REVERT: D 944 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8975 (mt) REVERT: D 981 MET cc_start: 0.7778 (ppp) cc_final: 0.7542 (ppp) REVERT: D 1174 MET cc_start: 0.7430 (pmm) cc_final: 0.7119 (pmm) REVERT: D 1487 MET cc_start: 0.8685 (mtp) cc_final: 0.8305 (mtp) REVERT: D 2150 MET cc_start: 0.8716 (mmm) cc_final: 0.8465 (mtt) REVERT: D 2234 MET cc_start: 0.8642 (mmm) cc_final: 0.8194 (mtp) REVERT: D 2757 MET cc_start: 0.7442 (mmt) cc_final: 0.6925 (mmt) REVERT: D 2828 MET cc_start: 0.7276 (mmp) cc_final: 0.6499 (mmp) REVERT: D 2843 MET cc_start: 0.8666 (ttp) cc_final: 0.8333 (tmm) REVERT: D 2943 PHE cc_start: 0.8787 (t80) cc_final: 0.8551 (m-10) REVERT: D 3104 MET cc_start: 0.8579 (tmm) cc_final: 0.8183 (tmm) REVERT: D 3105 LEU cc_start: 0.8950 (mt) cc_final: 0.8650 (mt) REVERT: D 3241 MET cc_start: 0.9157 (ttm) cc_final: 0.8765 (tmm) REVERT: D 3318 HIS cc_start: 0.6786 (m90) cc_final: 0.6507 (m-70) REVERT: D 3719 MET cc_start: 0.8675 (mmm) cc_final: 0.8217 (mmm) REVERT: D 4274 MET cc_start: 0.5233 (ptt) cc_final: 0.4987 (ptp) REVERT: D 4707 MET cc_start: 0.8267 (tmm) cc_final: 0.7782 (tmm) REVERT: D 4726 MET cc_start: 0.8506 (tpt) cc_final: 0.8240 (tpp) REVERT: D 4943 MET cc_start: 0.8365 (mtp) cc_final: 0.8128 (ttp) outliers start: 103 outliers final: 60 residues processed: 815 average time/residue: 1.2436 time to fit residues: 1823.4872 Evaluate side-chains 808 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 734 time to evaluate : 11.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 127 ARG Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 2931 ARG Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3287 ASN Chi-restraints excluded: chain C residue 3587 TRP Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4306 PHE Chi-restraints excluded: chain C residue 4615 LEU Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 3038 GLN Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3287 ASN Chi-restraints excluded: chain D residue 3815 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 9.9990 chunk 1556 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 1014 optimal weight: 4.9990 chunk 426 optimal weight: 9.9990 chunk 1729 optimal weight: 2.9990 chunk 1436 optimal weight: 6.9990 chunk 800 optimal weight: 30.0000 chunk 143 optimal weight: 3.9990 chunk 572 optimal weight: 7.9990 chunk 908 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 ASN A1762 GLN ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 54 ASN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 ASN ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.791 146532 Z= 0.657 Angle : 0.594 20.905 197928 Z= 0.300 Chirality : 0.040 0.391 21684 Planarity : 0.005 0.118 25468 Dihedral : 5.580 84.835 19672 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 0.96 % Allowed : 7.18 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 1.26 (0.06), residues: 17804 helix: 1.90 (0.05), residues: 9292 sheet: 0.03 (0.13), residues: 1524 loop : -0.39 (0.07), residues: 6988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B3587 HIS 0.011 0.001 HIS B3111 PHE 0.021 0.001 PHE B3854 TYR 0.034 0.001 TYR D4567 ARG 0.016 0.000 ARG D2824 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 739 time to evaluate : 12.280 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: I 31 LYS cc_start: 0.9432 (mmtt) cc_final: 0.9160 (mmtp) REVERT: I 53 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9215 (tt) REVERT: I 72 MET cc_start: 0.8794 (tmm) cc_final: 0.8503 (ttt) REVERT: I 73 MET cc_start: 0.9058 (mmp) cc_final: 0.8417 (mmm) REVERT: I 145 MET cc_start: 0.7902 (ppp) cc_final: 0.7700 (ppp) REVERT: A 944 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9001 (mt) REVERT: A 981 MET cc_start: 0.8052 (ppp) cc_final: 0.7458 (ppp) REVERT: A 1842 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8554 (pt) REVERT: A 1953 MET cc_start: 0.8866 (tpp) cc_final: 0.8562 (tpp) REVERT: A 1975 MET cc_start: 0.8239 (ttm) cc_final: 0.8007 (ttm) REVERT: A 2689 MET cc_start: 0.5648 (pmm) cc_final: 0.5420 (pmm) REVERT: A 2943 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: A 3104 MET cc_start: 0.8794 (tmm) cc_final: 0.8447 (tmm) REVERT: A 3105 LEU cc_start: 0.8962 (mt) cc_final: 0.8683 (mt) REVERT: A 3241 MET cc_start: 0.9163 (ttm) cc_final: 0.8758 (tmm) REVERT: A 3318 HIS cc_start: 0.7200 (m90) cc_final: 0.6958 (m-70) REVERT: A 3719 MET cc_start: 0.8670 (mmm) cc_final: 0.8282 (mmm) REVERT: A 4707 MET cc_start: 0.8224 (tmm) cc_final: 0.7742 (tmm) REVERT: A 4726 MET cc_start: 0.8477 (tpt) cc_final: 0.8201 (tpp) REVERT: H 62 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: J 31 LYS cc_start: 0.9393 (mmtt) cc_final: 0.9072 (mmtp) REVERT: J 73 MET cc_start: 0.9008 (mmp) cc_final: 0.8411 (mmm) REVERT: J 130 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.5111 (t0) REVERT: L 31 LYS cc_start: 0.9392 (mmtt) cc_final: 0.9181 (mmtp) REVERT: L 37 MET cc_start: 0.9049 (ttm) cc_final: 0.8620 (ttm) REVERT: L 72 MET cc_start: 0.8913 (tmm) cc_final: 0.8696 (tmm) REVERT: L 73 MET cc_start: 0.8979 (mmp) cc_final: 0.8688 (mmm) REVERT: L 126 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7993 (pt) REVERT: L 130 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.4979 (t0) REVERT: K 14 LYS cc_start: 0.9315 (mmtm) cc_final: 0.9106 (tppt) REVERT: K 31 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9078 (mmtp) REVERT: K 37 MET cc_start: 0.9056 (ttm) cc_final: 0.8601 (ttm) REVERT: K 73 MET cc_start: 0.8651 (mmm) cc_final: 0.8075 (mmm) REVERT: K 93 PHE cc_start: 0.8492 (m-10) cc_final: 0.8266 (m-10) REVERT: K 125 MET cc_start: 0.8831 (tmm) cc_final: 0.8523 (tmm) REVERT: B 393 MET cc_start: 0.8500 (mmm) cc_final: 0.7926 (mmm) REVERT: B 944 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9008 (mt) REVERT: B 981 MET cc_start: 0.8183 (ppp) cc_final: 0.7480 (ppp) REVERT: B 1842 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8552 (pt) REVERT: B 1975 MET cc_start: 0.8372 (mtm) cc_final: 0.7745 (mtp) REVERT: B 2234 MET cc_start: 0.8691 (mmm) cc_final: 0.8158 (mtp) REVERT: B 2843 MET cc_start: 0.8742 (ttp) cc_final: 0.8362 (tmm) REVERT: B 2844 MET cc_start: 0.9021 (tmm) cc_final: 0.8754 (tmm) REVERT: B 3050 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 3104 MET cc_start: 0.8991 (tmm) cc_final: 0.8619 (tmm) REVERT: B 3241 MET cc_start: 0.9164 (ttm) cc_final: 0.8756 (tmm) REVERT: B 3296 MET cc_start: 0.8476 (mmt) cc_final: 0.7963 (ppp) REVERT: B 3318 HIS cc_start: 0.7358 (m90) cc_final: 0.7041 (m-70) REVERT: B 3719 MET cc_start: 0.8646 (mmm) cc_final: 0.8227 (mmm) REVERT: B 4707 MET cc_start: 0.8216 (tmm) cc_final: 0.7732 (tmm) REVERT: B 4943 MET cc_start: 0.8437 (mtp) cc_final: 0.8172 (ttp) REVERT: C 393 MET cc_start: 0.8399 (mmm) cc_final: 0.7946 (mmm) REVERT: C 944 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9017 (mt) REVERT: C 981 MET cc_start: 0.8068 (ppp) cc_final: 0.7406 (ppp) REVERT: C 1842 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8546 (pt) REVERT: C 2234 MET cc_start: 0.8640 (mmm) cc_final: 0.8338 (mtp) REVERT: C 2689 MET cc_start: 0.6122 (pmm) cc_final: 0.5686 (pmm) REVERT: C 2848 TYR cc_start: 0.8357 (t80) cc_final: 0.8060 (t80) REVERT: C 3104 MET cc_start: 0.8442 (tmm) cc_final: 0.8007 (tmm) REVERT: C 3105 LEU cc_start: 0.8953 (mt) cc_final: 0.8699 (mt) REVERT: C 3220 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7996 (pp20) REVERT: C 3241 MET cc_start: 0.9168 (ttm) cc_final: 0.8814 (tmm) REVERT: C 3318 HIS cc_start: 0.6690 (m90) cc_final: 0.6466 (m-70) REVERT: C 4615 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (tt) REVERT: C 4707 MET cc_start: 0.8321 (tmm) cc_final: 0.7846 (tmm) REVERT: C 4726 MET cc_start: 0.8409 (tpt) cc_final: 0.8194 (tpp) REVERT: C 4804 MET cc_start: 0.8748 (mmm) cc_final: 0.8254 (mmm) REVERT: D 393 MET cc_start: 0.8368 (mmm) cc_final: 0.8059 (mmm) REVERT: D 893 TRP cc_start: 0.8695 (t60) cc_final: 0.8438 (t60) REVERT: D 944 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8976 (mt) REVERT: D 964 MET cc_start: 0.2887 (ppp) cc_final: 0.2651 (ppp) REVERT: D 981 MET cc_start: 0.7797 (ppp) cc_final: 0.6984 (ppp) REVERT: D 1487 MET cc_start: 0.8668 (mtp) cc_final: 0.8323 (mtp) REVERT: D 1842 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8564 (pt) REVERT: D 2150 MET cc_start: 0.8712 (mmm) cc_final: 0.8442 (mtt) REVERT: D 2234 MET cc_start: 0.8628 (mmm) cc_final: 0.8153 (mtp) REVERT: D 2584 MET cc_start: 0.8833 (mmm) cc_final: 0.8531 (mtt) REVERT: D 2757 MET cc_start: 0.7494 (mmt) cc_final: 0.6961 (mmt) REVERT: D 2843 MET cc_start: 0.8667 (ttp) cc_final: 0.8282 (tmm) REVERT: D 2844 MET cc_start: 0.9083 (tmm) cc_final: 0.8644 (ppp) REVERT: D 2943 PHE cc_start: 0.8792 (t80) cc_final: 0.8547 (m-10) REVERT: D 3104 MET cc_start: 0.8575 (tmm) cc_final: 0.8175 (tmm) REVERT: D 3105 LEU cc_start: 0.8966 (mt) cc_final: 0.8661 (mt) REVERT: D 3241 MET cc_start: 0.9154 (ttm) cc_final: 0.8762 (tmm) REVERT: D 3296 MET cc_start: 0.8399 (mmm) cc_final: 0.7894 (ppp) REVERT: D 3318 HIS cc_start: 0.6820 (m90) cc_final: 0.6544 (m-70) REVERT: D 3719 MET cc_start: 0.8664 (mmm) cc_final: 0.8205 (mmm) REVERT: D 4707 MET cc_start: 0.8253 (tmm) cc_final: 0.7759 (tmm) REVERT: D 4814 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7603 (mmm) REVERT: D 4943 MET cc_start: 0.8474 (mtp) cc_final: 0.8202 (ttp) outliers start: 143 outliers final: 88 residues processed: 841 average time/residue: 1.2205 time to fit residues: 1839.1720 Evaluate side-chains 838 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 732 time to evaluate : 12.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain I residue 127 ARG Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2757 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2931 ARG Chi-restraints excluded: chain B residue 3050 LEU Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2931 ARG Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3287 ASN Chi-restraints excluded: chain C residue 3587 TRP Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4306 PHE Chi-restraints excluded: chain C residue 4615 LEU Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3181 TYR Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3287 ASN Chi-restraints excluded: chain D residue 3797 MET Chi-restraints excluded: chain D residue 3815 GLU Chi-restraints excluded: chain D residue 4814 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 6.9990 chunk 194 optimal weight: 0.2980 chunk 985 optimal weight: 5.9990 chunk 1263 optimal weight: 3.9990 chunk 978 optimal weight: 6.9990 chunk 1456 optimal weight: 50.0000 chunk 966 optimal weight: 10.0000 chunk 1723 optimal weight: 1.9990 chunk 1078 optimal weight: 2.9990 chunk 1050 optimal weight: 6.9990 chunk 795 optimal weight: 8.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN K 54 ASN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.791 146532 Z= 0.622 Angle : 0.579 20.923 197928 Z= 0.291 Chirality : 0.039 0.325 21684 Planarity : 0.004 0.117 25468 Dihedral : 5.506 86.114 19670 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 0.92 % Allowed : 7.53 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 1.32 (0.06), residues: 17804 helix: 1.96 (0.06), residues: 9288 sheet: 0.08 (0.14), residues: 1512 loop : -0.38 (0.07), residues: 7004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D2773 HIS 0.011 0.001 HIS A3111 PHE 0.022 0.001 PHE C4246 TYR 0.035 0.001 TYR D4567 ARG 0.016 0.000 ARG B2824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 737 time to evaluate : 12.170 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: I 31 LYS cc_start: 0.9424 (mmtt) cc_final: 0.9151 (mmtp) REVERT: I 53 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9200 (tt) REVERT: I 72 MET cc_start: 0.8762 (tmm) cc_final: 0.8432 (ttt) REVERT: I 73 MET cc_start: 0.8985 (mmp) cc_final: 0.8337 (mmm) REVERT: A 944 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8995 (mt) REVERT: A 981 MET cc_start: 0.8038 (ppp) cc_final: 0.7434 (ppp) REVERT: A 1842 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8543 (pt) REVERT: A 1953 MET cc_start: 0.8807 (tpp) cc_final: 0.8511 (tpp) REVERT: A 1975 MET cc_start: 0.8234 (ttm) cc_final: 0.7999 (ttm) REVERT: A 2134 MET cc_start: 0.9054 (mmm) cc_final: 0.8667 (tpp) REVERT: A 2234 MET cc_start: 0.8703 (mmm) cc_final: 0.8068 (mtp) REVERT: A 2689 MET cc_start: 0.5645 (pmm) cc_final: 0.5402 (pmm) REVERT: A 2943 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8529 (m-10) REVERT: A 3104 MET cc_start: 0.8766 (tmm) cc_final: 0.8414 (tmm) REVERT: A 3105 LEU cc_start: 0.8954 (mt) cc_final: 0.8671 (mt) REVERT: A 3215 MET cc_start: 0.9115 (mmm) cc_final: 0.8830 (ptp) REVERT: A 3241 MET cc_start: 0.9137 (ttm) cc_final: 0.8734 (tmm) REVERT: A 3318 HIS cc_start: 0.7172 (m90) cc_final: 0.6943 (m-70) REVERT: A 3719 MET cc_start: 0.8644 (mmm) cc_final: 0.8256 (mmm) REVERT: A 4274 MET cc_start: 0.4983 (ptt) cc_final: 0.4730 (mtt) REVERT: A 4707 MET cc_start: 0.8224 (tmm) cc_final: 0.7759 (tmm) REVERT: A 4726 MET cc_start: 0.8479 (tpt) cc_final: 0.8209 (tpp) REVERT: A 4943 MET cc_start: 0.8560 (mmm) cc_final: 0.7442 (mmm) REVERT: H 62 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: J 31 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9060 (mmtp) REVERT: J 73 MET cc_start: 0.8938 (mmp) cc_final: 0.8430 (mmm) REVERT: J 130 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.5048 (t0) REVERT: L 31 LYS cc_start: 0.9376 (mmtt) cc_final: 0.9169 (mmtp) REVERT: L 37 MET cc_start: 0.9044 (ttm) cc_final: 0.8629 (ttm) REVERT: L 72 MET cc_start: 0.8875 (tmm) cc_final: 0.8620 (tmm) REVERT: L 73 MET cc_start: 0.8912 (mmp) cc_final: 0.8610 (mmm) REVERT: L 126 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7776 (pt) REVERT: L 130 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.5119 (t0) REVERT: K 31 LYS cc_start: 0.9353 (mmtt) cc_final: 0.9069 (mmtp) REVERT: K 37 MET cc_start: 0.9047 (ttm) cc_final: 0.8581 (ttm) REVERT: K 93 PHE cc_start: 0.8506 (m-10) cc_final: 0.8294 (m-10) REVERT: K 125 MET cc_start: 0.8849 (tmm) cc_final: 0.8516 (tmm) REVERT: K 130 ASP cc_start: 0.5510 (OUTLIER) cc_final: 0.4887 (t0) REVERT: B 393 MET cc_start: 0.8478 (mmm) cc_final: 0.7891 (mmm) REVERT: B 981 MET cc_start: 0.8178 (ppp) cc_final: 0.7499 (ppp) REVERT: B 1168 MET cc_start: 0.8510 (mmm) cc_final: 0.8298 (mmm) REVERT: B 1842 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8541 (pt) REVERT: B 1975 MET cc_start: 0.8347 (mtm) cc_final: 0.7702 (mtp) REVERT: B 2234 MET cc_start: 0.8651 (mmm) cc_final: 0.8132 (mtp) REVERT: B 2828 MET cc_start: 0.7449 (mmp) cc_final: 0.6615 (mmp) REVERT: B 2844 MET cc_start: 0.9025 (tmm) cc_final: 0.8818 (tmm) REVERT: B 3050 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 3104 MET cc_start: 0.8979 (tmm) cc_final: 0.8595 (tmm) REVERT: B 3235 MET cc_start: 0.7691 (ppp) cc_final: 0.7063 (ppp) REVERT: B 3241 MET cc_start: 0.9141 (ttm) cc_final: 0.8730 (tmm) REVERT: B 3296 MET cc_start: 0.8462 (mmt) cc_final: 0.8035 (ppp) REVERT: B 3318 HIS cc_start: 0.7329 (m90) cc_final: 0.6992 (m90) REVERT: B 4707 MET cc_start: 0.8198 (tmm) cc_final: 0.7705 (tmm) REVERT: B 4943 MET cc_start: 0.8423 (mtp) cc_final: 0.8139 (ttp) REVERT: C 393 MET cc_start: 0.8400 (mmm) cc_final: 0.7220 (mmm) REVERT: C 981 MET cc_start: 0.8069 (ppp) cc_final: 0.7409 (ppp) REVERT: C 1842 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8538 (pt) REVERT: C 2234 MET cc_start: 0.8649 (mmm) cc_final: 0.8351 (mtp) REVERT: C 2689 MET cc_start: 0.6009 (pmm) cc_final: 0.5610 (pmm) REVERT: C 2848 TYR cc_start: 0.8344 (t80) cc_final: 0.8057 (t80) REVERT: C 3104 MET cc_start: 0.8438 (tmm) cc_final: 0.8024 (tmm) REVERT: C 3105 LEU cc_start: 0.8959 (mt) cc_final: 0.8700 (mt) REVERT: C 3220 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7978 (pp20) REVERT: C 3241 MET cc_start: 0.9146 (ttm) cc_final: 0.8790 (tmm) REVERT: C 3318 HIS cc_start: 0.6678 (m90) cc_final: 0.6445 (m-70) REVERT: C 4707 MET cc_start: 0.8314 (tmm) cc_final: 0.7834 (tmm) REVERT: C 4726 MET cc_start: 0.8393 (tpt) cc_final: 0.8172 (tpp) REVERT: C 4804 MET cc_start: 0.8742 (mmm) cc_final: 0.8262 (mmm) REVERT: D 393 MET cc_start: 0.8372 (mmm) cc_final: 0.8032 (mmm) REVERT: D 893 TRP cc_start: 0.8681 (t60) cc_final: 0.8408 (t60) REVERT: D 944 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8959 (mt) REVERT: D 964 MET cc_start: 0.2924 (ppp) cc_final: 0.2690 (ppp) REVERT: D 981 MET cc_start: 0.7795 (ppp) cc_final: 0.7004 (ppp) REVERT: D 1174 MET cc_start: 0.7456 (pmm) cc_final: 0.7170 (pmm) REVERT: D 1487 MET cc_start: 0.8684 (mtp) cc_final: 0.8373 (mtp) REVERT: D 1842 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8549 (pt) REVERT: D 2150 MET cc_start: 0.8687 (mmm) cc_final: 0.8444 (mtt) REVERT: D 2234 MET cc_start: 0.8609 (mmm) cc_final: 0.8090 (mtp) REVERT: D 2584 MET cc_start: 0.8842 (mmm) cc_final: 0.8417 (mtt) REVERT: D 2757 MET cc_start: 0.7434 (mmt) cc_final: 0.6882 (mmt) REVERT: D 2828 MET cc_start: 0.7357 (mmp) cc_final: 0.6525 (mmp) REVERT: D 2843 MET cc_start: 0.8646 (ttp) cc_final: 0.8272 (tmm) REVERT: D 2844 MET cc_start: 0.9085 (tmm) cc_final: 0.8675 (ppp) REVERT: D 2943 PHE cc_start: 0.8801 (t80) cc_final: 0.8547 (m-10) REVERT: D 3104 MET cc_start: 0.8558 (tmm) cc_final: 0.8209 (tmm) REVERT: D 3105 LEU cc_start: 0.8962 (mt) cc_final: 0.8661 (mt) REVERT: D 3241 MET cc_start: 0.9150 (ttm) cc_final: 0.8765 (tmm) REVERT: D 3296 MET cc_start: 0.8372 (mmm) cc_final: 0.7981 (ppp) REVERT: D 3318 HIS cc_start: 0.6782 (m90) cc_final: 0.6506 (m-70) REVERT: D 4274 MET cc_start: 0.5203 (ptt) cc_final: 0.4976 (ptp) REVERT: D 4707 MET cc_start: 0.8231 (tmm) cc_final: 0.7721 (tmm) REVERT: D 4726 MET cc_start: 0.8496 (tpt) cc_final: 0.8234 (tpp) REVERT: D 4817 MET cc_start: 0.8649 (mmm) cc_final: 0.8422 (tpp) REVERT: D 4943 MET cc_start: 0.8424 (mtp) cc_final: 0.8133 (ttp) outliers start: 136 outliers final: 84 residues processed: 836 average time/residue: 1.2353 time to fit residues: 1851.0126 Evaluate side-chains 821 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 722 time to evaluate : 12.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3128 VAL Chi-restraints excluded: chain A residue 3181 TYR Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2983 LEU Chi-restraints excluded: chain B residue 3050 LEU Chi-restraints excluded: chain B residue 3128 VAL Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 2931 ARG Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4306 PHE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3128 VAL Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3287 ASN Chi-restraints excluded: chain D residue 3797 MET Chi-restraints excluded: chain D residue 3815 GLU Chi-restraints excluded: chain D residue 4814 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 4.9990 chunk 688 optimal weight: 7.9990 chunk 1029 optimal weight: 20.0000 chunk 519 optimal weight: 30.0000 chunk 338 optimal weight: 6.9990 chunk 333 optimal weight: 7.9990 chunk 1095 optimal weight: 10.0000 chunk 1174 optimal weight: 4.9990 chunk 852 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 1354 optimal weight: 0.0470 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 50 GLN I 54 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2217 HIS ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.791 146532 Z= 0.625 Angle : 0.583 20.940 197928 Z= 0.292 Chirality : 0.039 0.297 21684 Planarity : 0.004 0.117 25468 Dihedral : 5.449 88.048 19666 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 0.87 % Allowed : 7.72 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.06), residues: 17804 helix: 1.97 (0.06), residues: 9320 sheet: 0.09 (0.13), residues: 1568 loop : -0.35 (0.08), residues: 6916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP D2773 HIS 0.011 0.001 HIS D3111 PHE 0.047 0.001 PHE L 93 TYR 0.034 0.001 TYR D4567 ARG 0.014 0.000 ARG B2824 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 730 time to evaluate : 14.733 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: I 31 LYS cc_start: 0.9418 (mmtt) cc_final: 0.9152 (mmtp) REVERT: I 53 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9201 (tt) REVERT: I 72 MET cc_start: 0.8747 (tmm) cc_final: 0.8401 (ttt) REVERT: I 73 MET cc_start: 0.8946 (mmp) cc_final: 0.8353 (mmm) REVERT: A 944 LEU cc_start: 0.9196 (tt) cc_final: 0.8994 (mt) REVERT: A 981 MET cc_start: 0.8068 (ppp) cc_final: 0.7463 (ppp) REVERT: A 1168 MET cc_start: 0.8542 (mmm) cc_final: 0.8318 (mmt) REVERT: A 1842 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8545 (pt) REVERT: A 1953 MET cc_start: 0.8815 (tpp) cc_final: 0.8528 (tpp) REVERT: A 1975 MET cc_start: 0.8237 (ttm) cc_final: 0.7957 (ttm) REVERT: A 2234 MET cc_start: 0.8671 (mmm) cc_final: 0.8048 (mtp) REVERT: A 2681 MET cc_start: 0.8050 (mmm) cc_final: 0.7833 (mmp) REVERT: A 2689 MET cc_start: 0.5825 (pmm) cc_final: 0.5592 (pmm) REVERT: A 2843 MET cc_start: 0.8883 (ptt) cc_final: 0.8573 (ppp) REVERT: A 2943 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (m-10) REVERT: A 3104 MET cc_start: 0.8745 (tmm) cc_final: 0.8434 (tmm) REVERT: A 3105 LEU cc_start: 0.8947 (mt) cc_final: 0.8690 (mt) REVERT: A 3215 MET cc_start: 0.9151 (mmm) cc_final: 0.8883 (ptp) REVERT: A 3241 MET cc_start: 0.9143 (ttm) cc_final: 0.8745 (tmm) REVERT: A 3318 HIS cc_start: 0.7196 (m90) cc_final: 0.6934 (m-70) REVERT: A 3719 MET cc_start: 0.8630 (mmm) cc_final: 0.8226 (mmm) REVERT: A 4274 MET cc_start: 0.4937 (ptt) cc_final: 0.4689 (mtt) REVERT: A 4707 MET cc_start: 0.8214 (tmm) cc_final: 0.7733 (tmm) REVERT: A 4726 MET cc_start: 0.8481 (tpt) cc_final: 0.8216 (tpp) REVERT: A 4817 MET cc_start: 0.8634 (mmm) cc_final: 0.8411 (tpp) REVERT: A 4943 MET cc_start: 0.8552 (mmm) cc_final: 0.7422 (mmm) REVERT: J 31 LYS cc_start: 0.9385 (mmtt) cc_final: 0.9112 (mmtp) REVERT: J 73 MET cc_start: 0.8933 (mmp) cc_final: 0.8487 (mmm) REVERT: J 130 ASP cc_start: 0.5692 (OUTLIER) cc_final: 0.5008 (t0) REVERT: L 37 MET cc_start: 0.9043 (ttm) cc_final: 0.8613 (ttm) REVERT: L 72 MET cc_start: 0.8884 (tmm) cc_final: 0.8571 (tmm) REVERT: L 73 MET cc_start: 0.8908 (mmp) cc_final: 0.8612 (mmm) REVERT: L 126 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7971 (pt) REVERT: L 130 ASP cc_start: 0.5806 (OUTLIER) cc_final: 0.5124 (t0) REVERT: K 31 LYS cc_start: 0.9350 (mmtt) cc_final: 0.9064 (mmtp) REVERT: K 37 MET cc_start: 0.9025 (ttm) cc_final: 0.8597 (ttm) REVERT: K 77 MET cc_start: 0.7410 (tmm) cc_final: 0.7011 (tmm) REVERT: K 125 MET cc_start: 0.8870 (tmm) cc_final: 0.8524 (tmm) REVERT: K 130 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.4936 (t0) REVERT: B 981 MET cc_start: 0.8192 (ppp) cc_final: 0.7499 (ppp) REVERT: B 1168 MET cc_start: 0.8510 (mmm) cc_final: 0.8290 (mmm) REVERT: B 1842 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8542 (pt) REVERT: B 1975 MET cc_start: 0.8346 (mtm) cc_final: 0.7701 (mtp) REVERT: B 2234 MET cc_start: 0.8632 (mmm) cc_final: 0.8082 (mtp) REVERT: B 3046 MET cc_start: 0.9223 (mpp) cc_final: 0.8952 (pmm) REVERT: B 3050 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 3104 MET cc_start: 0.8977 (tmm) cc_final: 0.8625 (tmm) REVERT: B 3235 MET cc_start: 0.7737 (ppp) cc_final: 0.7126 (ppp) REVERT: B 3241 MET cc_start: 0.9134 (ttm) cc_final: 0.8728 (tmm) REVERT: B 3296 MET cc_start: 0.8526 (mmt) cc_final: 0.8122 (ppp) REVERT: B 3318 HIS cc_start: 0.7322 (m90) cc_final: 0.6980 (m90) REVERT: B 3719 MET cc_start: 0.8617 (mmm) cc_final: 0.8243 (mmm) REVERT: B 4707 MET cc_start: 0.8181 (tmm) cc_final: 0.7697 (tmm) REVERT: B 4943 MET cc_start: 0.8382 (mtp) cc_final: 0.8105 (ttp) REVERT: C 393 MET cc_start: 0.8394 (mmm) cc_final: 0.7205 (mmm) REVERT: C 972 LEU cc_start: 0.3846 (OUTLIER) cc_final: 0.3635 (tp) REVERT: C 981 MET cc_start: 0.8105 (ppp) cc_final: 0.7472 (ppp) REVERT: C 1842 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8539 (pt) REVERT: C 2234 MET cc_start: 0.8656 (mmm) cc_final: 0.8351 (mtp) REVERT: C 2734 MET cc_start: 0.9010 (mtt) cc_final: 0.8528 (mpp) REVERT: C 2848 TYR cc_start: 0.8339 (t80) cc_final: 0.8059 (t80) REVERT: C 3104 MET cc_start: 0.8393 (tmm) cc_final: 0.7974 (tmm) REVERT: C 3105 LEU cc_start: 0.8946 (mt) cc_final: 0.8687 (mt) REVERT: C 3220 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7993 (pp20) REVERT: C 3241 MET cc_start: 0.9165 (ttm) cc_final: 0.8811 (tmm) REVERT: C 3318 HIS cc_start: 0.6672 (m90) cc_final: 0.6419 (m-70) REVERT: C 4654 MET cc_start: 0.8723 (tpp) cc_final: 0.8391 (tpp) REVERT: C 4707 MET cc_start: 0.8294 (tmm) cc_final: 0.7815 (tmm) REVERT: C 4726 MET cc_start: 0.8410 (tpt) cc_final: 0.8187 (tpp) REVERT: C 4804 MET cc_start: 0.8767 (mmm) cc_final: 0.8276 (mmm) REVERT: D 393 MET cc_start: 0.8399 (mmm) cc_final: 0.8111 (mmm) REVERT: D 893 TRP cc_start: 0.8673 (t60) cc_final: 0.8396 (t60) REVERT: D 944 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8963 (mt) REVERT: D 981 MET cc_start: 0.7805 (ppp) cc_final: 0.7023 (ppp) REVERT: D 1487 MET cc_start: 0.8679 (mtp) cc_final: 0.8399 (mtp) REVERT: D 1842 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8551 (pt) REVERT: D 2004 MET cc_start: 0.9272 (mmp) cc_final: 0.9056 (mmm) REVERT: D 2150 MET cc_start: 0.8680 (mmm) cc_final: 0.8456 (mtt) REVERT: D 2234 MET cc_start: 0.8623 (mmm) cc_final: 0.8095 (mtp) REVERT: D 2584 MET cc_start: 0.8845 (mmm) cc_final: 0.8429 (mtt) REVERT: D 2757 MET cc_start: 0.7430 (mmt) cc_final: 0.6858 (mmt) REVERT: D 2828 MET cc_start: 0.7349 (mmp) cc_final: 0.6526 (mmp) REVERT: D 2843 MET cc_start: 0.8645 (ttp) cc_final: 0.8281 (tmm) REVERT: D 2844 MET cc_start: 0.9078 (tmm) cc_final: 0.8684 (ppp) REVERT: D 2943 PHE cc_start: 0.8800 (t80) cc_final: 0.8546 (m-10) REVERT: D 3104 MET cc_start: 0.8484 (tmm) cc_final: 0.8116 (tmm) REVERT: D 3105 LEU cc_start: 0.8970 (mt) cc_final: 0.8705 (mt) REVERT: D 3241 MET cc_start: 0.9148 (ttm) cc_final: 0.8765 (tmm) REVERT: D 3296 MET cc_start: 0.8360 (mmm) cc_final: 0.8017 (ppp) REVERT: D 3318 HIS cc_start: 0.6750 (m90) cc_final: 0.6459 (m-70) REVERT: D 4274 MET cc_start: 0.5110 (ptt) cc_final: 0.4902 (ptp) REVERT: D 4707 MET cc_start: 0.8223 (tmm) cc_final: 0.7711 (tmm) REVERT: D 4726 MET cc_start: 0.8506 (tpt) cc_final: 0.8242 (tpp) REVERT: D 4814 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7596 (mmm) REVERT: D 4817 MET cc_start: 0.8635 (mmm) cc_final: 0.8424 (tpp) REVERT: D 4943 MET cc_start: 0.8421 (mtp) cc_final: 0.8140 (ttp) outliers start: 128 outliers final: 94 residues processed: 821 average time/residue: 1.2299 time to fit residues: 1815.3443 Evaluate side-chains 836 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 727 time to evaluate : 12.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3128 VAL Chi-restraints excluded: chain A residue 3181 TYR Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3798 GLN Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2983 LEU Chi-restraints excluded: chain B residue 3050 LEU Chi-restraints excluded: chain B residue 3128 VAL Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3798 GLN Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain B residue 4052 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 2931 ARG Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3128 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3587 TRP Chi-restraints excluded: chain C residue 3798 GLN Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4306 PHE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3128 VAL Chi-restraints excluded: chain D residue 3181 TYR Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3287 ASN Chi-restraints excluded: chain D residue 3797 MET Chi-restraints excluded: chain D residue 3798 GLN Chi-restraints excluded: chain D residue 3815 GLU Chi-restraints excluded: chain D residue 4814 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 10.0000 chunk 1651 optimal weight: 50.0000 chunk 1506 optimal weight: 0.3980 chunk 1605 optimal weight: 20.0000 chunk 1650 optimal weight: 6.9990 chunk 966 optimal weight: 10.0000 chunk 699 optimal weight: 9.9990 chunk 1261 optimal weight: 2.9990 chunk 492 optimal weight: 5.9990 chunk 1451 optimal weight: 50.0000 chunk 1518 optimal weight: 3.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 HIS ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.791 146532 Z= 0.637 Angle : 0.592 20.846 197928 Z= 0.297 Chirality : 0.040 0.293 21684 Planarity : 0.004 0.118 25468 Dihedral : 5.426 89.862 19664 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 0.82 % Allowed : 7.81 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.06), residues: 17804 helix: 1.97 (0.05), residues: 9316 sheet: 0.08 (0.13), residues: 1568 loop : -0.34 (0.08), residues: 6920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP D2773 HIS 0.011 0.001 HIS D3111 PHE 0.037 0.001 PHE L 93 TYR 0.022 0.001 TYR B2848 ARG 0.014 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 732 time to evaluate : 12.149 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: I 31 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9157 (mmtp) REVERT: I 53 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9200 (tt) REVERT: I 72 MET cc_start: 0.8753 (tmm) cc_final: 0.8399 (ttt) REVERT: I 73 MET cc_start: 0.8953 (mmp) cc_final: 0.8415 (mmm) REVERT: A 344 LYS cc_start: 0.8058 (tppt) cc_final: 0.7700 (tptp) REVERT: A 944 LEU cc_start: 0.9205 (tt) cc_final: 0.9000 (mt) REVERT: A 981 MET cc_start: 0.8093 (ppp) cc_final: 0.7475 (ppp) REVERT: A 1168 MET cc_start: 0.8547 (mmm) cc_final: 0.8328 (mmt) REVERT: A 1842 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8551 (pt) REVERT: A 1953 MET cc_start: 0.8837 (tpp) cc_final: 0.8540 (tpp) REVERT: A 1975 MET cc_start: 0.8233 (ttm) cc_final: 0.7957 (ttm) REVERT: A 2234 MET cc_start: 0.8677 (mmm) cc_final: 0.8078 (mtp) REVERT: A 2681 MET cc_start: 0.8085 (mmm) cc_final: 0.7855 (mmp) REVERT: A 2689 MET cc_start: 0.5855 (pmm) cc_final: 0.5617 (pmm) REVERT: A 2843 MET cc_start: 0.8906 (ptt) cc_final: 0.8571 (ppp) REVERT: A 2943 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: A 3104 MET cc_start: 0.8738 (tmm) cc_final: 0.8423 (tmm) REVERT: A 3105 LEU cc_start: 0.8953 (mt) cc_final: 0.8694 (mt) REVERT: A 3215 MET cc_start: 0.9154 (mmm) cc_final: 0.8892 (ptp) REVERT: A 3241 MET cc_start: 0.9151 (ttm) cc_final: 0.8751 (tmm) REVERT: A 3318 HIS cc_start: 0.7212 (m90) cc_final: 0.6943 (m-70) REVERT: A 4274 MET cc_start: 0.4811 (ptt) cc_final: 0.4483 (mtt) REVERT: A 4279 MET cc_start: 0.6460 (ptm) cc_final: 0.6198 (ppp) REVERT: A 4707 MET cc_start: 0.8210 (tmm) cc_final: 0.7711 (tmm) REVERT: A 4726 MET cc_start: 0.8490 (tpt) cc_final: 0.8233 (tpp) REVERT: A 4817 MET cc_start: 0.8630 (mmm) cc_final: 0.8410 (tpp) REVERT: A 4943 MET cc_start: 0.8566 (mmm) cc_final: 0.7339 (mmm) REVERT: J 31 LYS cc_start: 0.9378 (mmtt) cc_final: 0.9116 (mmtp) REVERT: J 73 MET cc_start: 0.8935 (mmp) cc_final: 0.8466 (mmm) REVERT: J 130 ASP cc_start: 0.5716 (OUTLIER) cc_final: 0.5091 (t0) REVERT: L 37 MET cc_start: 0.9040 (ttm) cc_final: 0.8605 (ttm) REVERT: L 72 MET cc_start: 0.8892 (tmm) cc_final: 0.8558 (tmm) REVERT: L 73 MET cc_start: 0.8930 (mmp) cc_final: 0.8634 (mmm) REVERT: L 126 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7846 (pt) REVERT: L 130 ASP cc_start: 0.5852 (OUTLIER) cc_final: 0.5195 (t0) REVERT: L 145 MET cc_start: 0.8213 (ppp) cc_final: 0.7908 (ppp) REVERT: K 31 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9064 (mmtp) REVERT: K 37 MET cc_start: 0.9029 (ttm) cc_final: 0.8582 (ttm) REVERT: K 125 MET cc_start: 0.8883 (tmm) cc_final: 0.8679 (tmm) REVERT: K 130 ASP cc_start: 0.5676 (OUTLIER) cc_final: 0.5113 (t0) REVERT: B 981 MET cc_start: 0.8179 (ppp) cc_final: 0.7509 (ppp) REVERT: B 1842 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8549 (pt) REVERT: B 1975 MET cc_start: 0.8361 (mtm) cc_final: 0.7770 (mtp) REVERT: B 2234 MET cc_start: 0.8630 (mmm) cc_final: 0.8075 (mtp) REVERT: B 2828 MET cc_start: 0.7486 (mmp) cc_final: 0.6555 (mmp) REVERT: B 3046 MET cc_start: 0.9254 (mpp) cc_final: 0.8972 (pmm) REVERT: B 3104 MET cc_start: 0.8979 (tmm) cc_final: 0.8630 (tmm) REVERT: B 3235 MET cc_start: 0.7980 (ppp) cc_final: 0.7384 (ppp) REVERT: B 3241 MET cc_start: 0.9146 (ttm) cc_final: 0.8734 (tmm) REVERT: B 3296 MET cc_start: 0.8564 (mmt) cc_final: 0.8165 (ppp) REVERT: B 3318 HIS cc_start: 0.7349 (m90) cc_final: 0.7003 (m90) REVERT: B 4707 MET cc_start: 0.8176 (tmm) cc_final: 0.7690 (tmm) REVERT: B 4943 MET cc_start: 0.8385 (mtp) cc_final: 0.8104 (ttp) REVERT: C 344 LYS cc_start: 0.8025 (tppt) cc_final: 0.7675 (tptp) REVERT: C 393 MET cc_start: 0.8386 (mmm) cc_final: 0.7195 (mmm) REVERT: C 981 MET cc_start: 0.8129 (ppp) cc_final: 0.7503 (ppp) REVERT: C 1842 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8548 (pt) REVERT: C 2234 MET cc_start: 0.8675 (mmm) cc_final: 0.8357 (mtp) REVERT: C 2848 TYR cc_start: 0.8349 (t80) cc_final: 0.8076 (t80) REVERT: C 3104 MET cc_start: 0.8354 (tmm) cc_final: 0.7935 (tmm) REVERT: C 3105 LEU cc_start: 0.8945 (mt) cc_final: 0.8687 (mt) REVERT: C 3220 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7995 (pp20) REVERT: C 3241 MET cc_start: 0.9150 (ttm) cc_final: 0.8787 (tmm) REVERT: C 3318 HIS cc_start: 0.6706 (m90) cc_final: 0.6445 (m-70) REVERT: C 3719 MET cc_start: 0.8669 (mmm) cc_final: 0.8327 (mmm) REVERT: C 4654 MET cc_start: 0.8732 (tpp) cc_final: 0.8405 (tpp) REVERT: C 4707 MET cc_start: 0.8285 (tmm) cc_final: 0.7810 (tmm) REVERT: C 4726 MET cc_start: 0.8423 (tpt) cc_final: 0.8206 (tpp) REVERT: C 4804 MET cc_start: 0.8758 (mmm) cc_final: 0.8260 (mmm) REVERT: C 4817 MET cc_start: 0.8646 (mmm) cc_final: 0.8429 (tpp) REVERT: D 393 MET cc_start: 0.8385 (mmm) cc_final: 0.8083 (mmm) REVERT: D 893 TRP cc_start: 0.8660 (t60) cc_final: 0.8404 (t60) REVERT: D 944 LEU cc_start: 0.9240 (tt) cc_final: 0.8989 (mt) REVERT: D 981 MET cc_start: 0.7823 (ppp) cc_final: 0.7067 (ppp) REVERT: D 1174 MET cc_start: 0.7462 (pmm) cc_final: 0.7194 (pmm) REVERT: D 1487 MET cc_start: 0.8668 (mtp) cc_final: 0.8381 (mtp) REVERT: D 1842 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8558 (pt) REVERT: D 2004 MET cc_start: 0.9278 (mmp) cc_final: 0.9063 (mmm) REVERT: D 2150 MET cc_start: 0.8678 (mmm) cc_final: 0.8473 (mtt) REVERT: D 2584 MET cc_start: 0.8893 (mmm) cc_final: 0.8467 (mtt) REVERT: D 2757 MET cc_start: 0.7484 (mmt) cc_final: 0.6902 (mmt) REVERT: D 2828 MET cc_start: 0.7412 (mmp) cc_final: 0.6634 (mmp) REVERT: D 2843 MET cc_start: 0.8655 (ttp) cc_final: 0.8255 (tmm) REVERT: D 2943 PHE cc_start: 0.8823 (t80) cc_final: 0.8553 (m-10) REVERT: D 3104 MET cc_start: 0.8477 (tmm) cc_final: 0.8103 (tmm) REVERT: D 3105 LEU cc_start: 0.8968 (mt) cc_final: 0.8708 (mt) REVERT: D 3241 MET cc_start: 0.9150 (ttm) cc_final: 0.8772 (tmm) REVERT: D 3318 HIS cc_start: 0.6760 (m90) cc_final: 0.6465 (m-70) REVERT: D 4707 MET cc_start: 0.8207 (tmm) cc_final: 0.7700 (tmm) REVERT: D 4814 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7596 (mmm) REVERT: D 4817 MET cc_start: 0.8628 (mmm) cc_final: 0.8423 (tpp) REVERT: D 4943 MET cc_start: 0.8399 (mtp) cc_final: 0.8115 (ttp) outliers start: 121 outliers final: 95 residues processed: 817 average time/residue: 1.1911 time to fit residues: 1752.5233 Evaluate side-chains 829 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 722 time to evaluate : 11.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3128 VAL Chi-restraints excluded: chain A residue 3181 TYR Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3798 GLN Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2983 LEU Chi-restraints excluded: chain B residue 3128 VAL Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3798 GLN Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain B residue 4052 MET Chi-restraints excluded: chain B residue 4672 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 2931 ARG Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3128 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3587 TRP Chi-restraints excluded: chain C residue 3798 GLN Chi-restraints excluded: chain C residue 3815 GLU Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4814 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3128 VAL Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3287 ASN Chi-restraints excluded: chain D residue 3797 MET Chi-restraints excluded: chain D residue 3798 GLN Chi-restraints excluded: chain D residue 3815 GLU Chi-restraints excluded: chain D residue 4814 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 1.9990 chunk 1054 optimal weight: 10.0000 chunk 1698 optimal weight: 2.9990 chunk 1036 optimal weight: 20.0000 chunk 805 optimal weight: 40.0000 chunk 1180 optimal weight: 8.9990 chunk 1781 optimal weight: 7.9990 chunk 1639 optimal weight: 3.9990 chunk 1418 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 1095 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2464 HIS ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2927 GLN ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.791 146532 Z= 0.615 Angle : 0.589 20.847 197928 Z= 0.294 Chirality : 0.039 0.285 21684 Planarity : 0.004 0.118 25468 Dihedral : 5.353 89.359 19662 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 0.70 % Allowed : 7.97 % Favored : 91.33 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.06), residues: 17804 helix: 2.00 (0.06), residues: 9340 sheet: 0.08 (0.13), residues: 1576 loop : -0.34 (0.08), residues: 6888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP D2773 HIS 0.019 0.001 HIS C3111 PHE 0.034 0.001 PHE L 93 TYR 0.038 0.001 TYR D4567 ARG 0.015 0.000 ARG F 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35608 Ramachandran restraints generated. 17804 Oldfield, 0 Emsley, 17804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 728 time to evaluate : 12.301 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: I 31 LYS cc_start: 0.9403 (mmtt) cc_final: 0.9140 (mmtp) REVERT: I 53 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9185 (tt) REVERT: I 72 MET cc_start: 0.8719 (tmm) cc_final: 0.8371 (ttt) REVERT: I 73 MET cc_start: 0.8878 (mmp) cc_final: 0.8360 (mmm) REVERT: I 145 MET cc_start: 0.8191 (ppp) cc_final: 0.7871 (ppp) REVERT: A 344 LYS cc_start: 0.8063 (tppt) cc_final: 0.7693 (tptp) REVERT: A 494 MET cc_start: 0.8652 (mmm) cc_final: 0.8329 (mmm) REVERT: A 944 LEU cc_start: 0.9193 (tt) cc_final: 0.8989 (mt) REVERT: A 981 MET cc_start: 0.8058 (ppp) cc_final: 0.7475 (ppp) REVERT: A 1842 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8542 (pt) REVERT: A 1953 MET cc_start: 0.8781 (tpp) cc_final: 0.8492 (tpp) REVERT: A 1975 MET cc_start: 0.8233 (ttm) cc_final: 0.7948 (ttm) REVERT: A 2234 MET cc_start: 0.8656 (mmm) cc_final: 0.8090 (mtp) REVERT: A 2681 MET cc_start: 0.8014 (mmm) cc_final: 0.7764 (mmp) REVERT: A 2689 MET cc_start: 0.5807 (pmm) cc_final: 0.5581 (pmm) REVERT: A 2734 MET cc_start: 0.9012 (mtt) cc_final: 0.8571 (mpp) REVERT: A 2843 MET cc_start: 0.8898 (ptt) cc_final: 0.8473 (tmm) REVERT: A 2943 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8524 (m-10) REVERT: A 3104 MET cc_start: 0.8684 (tmm) cc_final: 0.8368 (tmm) REVERT: A 3105 LEU cc_start: 0.8957 (mt) cc_final: 0.8694 (mt) REVERT: A 3215 MET cc_start: 0.9156 (mmm) cc_final: 0.8904 (ptp) REVERT: A 3241 MET cc_start: 0.9135 (ttm) cc_final: 0.8731 (tmm) REVERT: A 3318 HIS cc_start: 0.7209 (m90) cc_final: 0.6948 (m-70) REVERT: A 4274 MET cc_start: 0.4832 (ptt) cc_final: 0.4371 (ptp) REVERT: A 4279 MET cc_start: 0.6476 (ptm) cc_final: 0.6201 (ppp) REVERT: A 4654 MET cc_start: 0.8742 (tpp) cc_final: 0.8429 (tpp) REVERT: A 4707 MET cc_start: 0.8208 (tmm) cc_final: 0.7719 (tmm) REVERT: A 4726 MET cc_start: 0.8479 (tpt) cc_final: 0.8222 (tpp) REVERT: A 4817 MET cc_start: 0.8636 (mmm) cc_final: 0.8403 (tpp) REVERT: A 4943 MET cc_start: 0.8523 (mmm) cc_final: 0.7930 (mtp) REVERT: J 31 LYS cc_start: 0.9379 (mmtt) cc_final: 0.9113 (mmtp) REVERT: J 73 MET cc_start: 0.8871 (mmp) cc_final: 0.8458 (mmm) REVERT: J 130 ASP cc_start: 0.5649 (OUTLIER) cc_final: 0.5137 (t0) REVERT: L 37 MET cc_start: 0.9006 (ttm) cc_final: 0.8588 (ttm) REVERT: L 73 MET cc_start: 0.8859 (mmp) cc_final: 0.8639 (mmm) REVERT: L 126 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8103 (pt) REVERT: L 130 ASP cc_start: 0.5821 (OUTLIER) cc_final: 0.5204 (t0) REVERT: L 145 MET cc_start: 0.8166 (ppp) cc_final: 0.7838 (ppp) REVERT: K 31 LYS cc_start: 0.9329 (mmtt) cc_final: 0.9042 (mmtp) REVERT: K 37 MET cc_start: 0.9022 (ttm) cc_final: 0.8570 (ttm) REVERT: K 130 ASP cc_start: 0.5595 (OUTLIER) cc_final: 0.5080 (t0) REVERT: B 494 MET cc_start: 0.8643 (mmm) cc_final: 0.8293 (mmm) REVERT: B 981 MET cc_start: 0.8176 (ppp) cc_final: 0.7506 (ppp) REVERT: B 1729 MET cc_start: 0.8486 (mmm) cc_final: 0.8162 (mmt) REVERT: B 1842 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8541 (pt) REVERT: B 1975 MET cc_start: 0.8336 (mtm) cc_final: 0.7758 (mtp) REVERT: B 2234 MET cc_start: 0.8629 (mmm) cc_final: 0.8074 (mtp) REVERT: B 3046 MET cc_start: 0.9342 (mpp) cc_final: 0.9018 (pmm) REVERT: B 3050 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7746 (mp) REVERT: B 3104 MET cc_start: 0.8956 (tmm) cc_final: 0.8603 (tmm) REVERT: B 3241 MET cc_start: 0.9121 (ttm) cc_final: 0.8708 (tmm) REVERT: B 3296 MET cc_start: 0.8549 (mmt) cc_final: 0.8172 (ppp) REVERT: B 3318 HIS cc_start: 0.7311 (m90) cc_final: 0.6976 (m90) REVERT: B 3985 MET cc_start: 0.8701 (mmm) cc_final: 0.8467 (mmm) REVERT: B 4707 MET cc_start: 0.8172 (tmm) cc_final: 0.7684 (tmm) REVERT: B 4943 MET cc_start: 0.8345 (mtp) cc_final: 0.8078 (ttp) REVERT: C 344 LYS cc_start: 0.8020 (tppt) cc_final: 0.7693 (tptp) REVERT: C 393 MET cc_start: 0.8392 (mmm) cc_final: 0.7179 (mmm) REVERT: C 981 MET cc_start: 0.8132 (ppp) cc_final: 0.7469 (ppp) REVERT: C 1842 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8536 (pt) REVERT: C 2347 MET cc_start: 0.9323 (mmt) cc_final: 0.9052 (mmt) REVERT: C 2681 MET cc_start: 0.7685 (mmm) cc_final: 0.7423 (mmp) REVERT: C 2734 MET cc_start: 0.8948 (mtt) cc_final: 0.8468 (mpp) REVERT: C 2848 TYR cc_start: 0.8342 (t80) cc_final: 0.8083 (t80) REVERT: C 3220 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7991 (pp20) REVERT: C 3241 MET cc_start: 0.9154 (ttm) cc_final: 0.8785 (tmm) REVERT: C 3318 HIS cc_start: 0.6719 (m90) cc_final: 0.6452 (m-70) REVERT: C 3719 MET cc_start: 0.8633 (mmm) cc_final: 0.8280 (mmm) REVERT: C 4654 MET cc_start: 0.8763 (tpp) cc_final: 0.8446 (tpp) REVERT: C 4707 MET cc_start: 0.8274 (tmm) cc_final: 0.7788 (tmm) REVERT: C 4726 MET cc_start: 0.8411 (tpt) cc_final: 0.8200 (tpp) REVERT: C 4804 MET cc_start: 0.8761 (mmm) cc_final: 0.8279 (mmm) REVERT: C 4817 MET cc_start: 0.8616 (mmm) cc_final: 0.8391 (tpp) REVERT: C 4943 MET cc_start: 0.8598 (mmm) cc_final: 0.7377 (mmm) REVERT: D 393 MET cc_start: 0.8379 (mmm) cc_final: 0.8073 (mmm) REVERT: D 893 TRP cc_start: 0.8656 (t60) cc_final: 0.8387 (t60) REVERT: D 944 LEU cc_start: 0.9228 (tt) cc_final: 0.8977 (mt) REVERT: D 981 MET cc_start: 0.7818 (ppp) cc_final: 0.7063 (ppp) REVERT: D 1174 MET cc_start: 0.7459 (pmm) cc_final: 0.7190 (pmm) REVERT: D 1487 MET cc_start: 0.8672 (mtp) cc_final: 0.8411 (mtp) REVERT: D 1842 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8548 (pt) REVERT: D 2004 MET cc_start: 0.9270 (mmp) cc_final: 0.9054 (mmm) REVERT: D 2584 MET cc_start: 0.8892 (mmm) cc_final: 0.8478 (mtt) REVERT: D 2734 MET cc_start: 0.8995 (mtt) cc_final: 0.8700 (mpp) REVERT: D 2757 MET cc_start: 0.7433 (mmt) cc_final: 0.6855 (mmt) REVERT: D 2828 MET cc_start: 0.7346 (mmp) cc_final: 0.6583 (mmp) REVERT: D 2843 MET cc_start: 0.8655 (ttp) cc_final: 0.8250 (tmm) REVERT: D 2943 PHE cc_start: 0.8834 (t80) cc_final: 0.8551 (m-10) REVERT: D 3104 MET cc_start: 0.8450 (tmm) cc_final: 0.8089 (tmm) REVERT: D 3105 LEU cc_start: 0.8945 (mt) cc_final: 0.8699 (mt) REVERT: D 3241 MET cc_start: 0.9134 (ttm) cc_final: 0.8750 (tmm) REVERT: D 3318 HIS cc_start: 0.6768 (m90) cc_final: 0.6463 (m-70) REVERT: D 4707 MET cc_start: 0.8194 (tmm) cc_final: 0.7709 (tmm) REVERT: D 4726 MET cc_start: 0.8484 (tpt) cc_final: 0.8222 (tpp) REVERT: D 4817 MET cc_start: 0.8626 (mmm) cc_final: 0.8391 (tpp) REVERT: D 4943 MET cc_start: 0.8377 (mtp) cc_final: 0.8112 (ttp) outliers start: 102 outliers final: 86 residues processed: 801 average time/residue: 1.3153 time to fit residues: 1910.0276 Evaluate side-chains 816 residues out of total 15708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 718 time to evaluate : 12.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3128 VAL Chi-restraints excluded: chain A residue 3181 TYR Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3798 GLN Chi-restraints excluded: chain A residue 3815 GLU Chi-restraints excluded: chain A residue 4052 MET Chi-restraints excluded: chain A residue 4814 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 108 HIS Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 108 HIS Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2983 LEU Chi-restraints excluded: chain B residue 3050 LEU Chi-restraints excluded: chain B residue 3128 VAL Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3798 GLN Chi-restraints excluded: chain B residue 3815 GLU Chi-restraints excluded: chain B residue 4672 MET Chi-restraints excluded: chain B residue 4814 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2843 MET Chi-restraints excluded: chain C residue 2931 ARG Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3128 VAL Chi-restraints excluded: chain C residue 3174 HIS Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3220 GLU Chi-restraints excluded: chain C residue 3798 GLN Chi-restraints excluded: chain C residue 3815 GLU 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 669 GLN Chi-restraints excluded: chain D residue 913 ARG Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 2890 GLN Chi-restraints excluded: chain D residue 3128 VAL Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3797 MET Chi-restraints excluded: chain D residue 3798 GLN Chi-restraints excluded: chain D residue 3815 GLU Chi-restraints excluded: chain D residue 4814 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 5.9990 chunk 1126 optimal weight: 5.9990 chunk 1510 optimal weight: 4.9990 chunk 434 optimal weight: 10.0000 chunk 1307 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 1420 optimal weight: 3.9990 chunk 594 optimal weight: 0.0870 chunk 1458 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4514 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D 932 ASN ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.038131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.027605 restraints weight = 2102464.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.028622 restraints weight = 873198.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.029055 restraints weight = 536227.528| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.791 146532 Z= 0.622 Angle : 0.592 20.802 197928 Z= 0.295 Chirality : 0.039 0.283 21684 Planarity : 0.004 0.119 25468 Dihedral : 5.318 87.817 19662 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 0.79 % Allowed : 7.89 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.06), residues: 17804 helix: 2.03 (0.06), residues: 9304 sheet: 0.08 (0.13), residues: 1576 loop : -0.33 (0.08), residues: 6924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP D3587 HIS 0.020 0.001 HIS C3111 PHE 0.050 0.001 PHE C3117 TYR 0.035 0.001 TYR D4567 ARG 0.019 0.000 ARG B2824 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30867.34 seconds wall clock time: 545 minutes 40.44 seconds (32740.44 seconds total)