Starting phenix.real_space_refine on Sat Apr 13 17:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxe_42761/04_2024/8uxe_42761_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxe_42761/04_2024/8uxe_42761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxe_42761/04_2024/8uxe_42761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxe_42761/04_2024/8uxe_42761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxe_42761/04_2024/8uxe_42761_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxe_42761/04_2024/8uxe_42761_neut_updated.pdb" } resolution = 3.53 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= 0.017 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 940 5.16 5 C 88276 2.51 5 N 23592 2.21 5 O 25856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A GLU 928": "OE1" <-> "OE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1309": "OE1" <-> "OE2" Residue "A TYR 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1946": "OE1" <-> "OE2" Residue "A GLU 2315": "OE1" <-> "OE2" Residue "A ASP 2511": "OD1" <-> "OD2" Residue "A ASP 2679": "OD1" <-> "OD2" Residue "A ASP 2696": "OD1" <-> "OD2" Residue "A GLU 2794": "OE1" <-> "OE2" Residue "A ASP 2885": "OD1" <-> "OD2" Residue "A GLU 2952": "OE1" <-> "OE2" Residue "A ARG 3150": "NH1" <-> "NH2" Residue "A TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3337": "OE1" <-> "OE2" Residue "A TYR 3609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4089": "OE1" <-> "OE2" Residue "A GLU 4184": "OE1" <-> "OE2" Residue "A PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4562": "OE1" <-> "OE2" Residue "A GLU 4668": "OE1" <-> "OE2" Residue "A ASP 4691": "OD1" <-> "OD2" Residue "A ASP 4837": "OD1" <-> "OD2" Residue "A GLU 4906": "OE1" <-> "OE2" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 891": "OE1" <-> "OE2" Residue "B GLU 928": "OE1" <-> "OE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1309": "OE1" <-> "OE2" Residue "B TYR 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1946": "OE1" <-> "OE2" Residue "B GLU 2315": "OE1" <-> "OE2" Residue "B ASP 2511": "OD1" <-> "OD2" Residue "B ASP 2679": "OD1" <-> "OD2" Residue "B ASP 2696": "OD1" <-> "OD2" Residue "B GLU 2794": "OE1" <-> "OE2" Residue "B ASP 2885": "OD1" <-> "OD2" Residue "B GLU 2952": "OE1" <-> "OE2" Residue "B ARG 3150": "NH1" <-> "NH2" Residue "B TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3337": "OE1" <-> "OE2" Residue "B TYR 3609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4089": "OE1" <-> "OE2" Residue "B GLU 4184": "OE1" <-> "OE2" Residue "B PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4562": "OE1" <-> "OE2" Residue "B GLU 4668": "OE1" <-> "OE2" Residue "B ASP 4691": "OD1" <-> "OD2" Residue "B ASP 4837": "OD1" <-> "OD2" Residue "B GLU 4906": "OE1" <-> "OE2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "C PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 891": "OE1" <-> "OE2" Residue "C GLU 928": "OE1" <-> "OE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1309": "OE1" <-> "OE2" Residue "C TYR 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1946": "OE1" <-> "OE2" Residue "C GLU 2315": "OE1" <-> "OE2" Residue "C ASP 2511": "OD1" <-> "OD2" Residue "C ASP 2679": "OD1" <-> "OD2" Residue "C ASP 2696": "OD1" <-> "OD2" Residue "C GLU 2794": "OE1" <-> "OE2" Residue "C ASP 2885": "OD1" <-> "OD2" Residue "C GLU 2952": "OE1" <-> "OE2" Residue "C ARG 3150": "NH1" <-> "NH2" Residue "C TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3337": "OE1" <-> "OE2" Residue "C TYR 3609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4089": "OE1" <-> "OE2" Residue "C GLU 4184": "OE1" <-> "OE2" Residue "C PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4562": "OE1" <-> "OE2" Residue "C GLU 4668": "OE1" <-> "OE2" Residue "C ASP 4691": "OD1" <-> "OD2" Residue "C ASP 4837": "OD1" <-> "OD2" Residue "C GLU 4906": "OE1" <-> "OE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 676": "OE1" <-> "OE2" Residue "D PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "D GLU 928": "OE1" <-> "OE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1309": "OE1" <-> "OE2" Residue "D TYR 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1946": "OE1" <-> "OE2" Residue "D GLU 2315": "OE1" <-> "OE2" Residue "D ASP 2511": "OD1" <-> "OD2" Residue "D ASP 2679": "OD1" <-> "OD2" Residue "D ASP 2696": "OD1" <-> "OD2" Residue "D GLU 2794": "OE1" <-> "OE2" Residue "D ASP 2885": "OD1" <-> "OD2" Residue "D GLU 2952": "OE1" <-> "OE2" Residue "D ARG 3150": "NH1" <-> "NH2" Residue "D TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3337": "OE1" <-> "OE2" Residue "D TYR 3609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4089": "OE1" <-> "OE2" Residue "D GLU 4184": "OE1" <-> "OE2" Residue "D PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4562": "OE1" <-> "OE2" Residue "D GLU 4668": "OE1" <-> "OE2" Residue "D ASP 4691": "OD1" <-> "OD2" Residue "D ASP 4837": "OD1" <-> "OD2" Residue "D GLU 4906": "OE1" <-> "OE2" Time to flip residues: 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 138692 Number of models: 1 Model: "" Number of chains: 12 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: "A" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "B" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "C" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "D" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36362 SG CYS A4888 175.906 202.309 87.793 1.00110.41 S ATOM 36387 SG CYS A4891 178.457 202.176 90.562 1.00101.79 S ATOM 70131 SG CYS B4888 174.443 175.907 87.838 1.00110.41 S ATOM 70156 SG CYS B4891 174.578 178.448 90.616 1.00101.79 S ATOM A030C SG CYS C4888 200.842 174.438 87.832 1.00110.41 S ATOM A0311 SG CYS C4891 198.300 174.573 90.610 1.00101.79 S ATOM A0T2D SG CYS D4888 202.292 200.829 87.841 1.00110.41 S ATOM A0T32 SG CYS D4891 202.158 198.287 90.619 1.00101.79 S Time building chain proxies: 94.73, per 1000 atoms: 0.68 Number of scatterers: 138692 At special positions: 0 Unit cell: (377.576, 377.576, 211.709, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 940 16.00 P 24 15.00 O 25856 8.00 N 23592 7.00 C 88276 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: 44.55 Conformation dependent library (CDL) restraints added in 33.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32464 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 716 helices and 80 sheets defined 59.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 38.44 Creating SS restraints... Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.084A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.876A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.085A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.876A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.084A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.876A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.084A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.876A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.596A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.742A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 5.012A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 271' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.557A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.033A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.713A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.816A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.672A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.133A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.973A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.723A 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: 3.655A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.513A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.771A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.719A 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: 4.575A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.998A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 4.401A pdb=" N VAL A 919 " --> pdb=" O HIS A 915 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.440A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 4.206A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.801A pdb=" N LYS A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.855A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.922A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.513A 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: 6.891A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.661A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1494 Processing helix chain 'A' and resid 1498 through 1503 removed outlier: 3.766A pdb=" N ASN A1502 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 3.818A 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: 3.790A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.180A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.629A 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: 3.589A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.836A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 removed outlier: 3.637A pdb=" N HIS A1710 " --> pdb=" O LEU A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1722 Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.637A pdb=" N SER A1735 " --> pdb=" O GLU A1731 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 4.265A pdb=" N GLN A1777 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 5.336A 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: 4.156A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) removed outlier: 3.617A 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 1835 through 1847 removed outlier: 4.134A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 4.009A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1901 through 1948 removed outlier: 4.207A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1960 removed outlier: 4.453A pdb=" N THR A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA A1959 " --> pdb=" O ALA A1955 " (cutoff:3.500A) Processing helix chain 'A' and resid 1962 through 1967 removed outlier: 4.577A pdb=" N ARG A1966 " --> pdb=" O THR A1962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 3.792A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.677A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.772A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.801A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A2129 " --> pdb=" O GLN A2125 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.545A 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 2182 Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.535A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.210A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.182A 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: 3.578A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) removed outlier: 3.549A 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 2292 through 2307 removed outlier: 3.915A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2332 through 2337 removed outlier: 5.092A pdb=" N GLY A2337 " --> pdb=" O PRO A2333 " (cutoff:3.500A) Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 3.518A pdb=" N ILE A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2439 removed outlier: 5.595A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2460 removed outlier: 4.652A pdb=" N GLY A2459 " --> pdb=" O ASP A2455 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE A2460 " --> pdb=" O MET A2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2455 through 2460' Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.662A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 3.860A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2510 removed outlier: 3.993A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2510' Processing helix chain 'A' and resid 2511 through 2532 removed outlier: 5.396A 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: 5.227A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 3.650A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2584 through 2593 removed outlier: 4.783A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2618 removed outlier: 3.988A pdb=" N LYS A2604 " --> pdb=" O ASN A2600 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N MET A2605 " --> pdb=" O GLU A2601 " (cutoff:3.500A) Proline residue: A2606 - end of helix Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.082A 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 2690 through 2696 removed outlier: 4.657A pdb=" N SER A2694 " --> pdb=" O GLU A2690 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A2696 " --> pdb=" O GLN A2692 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2740 removed outlier: 3.773A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2786 Proline residue: A2774 - end of helix removed outlier: 3.683A pdb=" N GLY A2786 " --> pdb=" O MET A2782 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2827 through 2832 removed outlier: 5.153A pdb=" N THR A2832 " --> pdb=" O MET A2828 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.325A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2881 through 2900 removed outlier: 4.608A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A2888 " --> pdb=" O LYS A2884 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2945 removed outlier: 4.373A pdb=" N GLY A2945 " --> pdb=" O LEU A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.646A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.923A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.700A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) Processing helix chain 'A' and resid 3042 through 3048 Processing helix chain 'A' and resid 3050 through 3078 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.847A 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 removed outlier: 3.506A pdb=" N LEU A3121 " --> pdb=" O PHE A3117 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A3122 " --> pdb=" O GLY A3118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3117 through 3122' Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.300A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3150 removed outlier: 3.749A pdb=" N GLU A3149 " --> pdb=" O SER A3145 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3145 through 3150' Processing helix chain 'A' and resid 3151 through 3166 removed outlier: 3.596A pdb=" N ALA A3165 " --> pdb=" O ALA A3161 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A3166 " --> pdb=" O PHE A3162 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3180 removed outlier: 4.287A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3175 through 3180' Processing helix chain 'A' and resid 3182 through 3188 Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.712A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 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 3236 through 3254 Proline residue: A3240 - end of helix removed outlier: 4.725A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N HIS A3252 " --> pdb=" O ARG A3248 " (cutoff:3.500A) Proline residue: A3254 - end of helix Processing helix chain 'A' and resid 3269 through 3291 Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.454A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 6.204A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3330 removed outlier: 5.408A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix Processing helix chain 'A' and resid 3599 through 3605 removed outlier: 4.535A pdb=" N MET A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3613 through 3628 Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.791A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.613A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.863A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.960A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.735A pdb=" N ILE A3744 " --> pdb=" O VAL A3740 " (cutoff:3.500A) removed outlier: 3.872A 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: 4.575A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3826 through 3848 removed outlier: 4.978A pdb=" N LEU A3830 " --> pdb=" O GLY A3826 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A3831 " --> pdb=" O GLU A3827 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A3832 " --> pdb=" O LYS A3828 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP A3833 " --> pdb=" O VAL A3829 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU A3834 " --> pdb=" O LEU A3830 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE A3835 " --> pdb=" O GLN A3831 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.563A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.436A 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: 3.711A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.859A 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 4029 removed outlier: 4.346A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.798A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4070 Processing helix chain 'A' and resid 4079 through 4110 Proline residue: A4090 - end of helix Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 Processing helix chain 'A' and resid 4124 through 4131 removed outlier: 3.613A pdb=" N GLN A4130 " --> pdb=" O LEU A4126 " (cutoff:3.500A) 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 4181 through 4208 removed outlier: 4.839A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4260 removed outlier: 4.165A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4273 removed outlier: 4.282A pdb=" N LYS A4273 " --> pdb=" O LYS A4269 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.868A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 3.675A pdb=" N ILE A4485 " --> pdb=" O TRP A4481 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.247A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4566 through 4612 Proline residue: A4570 - end of helix removed outlier: 4.389A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.338A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4674 through 4683 removed outlier: 4.231A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A4679 " --> pdb=" O ALA A4675 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.490A 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: 3.882A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.604A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.550A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 3.874A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A4823 " --> pdb=" O VAL A4819 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4832 removed outlier: 4.274A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A4832 " --> pdb=" O GLY A4828 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.071A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 2594 through 2599 Proline residue: A2597 - end of helix No H-bonds generated for 'chain 'A' and resid 2594 through 2599' 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: 3.596A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.742A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 5.011A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 271' Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.555A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.033A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.713A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.816A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.672A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.133A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.973A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.722A 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: 3.655A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.513A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.771A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.718A 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: 4.575A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.998A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 4.400A pdb=" N VAL B 919 " --> pdb=" O HIS B 915 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B 920 " --> pdb=" O PRO B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 915 through 920' Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.441A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 4.205A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.801A pdb=" N LYS B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.855A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.922A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.513A 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: 6.891A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.662A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1494 Processing helix chain 'B' and resid 1498 through 1503 removed outlier: 3.765A pdb=" N ASN B1502 " --> pdb=" O GLN B1498 " (cutoff:3.500A) removed outlier: 3.818A 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: 3.790A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.180A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.629A 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: 3.590A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.836A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 removed outlier: 3.637A pdb=" N HIS B1710 " --> pdb=" O LEU B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1722 Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.637A pdb=" N SER B1735 " --> pdb=" O GLU B1731 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1773 through 1778 removed outlier: 4.265A pdb=" N GLN B1777 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 5.337A 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: 4.156A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) removed outlier: 3.618A 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 1835 through 1847 removed outlier: 4.134A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 4.009A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1901 through 1948 removed outlier: 4.206A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1960 removed outlier: 4.454A pdb=" N THR B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA B1959 " --> pdb=" O ALA B1955 " (cutoff:3.500A) Processing helix chain 'B' and resid 1962 through 1967 removed outlier: 4.578A pdb=" N ARG B1966 " --> pdb=" O THR B1962 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 3.792A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.677A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.772A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.801A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B2129 " --> pdb=" O GLN B2125 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.546A 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 2182 Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.535A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.211A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.182A 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: 3.578A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) removed outlier: 3.549A 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 2292 through 2307 removed outlier: 3.915A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B2298 " --> pdb=" O GLU B2294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2332 through 2337 removed outlier: 5.091A pdb=" N GLY B2337 " --> pdb=" O PRO B2333 " (cutoff:3.500A) Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2377 through 2382 removed outlier: 3.518A pdb=" N ILE B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2439 removed outlier: 5.596A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2455 through 2460 removed outlier: 4.653A pdb=" N GLY B2459 " --> pdb=" O ASP B2455 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE B2460 " --> pdb=" O MET B2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2455 through 2460' Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.663A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 3.861A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2510 removed outlier: 3.993A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2510' Processing helix chain 'B' and resid 2511 through 2532 removed outlier: 5.396A 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: 5.226A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 3.650A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2584 through 2593 removed outlier: 4.784A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) Processing helix chain 'B' and resid 2600 through 2618 removed outlier: 3.988A pdb=" N LYS B2604 " --> pdb=" O ASN B2600 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N MET B2605 " --> pdb=" O GLU B2601 " (cutoff:3.500A) Proline residue: B2606 - end of helix Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.082A 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 2690 through 2696 removed outlier: 4.657A pdb=" N SER B2694 " --> pdb=" O GLU B2690 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B2696 " --> pdb=" O GLN B2692 " (cutoff:3.500A) Processing helix chain 'B' and resid 2715 through 2740 removed outlier: 3.773A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2766 through 2786 Proline residue: B2774 - end of helix removed outlier: 3.684A pdb=" N GLY B2786 " --> pdb=" O MET B2782 " (cutoff:3.500A) Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2827 through 2832 removed outlier: 5.152A pdb=" N THR B2832 " --> pdb=" O MET B2828 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.324A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2881 through 2900 removed outlier: 4.607A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS B2888 " --> pdb=" O LYS B2884 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2945 removed outlier: 4.372A pdb=" N GLY B2945 " --> pdb=" O LEU B2941 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.646A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.922A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.700A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) Processing helix chain 'B' and resid 3042 through 3048 Processing helix chain 'B' and resid 3050 through 3078 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.846A 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 removed outlier: 3.506A pdb=" N LEU B3121 " --> pdb=" O PHE B3117 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B3122 " --> pdb=" O GLY B3118 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3117 through 3122' Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.300A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3150 removed outlier: 3.749A pdb=" N GLU B3149 " --> pdb=" O SER B3145 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3145 through 3150' Processing helix chain 'B' and resid 3151 through 3166 removed outlier: 3.596A pdb=" N ALA B3165 " --> pdb=" O ALA B3161 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE B3166 " --> pdb=" O PHE B3162 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3180 removed outlier: 4.286A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3175 through 3180' Processing helix chain 'B' and resid 3182 through 3188 Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.712A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 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 3236 through 3254 Proline residue: B3240 - end of helix removed outlier: 4.725A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS B3252 " --> pdb=" O ARG B3248 " (cutoff:3.500A) Proline residue: B3254 - end of helix Processing helix chain 'B' and resid 3269 through 3291 Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.453A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 6.203A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3330 removed outlier: 5.408A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix Processing helix chain 'B' and resid 3599 through 3605 removed outlier: 4.536A pdb=" N MET B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3613 through 3628 Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.791A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.614A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.862A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.960A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.735A pdb=" N ILE B3744 " --> pdb=" O VAL B3740 " (cutoff:3.500A) removed outlier: 3.872A 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: 4.575A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3826 through 3848 removed outlier: 4.978A pdb=" N LEU B3830 " --> pdb=" O GLY B3826 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B3831 " --> pdb=" O GLU B3827 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B3832 " --> pdb=" O LYS B3828 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP B3833 " --> pdb=" O VAL B3829 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU B3834 " --> pdb=" O LEU B3830 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE B3835 " --> pdb=" O GLN B3831 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.563A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.436A 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: 3.711A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.859A 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 4029 removed outlier: 4.346A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.798A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4070 Processing helix chain 'B' and resid 4079 through 4110 Proline residue: B4090 - end of helix Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 Processing helix chain 'B' and resid 4124 through 4131 removed outlier: 3.614A pdb=" N GLN B4130 " --> pdb=" O LEU B4126 " (cutoff:3.500A) 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 4181 through 4208 removed outlier: 4.840A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4260 removed outlier: 4.165A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4273 removed outlier: 4.282A pdb=" N LYS B4273 " --> pdb=" O LYS B4269 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.867A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 3.674A pdb=" N ILE B4485 " --> pdb=" O TRP B4481 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.247A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4566 through 4612 Proline residue: B4570 - end of helix removed outlier: 4.389A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.338A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4674 through 4683 removed outlier: 4.231A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B4679 " --> pdb=" O ALA B4675 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.491A 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: 3.882A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.604A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.550A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 3.873A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B4823 " --> pdb=" O VAL B4819 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4832 removed outlier: 4.274A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU B4832 " --> pdb=" O GLY B4828 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.071A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 2594 through 2599 Proline residue: B2597 - end of helix No H-bonds generated for 'chain 'B' and resid 2594 through 2599' 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: 3.596A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.742A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 5.012A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 271' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.556A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.032A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.713A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.816A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.671A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.133A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.974A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 5.723A 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: 3.655A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.513A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.771A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.718A 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: 4.576A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.107A 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: 4.997A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 4.400A pdb=" N VAL C 919 " --> pdb=" O HIS C 915 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU C 920 " --> pdb=" O PRO C 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 915 through 920' Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.441A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 4.206A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 4.801A pdb=" N LYS C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.855A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.922A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.514A 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: 6.891A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.661A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1494 Processing helix chain 'C' and resid 1498 through 1503 removed outlier: 3.766A pdb=" N ASN C1502 " --> pdb=" O GLN C1498 " (cutoff:3.500A) removed outlier: 3.817A 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: 3.790A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.181A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.629A 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: 3.589A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.837A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 removed outlier: 3.637A pdb=" N HIS C1710 " --> pdb=" O LEU C1706 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1722 Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.637A pdb=" N SER C1735 " --> pdb=" O GLU C1731 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1773 through 1778 removed outlier: 4.265A pdb=" N GLN C1777 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 5.336A 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: 4.156A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) removed outlier: 3.617A 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 1835 through 1847 removed outlier: 4.134A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 4.008A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1901 through 1948 removed outlier: 4.207A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1960 removed outlier: 4.454A pdb=" N THR C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA C1959 " --> pdb=" O ALA C1955 " (cutoff:3.500A) Processing helix chain 'C' and resid 1962 through 1967 removed outlier: 4.577A pdb=" N ARG C1966 " --> pdb=" O THR C1962 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 3.792A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.677A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.772A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.801A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C2129 " --> pdb=" O GLN C2125 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.545A 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 2182 Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.535A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.211A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.183A 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: 3.578A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) removed outlier: 3.549A 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 2292 through 2307 removed outlier: 3.915A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C2298 " --> pdb=" O GLU C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2332 through 2337 removed outlier: 5.091A pdb=" N GLY C2337 " --> pdb=" O PRO C2333 " (cutoff:3.500A) Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2377 through 2382 removed outlier: 3.518A pdb=" N ILE C2382 " --> pdb=" O GLU C2378 " (cutoff:3.500A) Processing helix chain 'C' and resid 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2439 removed outlier: 5.596A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2455 through 2460 removed outlier: 4.653A pdb=" N GLY C2459 " --> pdb=" O ASP C2455 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE C2460 " --> pdb=" O MET C2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2455 through 2460' Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.662A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 3.861A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2510 removed outlier: 3.993A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2510' Processing helix chain 'C' and resid 2511 through 2532 removed outlier: 5.395A 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: 5.227A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 3.650A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2584 through 2593 removed outlier: 4.783A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) Processing helix chain 'C' and resid 2600 through 2618 removed outlier: 3.988A pdb=" N LYS C2604 " --> pdb=" O ASN C2600 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N MET C2605 " --> pdb=" O GLU C2601 " (cutoff:3.500A) Proline residue: C2606 - end of helix Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.081A 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 2690 through 2696 removed outlier: 4.658A pdb=" N SER C2694 " --> pdb=" O GLU C2690 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C2696 " --> pdb=" O GLN C2692 " (cutoff:3.500A) Processing helix chain 'C' and resid 2715 through 2740 removed outlier: 3.773A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2766 through 2786 Proline residue: C2774 - end of helix removed outlier: 3.683A pdb=" N GLY C2786 " --> pdb=" O MET C2782 " (cutoff:3.500A) Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2827 through 2832 removed outlier: 5.154A pdb=" N THR C2832 " --> pdb=" O MET C2828 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.324A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2881 through 2900 removed outlier: 4.607A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS C2888 " --> pdb=" O LYS C2884 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2945 removed outlier: 4.373A pdb=" N GLY C2945 " --> pdb=" O LEU C2941 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.646A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.923A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.700A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) Processing helix chain 'C' and resid 3042 through 3048 Processing helix chain 'C' and resid 3050 through 3078 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.847A 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 removed outlier: 3.506A pdb=" N LEU C3121 " --> pdb=" O PHE C3117 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE C3122 " --> pdb=" O GLY C3118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3117 through 3122' Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.300A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3150 removed outlier: 3.749A pdb=" N GLU C3149 " --> pdb=" O SER C3145 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3145 through 3150' Processing helix chain 'C' and resid 3151 through 3166 removed outlier: 3.597A pdb=" N ALA C3165 " --> pdb=" O ALA C3161 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C3166 " --> pdb=" O PHE C3162 " (cutoff:3.500A) Processing helix chain 'C' and resid 3175 through 3180 removed outlier: 4.286A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3175 through 3180' Processing helix chain 'C' and resid 3182 through 3188 Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.712A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 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 3236 through 3254 Proline residue: C3240 - end of helix removed outlier: 4.726A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N HIS C3252 " --> pdb=" O ARG C3248 " (cutoff:3.500A) Proline residue: C3254 - end of helix Processing helix chain 'C' and resid 3269 through 3291 Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.453A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 6.203A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3330 removed outlier: 5.409A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix Processing helix chain 'C' and resid 3599 through 3605 removed outlier: 4.535A pdb=" N MET C3605 " --> pdb=" O ALA C3601 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3613 through 3628 Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.790A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.613A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.862A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.959A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.735A pdb=" N ILE C3744 " --> pdb=" O VAL C3740 " (cutoff:3.500A) removed outlier: 3.872A 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: 4.575A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3826 through 3848 removed outlier: 4.979A pdb=" N LEU C3830 " --> pdb=" O GLY C3826 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C3831 " --> pdb=" O GLU C3827 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP C3832 " --> pdb=" O LYS C3828 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP C3833 " --> pdb=" O VAL C3829 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU C3834 " --> pdb=" O LEU C3830 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE C3835 " --> pdb=" O GLN C3831 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.564A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.436A 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: 3.711A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.859A 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 4029 removed outlier: 4.346A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.798A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4070 Processing helix chain 'C' and resid 4079 through 4110 Proline residue: C4090 - end of helix Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 Processing helix chain 'C' and resid 4124 through 4131 removed outlier: 3.613A pdb=" N GLN C4130 " --> pdb=" O LEU C4126 " (cutoff:3.500A) 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 4181 through 4208 removed outlier: 4.839A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4260 removed outlier: 4.164A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4273 removed outlier: 4.282A pdb=" N LYS C4273 " --> pdb=" O LYS C4269 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.867A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 3.675A pdb=" N ILE C4485 " --> pdb=" O TRP C4481 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.247A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4566 through 4612 Proline residue: C4570 - end of helix removed outlier: 4.388A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.339A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4674 through 4683 removed outlier: 4.231A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C4679 " --> pdb=" O ALA C4675 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.491A 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: 3.882A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.604A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.550A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 3.874A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C4823 " --> pdb=" O VAL C4819 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4832 removed outlier: 4.274A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU C4832 " --> pdb=" O GLY C4828 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.071A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 2594 through 2599 Proline residue: C2597 - end of helix No H-bonds generated for 'chain 'C' and resid 2594 through 2599' 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: 3.597A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.742A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 5.012A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 271' Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.556A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.033A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.713A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.816A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.672A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.133A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.973A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 5.722A 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: 3.654A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.513A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.771A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.719A 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: 4.575A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.998A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 4.400A pdb=" N VAL D 919 " --> pdb=" O HIS D 915 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU D 920 " --> pdb=" O PRO D 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 915 through 920' Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.440A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 4.206A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.802A pdb=" N LYS D 987 " --> pdb=" O LEU D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.854A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.922A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.512A 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: 6.891A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.662A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1494 Processing helix chain 'D' and resid 1498 through 1503 removed outlier: 3.767A pdb=" N ASN D1502 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 3.817A 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: 3.790A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.180A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.629A 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: 3.589A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.836A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 removed outlier: 3.637A pdb=" N HIS D1710 " --> pdb=" O LEU D1706 " (cutoff:3.500A) Processing helix chain 'D' and resid 1711 through 1722 Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.636A pdb=" N SER D1735 " --> pdb=" O GLU D1731 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1773 through 1778 removed outlier: 4.264A pdb=" N GLN D1777 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 5.337A 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: 4.156A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) removed outlier: 3.617A 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 1835 through 1847 removed outlier: 4.133A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 4.009A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1901 through 1948 removed outlier: 4.206A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1954 through 1960 removed outlier: 4.453A pdb=" N THR D1958 " --> pdb=" O SER D1954 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA D1959 " --> pdb=" O ALA D1955 " (cutoff:3.500A) Processing helix chain 'D' and resid 1962 through 1967 removed outlier: 4.577A pdb=" N ARG D1966 " --> pdb=" O THR D1962 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 3.791A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.677A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.773A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.802A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D2129 " --> pdb=" O GLN D2125 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.546A 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 2182 Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.535A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.210A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.182A 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: 3.578A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) removed outlier: 3.549A 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 2292 through 2307 removed outlier: 3.915A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D2298 " --> pdb=" O GLU D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2332 through 2337 removed outlier: 5.092A pdb=" N GLY D2337 " --> pdb=" O PRO D2333 " (cutoff:3.500A) Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2377 through 2382 removed outlier: 3.519A pdb=" N ILE D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) Processing helix chain 'D' and resid 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2439 removed outlier: 5.595A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2455 through 2460 removed outlier: 4.652A pdb=" N GLY D2459 " --> pdb=" O ASP D2455 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE D2460 " --> pdb=" O MET D2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2455 through 2460' Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.662A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 3.860A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2510 removed outlier: 3.993A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2510' Processing helix chain 'D' and resid 2511 through 2532 removed outlier: 5.396A 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: 5.227A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 3.650A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2584 through 2593 removed outlier: 4.783A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) Processing helix chain 'D' and resid 2600 through 2618 removed outlier: 3.988A pdb=" N LYS D2604 " --> pdb=" O ASN D2600 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N MET D2605 " --> pdb=" O GLU D2601 " (cutoff:3.500A) Proline residue: D2606 - end of helix Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.081A 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 2690 through 2696 removed outlier: 4.657A pdb=" N SER D2694 " --> pdb=" O GLU D2690 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP D2696 " --> pdb=" O GLN D2692 " (cutoff:3.500A) Processing helix chain 'D' and resid 2715 through 2740 removed outlier: 3.773A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2766 through 2786 Proline residue: D2774 - end of helix removed outlier: 3.684A pdb=" N GLY D2786 " --> pdb=" O MET D2782 " (cutoff:3.500A) Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2827 through 2832 removed outlier: 5.153A pdb=" N THR D2832 " --> pdb=" O MET D2828 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.324A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2881 through 2900 removed outlier: 4.608A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS D2888 " --> pdb=" O LYS D2884 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2945 removed outlier: 4.372A pdb=" N GLY D2945 " --> pdb=" O LEU D2941 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.646A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.923A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.700A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) Processing helix chain 'D' and resid 3042 through 3048 Processing helix chain 'D' and resid 3050 through 3078 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.847A 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 removed outlier: 3.506A pdb=" N LEU D3121 " --> pdb=" O PHE D3117 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D3122 " --> pdb=" O GLY D3118 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3117 through 3122' Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.299A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3150 removed outlier: 3.750A pdb=" N GLU D3149 " --> pdb=" O SER D3145 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3145 through 3150' Processing helix chain 'D' and resid 3151 through 3166 removed outlier: 3.597A pdb=" N ALA D3165 " --> pdb=" O ALA D3161 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE D3166 " --> pdb=" O PHE D3162 " (cutoff:3.500A) Processing helix chain 'D' and resid 3175 through 3180 removed outlier: 4.287A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3175 through 3180' Processing helix chain 'D' and resid 3182 through 3188 Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.713A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 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 3236 through 3254 Proline residue: D3240 - end of helix removed outlier: 4.725A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N HIS D3252 " --> pdb=" O ARG D3248 " (cutoff:3.500A) Proline residue: D3254 - end of helix Processing helix chain 'D' and resid 3269 through 3291 Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.453A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 6.204A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3330 removed outlier: 5.408A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix Processing helix chain 'D' and resid 3599 through 3605 removed outlier: 4.536A pdb=" N MET D3605 " --> pdb=" O ALA D3601 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3613 through 3628 Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.791A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.613A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.862A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.959A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.736A pdb=" N ILE D3744 " --> pdb=" O VAL D3740 " (cutoff:3.500A) removed outlier: 3.872A 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: 4.575A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3826 through 3848 removed outlier: 4.979A pdb=" N LEU D3830 " --> pdb=" O GLY D3826 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D3831 " --> pdb=" O GLU D3827 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP D3832 " --> pdb=" O LYS D3828 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP D3833 " --> pdb=" O VAL D3829 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU D3834 " --> pdb=" O LEU D3830 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE D3835 " --> pdb=" O GLN D3831 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.563A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.436A 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: 3.711A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.859A 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 4029 removed outlier: 4.347A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.798A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4070 Processing helix chain 'D' and resid 4079 through 4110 Proline residue: D4090 - end of helix Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 Processing helix chain 'D' and resid 4124 through 4131 removed outlier: 3.613A pdb=" N GLN D4130 " --> pdb=" O LEU D4126 " (cutoff:3.500A) 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 4181 through 4208 removed outlier: 4.840A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4260 removed outlier: 4.164A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4273 removed outlier: 4.282A pdb=" N LYS D4273 " --> pdb=" O LYS D4269 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.867A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 3.674A pdb=" N ILE D4485 " --> pdb=" O TRP D4481 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.248A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4566 through 4612 Proline residue: D4570 - end of helix removed outlier: 4.389A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.337A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4674 through 4683 removed outlier: 4.231A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE D4679 " --> pdb=" O ALA D4675 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.490A 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: 3.882A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.604A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.550A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 3.873A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D4823 " --> pdb=" O VAL D4819 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4832 removed outlier: 4.274A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU D4832 " --> pdb=" O GLY D4828 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.072A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 2594 through 2599 Proline residue: D2597 - end of helix No H-bonds generated for 'chain 'D' and resid 2594 through 2599' 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 sheet with id= 1, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.568A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP E 101 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.567A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP F 101 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.567A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP G 101 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.567A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP H 101 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.505A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.213A 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= 6, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.716A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= 8, first strand: chain 'A' and resid 260 through 264 removed outlier: 5.800A pdb=" N LEU A 236 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N VAL A 247 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 15.115A pdb=" N LEU A 234 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id= 10, first strand: chain 'A' and resid 329 through 332 Processing sheet with id= 11, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 12, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.590A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.766A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 15, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.452A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 948 through 952 Processing sheet with id= 17, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 3.944A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 1268 through 1275 removed outlier: 5.390A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.963A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 2741 through 2744 Processing sheet with id= 21, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 3.926A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.903A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'A' and resid 233 through 238 removed outlier: 5.932A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.504A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.214A 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= 25, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.715A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= 27, first strand: chain 'B' and resid 260 through 264 removed outlier: 5.800A pdb=" N LEU B 236 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N VAL B 247 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 15.115A pdb=" N LEU B 234 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 304 through 308 Processing sheet with id= 29, first strand: chain 'B' and resid 329 through 332 Processing sheet with id= 30, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 31, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.590A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.767A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 34, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.451A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 948 through 952 Processing sheet with id= 36, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 3.944A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 1268 through 1275 removed outlier: 5.390A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 1307 through 1310 removed outlier: 4.963A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 2741 through 2744 Processing sheet with id= 40, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 3.926A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.902A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 233 through 238 removed outlier: 5.932A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.505A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.091A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.715A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= 46, first strand: chain 'C' and resid 260 through 264 removed outlier: 5.800A pdb=" N LEU C 236 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N VAL C 247 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 15.116A pdb=" N LEU C 234 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 304 through 308 Processing sheet with id= 48, first strand: chain 'C' and resid 329 through 332 Processing sheet with id= 49, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 50, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.590A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.766A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 53, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.451A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 948 through 952 Processing sheet with id= 55, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 3.944A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 1268 through 1275 removed outlier: 5.390A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 1307 through 1310 removed outlier: 4.963A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 2741 through 2744 Processing sheet with id= 59, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 3.925A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.903A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'C' and resid 233 through 238 removed outlier: 5.933A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.504A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.090A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.715A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 193 through 196 Processing sheet with id= 65, first strand: chain 'D' and resid 260 through 264 removed outlier: 5.800A pdb=" N LEU D 236 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N VAL D 247 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 15.115A pdb=" N LEU D 234 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 304 through 308 Processing sheet with id= 67, first strand: chain 'D' and resid 329 through 332 Processing sheet with id= 68, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 69, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.590A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.766A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 72, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.452A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 948 through 952 Processing sheet with id= 74, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 3.944A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 1268 through 1275 removed outlier: 5.390A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 1307 through 1310 removed outlier: 4.963A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 2741 through 2744 Processing sheet with id= 78, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 3.925A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.903A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 233 through 238 removed outlier: 5.932A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) 7392 hydrogen bonds defined for protein. 22060 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: 115.46 Time building geometry restraints manager: 49.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 44559 1.34 - 1.46: 29988 1.46 - 1.58: 65617 1.58 - 1.71: 36 1.71 - 1.83: 1520 Bond restraints: 141720 Sorted by residual: bond pdb=" N ILE A 898 " pdb=" CA ILE A 898 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.49e+00 bond pdb=" N ILE D 898 " pdb=" CA ILE D 898 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.22e+00 bond pdb=" N ILE B 898 " pdb=" CA ILE B 898 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.22e+00 bond pdb=" N ILE C 898 " pdb=" CA ILE C 898 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.22e+00 bond pdb=" N ILE B1012 " pdb=" CA ILE B1012 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.01e+00 ... (remaining 141715 not shown) Histogram of bond angle deviations from ideal: 95.99 - 104.78: 2528 104.78 - 113.56: 78870 113.56 - 122.35: 91241 122.35 - 131.13: 18235 131.13 - 139.92: 610 Bond angle restraints: 191484 Sorted by residual: angle pdb=" PB ATP D5003 " pdb=" O3B ATP D5003 " pdb=" PG ATP D5003 " ideal model delta sigma weight residual 139.87 130.60 9.27 1.00e+00 1.00e+00 8.59e+01 angle pdb=" PB ATP B5003 " pdb=" O3B ATP B5003 " pdb=" PG ATP B5003 " ideal model delta sigma weight residual 139.87 130.63 9.24 1.00e+00 1.00e+00 8.54e+01 angle pdb=" PB ATP A5003 " pdb=" O3B ATP A5003 " pdb=" PG ATP A5003 " ideal model delta sigma weight residual 139.87 130.66 9.21 1.00e+00 1.00e+00 8.47e+01 angle pdb=" PB ATP C5003 " pdb=" O3B ATP C5003 " pdb=" PG ATP C5003 " ideal model delta sigma weight residual 139.87 130.67 9.20 1.00e+00 1.00e+00 8.46e+01 angle pdb=" CA GLU A3262 " pdb=" CB GLU A3262 " pdb=" CG GLU A3262 " ideal model delta sigma weight residual 114.10 129.31 -15.21 2.00e+00 2.50e-01 5.78e+01 ... (remaining 191479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.38: 82475 30.38 - 60.75: 2649 60.75 - 91.13: 332 91.13 - 121.51: 12 121.51 - 151.89: 16 Dihedral angle restraints: 85484 sinusoidal: 35124 harmonic: 50360 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 -134.77 -45.23 0 5.00e+00 4.00e-02 8.18e+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 -134.80 -45.20 0 5.00e+00 4.00e-02 8.17e+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 -134.84 -45.16 0 5.00e+00 4.00e-02 8.16e+01 ... (remaining 85481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 17230 0.054 - 0.107: 3328 0.107 - 0.161: 355 0.161 - 0.214: 59 0.214 - 0.268: 16 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CB ILE B3122 " pdb=" CA ILE B3122 " pdb=" CG1 ILE B3122 " pdb=" CG2 ILE B3122 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A3122 " pdb=" CA ILE A3122 " pdb=" CG1 ILE A3122 " pdb=" CG2 ILE A3122 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO D1030 " pdb=" N PRO D1030 " pdb=" C PRO D1030 " pdb=" CB PRO D1030 " both_signs ideal model delta sigma weight residual False 2.72 2.98 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 20985 not shown) Planarity restraints: 24600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C4640 " 0.104 5.00e-02 4.00e+02 1.60e-01 4.12e+01 pdb=" N PRO C4641 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO C4641 " 0.093 5.00e-02 4.00e+02 pdb=" CD PRO C4641 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B4640 " -0.104 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO B4641 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " -0.104 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO A4641 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " -0.080 5.00e-02 4.00e+02 ... (remaining 24597 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 1716 2.64 - 3.21: 134674 3.21 - 3.77: 231800 3.77 - 4.34: 315610 4.34 - 4.90: 502629 Nonbonded interactions: 1186429 Sorted by model distance: nonbonded pdb=" OE2 GLU A2635 " pdb=" OH TYR A2680 " model vdw 2.079 2.440 nonbonded pdb=" OE2 GLU B2635 " pdb=" OH TYR B2680 " model vdw 2.079 2.440 nonbonded pdb=" OE2 GLU C2635 " pdb=" OH TYR C2680 " model vdw 2.079 2.440 nonbonded pdb=" OE2 GLU D2635 " pdb=" OH TYR D2680 " model vdw 2.080 2.440 nonbonded pdb=" OG1 THR A1286 " pdb=" O PRO A1550 " model vdw 2.126 2.440 ... (remaining 1186424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 13.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 31.910 Check model and map are aligned: 1.480 Set scattering table: 0.930 Process input model: 460.480 Find NCS groups from input model: 7.090 Set up NCS constraints: 0.970 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 519.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 141720 Z= 0.248 Angle : 0.740 19.867 191484 Z= 0.428 Chirality : 0.042 0.268 20988 Planarity : 0.005 0.160 24600 Dihedral : 15.073 151.887 53008 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 0.79 % Allowed : 0.57 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.06), residues: 17212 helix: 1.46 (0.06), residues: 9132 sheet: -0.18 (0.13), residues: 1644 loop : -0.60 (0.08), residues: 6436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1156 HIS 0.011 0.001 HIS A 395 PHE 0.064 0.001 PHE D4640 TYR 0.041 0.001 TYR C1703 ARG 0.016 0.001 ARG C3260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 707 time to evaluate : 11.658 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: E 67 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: F 67 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8494 (mtp) REVERT: G 67 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8437 (mtp) REVERT: A 241 MET cc_start: 0.7688 (pmm) cc_final: 0.7486 (pmm) REVERT: A 393 MET cc_start: 0.7699 (tpt) cc_final: 0.7228 (tpt) REVERT: A 494 MET cc_start: 0.8623 (mmm) cc_final: 0.8052 (mmp) REVERT: A 655 MET cc_start: 0.8464 (mmm) cc_final: 0.7981 (mmm) REVERT: A 891 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8885 (mm-30) REVERT: A 1046 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8144 (t0) REVERT: A 1975 MET cc_start: 0.7873 (pmm) cc_final: 0.7591 (pmm) REVERT: A 2384 MET cc_start: 0.9005 (mmm) cc_final: 0.8764 (mmp) REVERT: A 2605 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8419 (pmm) REVERT: A 2689 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6861 (mmp) REVERT: A 2724 TYR cc_start: 0.8881 (t80) cc_final: 0.8522 (t80) REVERT: A 2732 TRP cc_start: 0.9016 (t60) cc_final: 0.8534 (t60) REVERT: A 2840 MET cc_start: 0.8886 (mtt) cc_final: 0.7858 (mtt) REVERT: A 2844 MET cc_start: 0.9029 (ppp) cc_final: 0.8548 (ppp) REVERT: A 2848 TYR cc_start: 0.8919 (m-80) cc_final: 0.8568 (m-10) REVERT: A 2877 LEU cc_start: 0.8632 (mt) cc_final: 0.8324 (mt) REVERT: A 3046 MET cc_start: 0.8328 (mmm) cc_final: 0.7954 (mmm) REVERT: A 3072 MET cc_start: 0.8726 (mmp) cc_final: 0.8260 (mmm) REVERT: A 3104 MET cc_start: 0.8871 (ptp) cc_final: 0.7971 (tmm) REVERT: A 3260 ARG cc_start: 0.8240 (tmt170) cc_final: 0.7745 (tmt170) REVERT: A 3315 LEU cc_start: 0.9057 (mt) cc_final: 0.8769 (mm) REVERT: A 3319 PHE cc_start: 0.8509 (m-80) cc_final: 0.8106 (m-80) REVERT: A 3323 MET cc_start: 0.8864 (mpp) cc_final: 0.8483 (mpp) REVERT: A 3981 MET cc_start: 0.8326 (tmm) cc_final: 0.7834 (ttp) REVERT: A 4707 MET cc_start: 0.8295 (ttm) cc_final: 0.8072 (ttp) REVERT: B 393 MET cc_start: 0.7702 (tpt) cc_final: 0.7196 (tpt) REVERT: B 655 MET cc_start: 0.8571 (mmm) cc_final: 0.8035 (mmm) REVERT: B 891 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8859 (mm-30) REVERT: B 1975 MET cc_start: 0.7894 (pmm) cc_final: 0.7537 (pmm) REVERT: B 2724 TYR cc_start: 0.8978 (t80) cc_final: 0.8706 (t80) REVERT: B 2732 TRP cc_start: 0.9079 (t60) cc_final: 0.8863 (t60) REVERT: B 2828 MET cc_start: 0.7293 (tpp) cc_final: 0.6610 (tpp) REVERT: B 2840 MET cc_start: 0.8965 (mtt) cc_final: 0.7976 (mtt) REVERT: B 2844 MET cc_start: 0.9250 (ppp) cc_final: 0.8805 (ppp) REVERT: B 2877 LEU cc_start: 0.8859 (mt) cc_final: 0.8656 (mt) REVERT: B 2886 ARG cc_start: 0.9441 (OUTLIER) cc_final: 0.8818 (mtt90) REVERT: B 3072 MET cc_start: 0.8748 (mmp) cc_final: 0.8331 (mmm) REVERT: B 3109 PHE cc_start: 0.9069 (m-80) cc_final: 0.8428 (m-80) REVERT: B 3260 ARG cc_start: 0.8393 (tmt170) cc_final: 0.7939 (tmt170) REVERT: B 3315 LEU cc_start: 0.8851 (mt) cc_final: 0.8521 (mm) REVERT: B 3319 PHE cc_start: 0.8395 (m-80) cc_final: 0.8059 (m-80) REVERT: B 3323 MET cc_start: 0.8903 (mpp) cc_final: 0.8560 (mpp) REVERT: B 3605 MET cc_start: 0.6293 (ttp) cc_final: 0.6048 (ttp) REVERT: B 3981 MET cc_start: 0.8457 (tmm) cc_final: 0.8088 (tmm) REVERT: B 4707 MET cc_start: 0.8260 (ttm) cc_final: 0.8027 (ttp) REVERT: B 4817 MET cc_start: 0.8912 (mmm) cc_final: 0.8622 (mmm) REVERT: C 393 MET cc_start: 0.7692 (tpt) cc_final: 0.7185 (tpt) REVERT: C 655 MET cc_start: 0.8566 (mmm) cc_final: 0.8032 (mmm) REVERT: C 891 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8843 (mm-30) REVERT: C 1975 MET cc_start: 0.7889 (pmm) cc_final: 0.7537 (pmm) REVERT: C 2724 TYR cc_start: 0.8977 (t80) cc_final: 0.8705 (t80) REVERT: C 2828 MET cc_start: 0.7303 (tpp) cc_final: 0.6621 (tpp) REVERT: C 2840 MET cc_start: 0.8962 (mtt) cc_final: 0.7960 (mtt) REVERT: C 2844 MET cc_start: 0.9248 (ppp) cc_final: 0.8808 (ppp) REVERT: C 2886 ARG cc_start: 0.9446 (OUTLIER) cc_final: 0.8980 (ttm110) REVERT: C 3003 MET cc_start: 0.9052 (ptm) cc_final: 0.8449 (ppp) REVERT: C 3072 MET cc_start: 0.8751 (mmp) cc_final: 0.8336 (mmm) REVERT: C 3109 PHE cc_start: 0.9065 (m-80) cc_final: 0.8422 (m-80) REVERT: C 3260 ARG cc_start: 0.8374 (tmt170) cc_final: 0.8002 (tmt170) REVERT: C 3315 LEU cc_start: 0.8861 (mt) cc_final: 0.8547 (mm) REVERT: C 3319 PHE cc_start: 0.8404 (m-80) cc_final: 0.8095 (m-80) REVERT: C 3323 MET cc_start: 0.8913 (mpp) cc_final: 0.8574 (mpp) REVERT: C 3605 MET cc_start: 0.6263 (ttp) cc_final: 0.6047 (ttp) REVERT: C 3981 MET cc_start: 0.8465 (tmm) cc_final: 0.8099 (tmm) REVERT: C 4707 MET cc_start: 0.8274 (ttm) cc_final: 0.8050 (ttp) REVERT: C 4817 MET cc_start: 0.8917 (mmm) cc_final: 0.8630 (mmm) REVERT: D 393 MET cc_start: 0.7702 (tpt) cc_final: 0.7199 (tpt) REVERT: D 494 MET cc_start: 0.8678 (mmm) cc_final: 0.8152 (mmp) REVERT: D 655 MET cc_start: 0.8576 (mmm) cc_final: 0.8029 (mmm) REVERT: D 891 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8847 (mm-30) REVERT: D 1975 MET cc_start: 0.7885 (pmm) cc_final: 0.7516 (pmm) REVERT: D 2724 TYR cc_start: 0.8974 (t80) cc_final: 0.8702 (t80) REVERT: D 2732 TRP cc_start: 0.9079 (t60) cc_final: 0.8861 (t60) REVERT: D 2828 MET cc_start: 0.7284 (tpp) cc_final: 0.6601 (tpp) REVERT: D 2840 MET cc_start: 0.8972 (mtt) cc_final: 0.7979 (mtt) REVERT: D 2844 MET cc_start: 0.9246 (ppp) cc_final: 0.8807 (ppp) REVERT: D 2877 LEU cc_start: 0.8847 (mt) cc_final: 0.8644 (mt) REVERT: D 2886 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.8821 (mtt90) REVERT: D 3072 MET cc_start: 0.8765 (mmp) cc_final: 0.8343 (mmm) REVERT: D 3109 PHE cc_start: 0.9062 (m-80) cc_final: 0.8434 (m-80) REVERT: D 3260 ARG cc_start: 0.8394 (tmt170) cc_final: 0.8025 (tmt170) REVERT: D 3315 LEU cc_start: 0.8854 (mt) cc_final: 0.8526 (mm) REVERT: D 3319 PHE cc_start: 0.8401 (m-80) cc_final: 0.8063 (m-80) REVERT: D 3323 MET cc_start: 0.8897 (mpp) cc_final: 0.8554 (mpp) REVERT: D 3605 MET cc_start: 0.6320 (ttp) cc_final: 0.6068 (ttp) REVERT: D 3981 MET cc_start: 0.8448 (tmm) cc_final: 0.8082 (tmm) REVERT: D 4707 MET cc_start: 0.8259 (ttm) cc_final: 0.8023 (ttp) REVERT: D 4817 MET cc_start: 0.8910 (mmm) cc_final: 0.8620 (mmm) outliers start: 120 outliers final: 50 residues processed: 779 average time/residue: 1.2322 time to fit residues: 1700.3977 Evaluate side-chains 716 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 653 time to evaluate : 11.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain A residue 1021 GLN Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1049 SER Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2605 MET Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 2886 ARG Chi-restraints excluded: chain A residue 3262 GLU Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 1011 ARG Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1046 ASN Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 2134 MET Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2605 MET Chi-restraints excluded: chain B residue 2798 MET Chi-restraints excluded: chain B residue 2886 ARG Chi-restraints excluded: chain B residue 3262 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 917 CYS Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1046 ASN Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1049 SER Chi-restraints excluded: chain C residue 2134 MET Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2605 MET Chi-restraints excluded: chain C residue 2798 MET Chi-restraints excluded: chain C residue 2886 ARG Chi-restraints excluded: chain C residue 3262 GLU Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 4012 MET Chi-restraints excluded: chain D residue 891 GLU Chi-restraints excluded: chain D residue 1011 ARG Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 1046 ASN Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1049 SER Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2798 MET Chi-restraints excluded: chain D residue 2886 ARG Chi-restraints excluded: chain D residue 3262 GLU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 4012 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 9.9990 chunk 1309 optimal weight: 0.9990 chunk 726 optimal weight: 9.9990 chunk 447 optimal weight: 6.9990 chunk 883 optimal weight: 6.9990 chunk 699 optimal weight: 5.9990 chunk 1354 optimal weight: 6.9990 chunk 524 optimal weight: 20.0000 chunk 823 optimal weight: 7.9990 chunk 1008 optimal weight: 30.0000 chunk 1569 optimal weight: 0.0670 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 ASN A 890 HIS A 896 ASN A1978 ASN A2830 ASN ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 HIS B1978 ASN B2830 ASN ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3850 HIS ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 890 HIS C 896 ASN C1046 ASN ** C1978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2830 ASN ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3850 HIS ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 890 HIS D 896 ASN D1046 ASN ** D1978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2830 ASN ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3850 HIS ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 141720 Z= 0.260 Angle : 0.602 18.344 191484 Z= 0.306 Chirality : 0.040 0.229 20988 Planarity : 0.005 0.149 24600 Dihedral : 8.471 152.737 19285 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.05 % Favored : 96.84 % Rotamer: Outliers : 0.43 % Allowed : 3.52 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.06), residues: 17212 helix: 1.59 (0.05), residues: 9164 sheet: -0.29 (0.12), residues: 1768 loop : -0.51 (0.08), residues: 6280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2773 HIS 0.011 0.001 HIS C2729 PHE 0.043 0.001 PHE C4640 TYR 0.042 0.002 TYR B1703 ARG 0.008 0.001 ARG C 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 679 time to evaluate : 11.564 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: E 50 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.8389 (mtm-85) REVERT: F 50 ARG cc_start: 0.8682 (mtp-110) cc_final: 0.8425 (mtm-85) REVERT: G 50 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8409 (mtm-85) REVERT: A 241 MET cc_start: 0.7716 (pmm) cc_final: 0.7467 (pmm) REVERT: A 995 MET cc_start: 0.8725 (ptm) cc_final: 0.8037 (tmm) REVERT: A 1046 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8446 (m110) REVERT: A 1906 MET cc_start: 0.8648 (tpp) cc_final: 0.8041 (mmm) REVERT: A 1975 MET cc_start: 0.8037 (pmm) cc_final: 0.7777 (pmm) REVERT: A 2384 MET cc_start: 0.9019 (mmm) cc_final: 0.8810 (mmp) REVERT: A 2442 MET cc_start: 0.8468 (mmp) cc_final: 0.8040 (mmm) REVERT: A 2456 MET cc_start: 0.8896 (tpt) cc_final: 0.8561 (tpp) REVERT: A 2681 MET cc_start: 0.8614 (mmt) cc_final: 0.8261 (tpp) REVERT: A 2724 TYR cc_start: 0.8908 (t80) cc_final: 0.8568 (t80) REVERT: A 2732 TRP cc_start: 0.9004 (t60) cc_final: 0.8803 (t60) REVERT: A 2782 MET cc_start: 0.8925 (tmm) cc_final: 0.8250 (tmm) REVERT: A 2783 LEU cc_start: 0.9474 (mt) cc_final: 0.9075 (mt) REVERT: A 2840 MET cc_start: 0.8775 (mtt) cc_final: 0.8124 (mtt) REVERT: A 2844 MET cc_start: 0.9113 (ppp) cc_final: 0.8832 (ppp) REVERT: A 2848 TYR cc_start: 0.8886 (m-80) cc_final: 0.8589 (m-10) REVERT: A 2877 LEU cc_start: 0.8730 (mt) cc_final: 0.8435 (mt) REVERT: A 3046 MET cc_start: 0.8432 (mmm) cc_final: 0.8078 (mmm) REVERT: A 3072 MET cc_start: 0.8833 (mmp) cc_final: 0.8462 (mmm) REVERT: A 3104 MET cc_start: 0.8912 (ptp) cc_final: 0.8496 (ptt) REVERT: A 3273 MET cc_start: 0.8923 (mmm) cc_final: 0.7515 (mmm) REVERT: A 3315 LEU cc_start: 0.9067 (mt) cc_final: 0.8628 (mm) REVERT: A 3319 PHE cc_start: 0.8468 (m-80) cc_final: 0.8052 (m-80) REVERT: A 4279 MET cc_start: 0.7294 (ptt) cc_final: 0.7001 (mtm) REVERT: A 4707 MET cc_start: 0.8308 (ttm) cc_final: 0.8072 (ttp) REVERT: B 1046 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8456 (m110) REVERT: B 2456 MET cc_start: 0.8819 (tpp) cc_final: 0.7792 (tpt) REVERT: B 2512 MET cc_start: 0.8693 (tpp) cc_final: 0.8254 (tpp) REVERT: B 2724 TYR cc_start: 0.8992 (t80) cc_final: 0.8734 (t80) REVERT: B 2732 TRP cc_start: 0.9096 (t60) cc_final: 0.8884 (t60) REVERT: B 2840 MET cc_start: 0.9002 (mtt) cc_final: 0.8452 (mtp) REVERT: B 3072 MET cc_start: 0.8875 (mmp) cc_final: 0.8427 (mmm) REVERT: B 3104 MET cc_start: 0.9064 (ptp) cc_final: 0.8720 (ptt) REVERT: B 3109 PHE cc_start: 0.9036 (m-80) cc_final: 0.8395 (m-80) REVERT: B 3250 TRP cc_start: 0.8949 (t60) cc_final: 0.8613 (t-100) REVERT: B 3315 LEU cc_start: 0.8877 (mt) cc_final: 0.8638 (mt) REVERT: B 3972 MET cc_start: 0.8137 (mtm) cc_final: 0.7893 (mtm) REVERT: B 3981 MET cc_start: 0.8516 (tmm) cc_final: 0.8305 (tmm) REVERT: B 4279 MET cc_start: 0.7267 (ptt) cc_final: 0.6990 (mtm) REVERT: B 4707 MET cc_start: 0.8298 (ttm) cc_final: 0.8060 (ttp) REVERT: C 655 MET cc_start: 0.8718 (mmm) cc_final: 0.8410 (mmm) REVERT: C 2456 MET cc_start: 0.8815 (tpp) cc_final: 0.7801 (tpt) REVERT: C 2512 MET cc_start: 0.8682 (tpp) cc_final: 0.8250 (tpp) REVERT: C 2724 TYR cc_start: 0.8987 (t80) cc_final: 0.8740 (t80) REVERT: C 2840 MET cc_start: 0.9004 (mtt) cc_final: 0.8447 (mtp) REVERT: C 3072 MET cc_start: 0.8879 (mmp) cc_final: 0.8448 (mmm) REVERT: C 3104 MET cc_start: 0.9070 (ptp) cc_final: 0.8710 (ptt) REVERT: C 3109 PHE cc_start: 0.9045 (m-80) cc_final: 0.8413 (m-80) REVERT: C 3250 TRP cc_start: 0.8955 (t60) cc_final: 0.8608 (t-100) REVERT: C 3315 LEU cc_start: 0.8878 (mt) cc_final: 0.8641 (mt) REVERT: C 3972 MET cc_start: 0.8129 (mtm) cc_final: 0.7870 (mtm) REVERT: C 3981 MET cc_start: 0.8514 (tmm) cc_final: 0.8309 (tmm) REVERT: C 4279 MET cc_start: 0.7233 (ptt) cc_final: 0.6945 (mtm) REVERT: C 4707 MET cc_start: 0.8306 (ttm) cc_final: 0.8064 (ttp) REVERT: D 2456 MET cc_start: 0.8814 (tpp) cc_final: 0.7810 (tpt) REVERT: D 2512 MET cc_start: 0.8690 (tpp) cc_final: 0.8254 (tpp) REVERT: D 2724 TYR cc_start: 0.8989 (t80) cc_final: 0.8734 (t80) REVERT: D 2732 TRP cc_start: 0.9096 (t60) cc_final: 0.8880 (t60) REVERT: D 2840 MET cc_start: 0.9010 (mtt) cc_final: 0.8467 (mtp) REVERT: D 3072 MET cc_start: 0.8878 (mmp) cc_final: 0.8427 (mmm) REVERT: D 3104 MET cc_start: 0.9064 (ptp) cc_final: 0.8716 (ptt) REVERT: D 3109 PHE cc_start: 0.9040 (m-80) cc_final: 0.8411 (m-80) REVERT: D 3250 TRP cc_start: 0.8942 (t60) cc_final: 0.8602 (t-100) REVERT: D 3315 LEU cc_start: 0.8876 (mt) cc_final: 0.8647 (mt) REVERT: D 3972 MET cc_start: 0.8131 (mtm) cc_final: 0.7892 (mtm) REVERT: D 3981 MET cc_start: 0.8513 (tmm) cc_final: 0.8300 (tmm) REVERT: D 4279 MET cc_start: 0.7295 (ptt) cc_final: 0.7009 (mtm) REVERT: D 4707 MET cc_start: 0.8292 (ttm) cc_final: 0.8058 (ttp) outliers start: 65 outliers final: 34 residues processed: 708 average time/residue: 1.1727 time to fit residues: 1486.4114 Evaluate side-chains 688 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 652 time to evaluate : 11.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1021 GLN Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 917 CYS Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1046 ASN Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 917 CYS Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 3296 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 7.9990 chunk 487 optimal weight: 0.8980 chunk 1306 optimal weight: 20.0000 chunk 1068 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 chunk 1572 optimal weight: 6.9990 chunk 1698 optimal weight: 8.9990 chunk 1400 optimal weight: 4.9990 chunk 1558 optimal weight: 8.9990 chunk 535 optimal weight: 9.9990 chunk 1261 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN B 896 ASN ** B2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 ASN ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 141720 Z= 0.324 Angle : 0.597 16.418 191484 Z= 0.306 Chirality : 0.040 0.274 20988 Planarity : 0.005 0.142 24600 Dihedral : 7.930 157.088 19135 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 0.40 % Allowed : 4.97 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.06), residues: 17212 helix: 1.66 (0.05), residues: 9180 sheet: -0.19 (0.12), residues: 1720 loop : -0.52 (0.08), residues: 6312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 893 HIS 0.011 0.001 HIS C2729 PHE 0.030 0.002 PHE A4640 TYR 0.043 0.002 TYR C1703 ARG 0.006 0.001 ARG B 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 665 time to evaluate : 11.640 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: F 50 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8265 (mtm-85) REVERT: G 50 ARG cc_start: 0.8613 (mtp-110) cc_final: 0.8256 (mtm-85) REVERT: A 241 MET cc_start: 0.7697 (pmm) cc_final: 0.7483 (pmm) REVERT: A 393 MET cc_start: 0.7643 (tpt) cc_final: 0.7104 (mmm) REVERT: A 655 MET cc_start: 0.8731 (mmm) cc_final: 0.8382 (mmm) REVERT: A 933 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8190 (mt) REVERT: A 995 MET cc_start: 0.8750 (ptm) cc_final: 0.8021 (tmm) REVERT: A 1046 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8475 (m110) REVERT: A 1975 MET cc_start: 0.8090 (pmm) cc_final: 0.7769 (pmm) REVERT: A 2442 MET cc_start: 0.8701 (mmp) cc_final: 0.8365 (mmm) REVERT: A 2456 MET cc_start: 0.8818 (tpt) cc_final: 0.7950 (tpp) REVERT: A 2724 TYR cc_start: 0.8995 (t80) cc_final: 0.8617 (t80) REVERT: A 2732 TRP cc_start: 0.9047 (t60) cc_final: 0.8818 (t60) REVERT: A 2840 MET cc_start: 0.8814 (mtt) cc_final: 0.8249 (mtt) REVERT: A 2844 MET cc_start: 0.9156 (ppp) cc_final: 0.8933 (ppp) REVERT: A 2848 TYR cc_start: 0.8918 (m-80) cc_final: 0.8644 (m-10) REVERT: A 2877 LEU cc_start: 0.8717 (mt) cc_final: 0.8438 (mt) REVERT: A 3003 MET cc_start: 0.9022 (ptm) cc_final: 0.8344 (ppp) REVERT: A 3046 MET cc_start: 0.8541 (mmm) cc_final: 0.8211 (mmm) REVERT: A 3072 MET cc_start: 0.8909 (mmp) cc_final: 0.8506 (mmm) REVERT: A 3104 MET cc_start: 0.8932 (ptp) cc_final: 0.8495 (ptt) REVERT: A 3235 MET cc_start: 0.9003 (pmm) cc_final: 0.8789 (pmm) REVERT: A 3263 MET cc_start: 0.8832 (tpp) cc_final: 0.8623 (tpp) REVERT: A 3315 LEU cc_start: 0.9076 (mt) cc_final: 0.8614 (mm) REVERT: A 3319 PHE cc_start: 0.8467 (m-80) cc_final: 0.7942 (m-80) REVERT: A 4279 MET cc_start: 0.7273 (ptt) cc_final: 0.6974 (mtm) REVERT: A 4707 MET cc_start: 0.8286 (ttm) cc_final: 0.8051 (ttp) REVERT: B 393 MET cc_start: 0.7654 (tpt) cc_final: 0.7053 (mmm) REVERT: B 933 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8203 (mt) REVERT: B 1046 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8461 (m110) REVERT: B 1721 MET cc_start: 0.7847 (mmm) cc_final: 0.7607 (mmm) REVERT: B 1975 MET cc_start: 0.8112 (pmm) cc_final: 0.7754 (pmm) REVERT: B 2192 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8075 (tmm) REVERT: B 2442 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8622 (mmm) REVERT: B 2456 MET cc_start: 0.8812 (tpp) cc_final: 0.7996 (tpt) REVERT: B 2512 MET cc_start: 0.8687 (tpp) cc_final: 0.8424 (tpp) REVERT: B 2724 TYR cc_start: 0.8977 (t80) cc_final: 0.8714 (t80) REVERT: B 2798 MET cc_start: 0.7183 (mmp) cc_final: 0.6980 (mmp) REVERT: B 2840 MET cc_start: 0.9040 (mtt) cc_final: 0.8514 (mtt) REVERT: B 2852 TRP cc_start: 0.9109 (t60) cc_final: 0.8799 (t60) REVERT: B 3072 MET cc_start: 0.8915 (mmp) cc_final: 0.8567 (mmm) REVERT: B 3104 MET cc_start: 0.9061 (ptp) cc_final: 0.8698 (ptt) REVERT: B 3109 PHE cc_start: 0.9006 (m-80) cc_final: 0.8415 (m-80) REVERT: B 3981 MET cc_start: 0.8528 (tmm) cc_final: 0.8312 (ttp) REVERT: B 4279 MET cc_start: 0.7252 (ptt) cc_final: 0.6949 (mtm) REVERT: B 4707 MET cc_start: 0.8301 (ttm) cc_final: 0.8066 (ttp) REVERT: C 393 MET cc_start: 0.7645 (tpt) cc_final: 0.7033 (mmm) REVERT: C 655 MET cc_start: 0.8772 (mmm) cc_final: 0.8495 (mmt) REVERT: C 933 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8205 (mt) REVERT: C 964 MET cc_start: 0.4652 (OUTLIER) cc_final: 0.4191 (pmm) REVERT: C 1975 MET cc_start: 0.8085 (pmm) cc_final: 0.7726 (pmm) REVERT: C 2192 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8065 (tmm) REVERT: C 2456 MET cc_start: 0.8828 (tpp) cc_final: 0.8025 (tpt) REVERT: C 2512 MET cc_start: 0.8698 (tpp) cc_final: 0.8412 (tpp) REVERT: C 2724 TYR cc_start: 0.8976 (t80) cc_final: 0.8701 (t80) REVERT: C 2840 MET cc_start: 0.9050 (mtt) cc_final: 0.8521 (mtt) REVERT: C 2852 TRP cc_start: 0.9094 (t60) cc_final: 0.8780 (t60) REVERT: C 3072 MET cc_start: 0.8917 (mmp) cc_final: 0.8561 (mmm) REVERT: C 3104 MET cc_start: 0.9067 (ptp) cc_final: 0.8700 (ptt) REVERT: C 3109 PHE cc_start: 0.8997 (m-80) cc_final: 0.8404 (m-80) REVERT: C 3981 MET cc_start: 0.8524 (tmm) cc_final: 0.8308 (ttp) REVERT: C 4279 MET cc_start: 0.7236 (ptt) cc_final: 0.6928 (mtm) REVERT: C 4707 MET cc_start: 0.8310 (ttm) cc_final: 0.8068 (ttp) REVERT: D 393 MET cc_start: 0.7654 (tpt) cc_final: 0.7061 (mmm) REVERT: D 933 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8214 (mt) REVERT: D 1721 MET cc_start: 0.7849 (mmm) cc_final: 0.7608 (mmm) REVERT: D 1906 MET cc_start: 0.8733 (mmm) cc_final: 0.8298 (mmm) REVERT: D 1975 MET cc_start: 0.8090 (pmm) cc_final: 0.7725 (pmm) REVERT: D 2192 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8072 (tmm) REVERT: D 2442 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8644 (mmm) REVERT: D 2456 MET cc_start: 0.8810 (tpp) cc_final: 0.8006 (tpt) REVERT: D 2512 MET cc_start: 0.8688 (tpp) cc_final: 0.8423 (tpp) REVERT: D 2585 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7526 (mtm) REVERT: D 2724 TYR cc_start: 0.8974 (t80) cc_final: 0.8717 (t80) REVERT: D 2840 MET cc_start: 0.9042 (mtt) cc_final: 0.8516 (mtt) REVERT: D 2852 TRP cc_start: 0.9104 (t60) cc_final: 0.8792 (t60) REVERT: D 3072 MET cc_start: 0.8918 (mmp) cc_final: 0.8566 (mmm) REVERT: D 3104 MET cc_start: 0.9059 (ptp) cc_final: 0.8697 (ptt) REVERT: D 3109 PHE cc_start: 0.9007 (m-80) cc_final: 0.8406 (m-80) REVERT: D 3263 MET cc_start: 0.8893 (tpp) cc_final: 0.8692 (tpt) REVERT: D 3981 MET cc_start: 0.8525 (tmm) cc_final: 0.8303 (ttp) REVERT: D 4279 MET cc_start: 0.7255 (ptt) cc_final: 0.6964 (mtm) REVERT: D 4707 MET cc_start: 0.8301 (ttm) cc_final: 0.8059 (ttp) outliers start: 61 outliers final: 31 residues processed: 690 average time/residue: 1.2447 time to fit residues: 1549.9330 Evaluate side-chains 694 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 650 time to evaluate : 11.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1046 ASN Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 2442 MET Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2442 MET Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 3296 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 7.9990 chunk 1181 optimal weight: 30.0000 chunk 815 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 750 optimal weight: 4.9990 chunk 1055 optimal weight: 6.9990 chunk 1577 optimal weight: 10.0000 chunk 1670 optimal weight: 4.9990 chunk 824 optimal weight: 9.9990 chunk 1495 optimal weight: 4.9990 chunk 450 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 HIS F 26 HIS G 26 HIS H 26 HIS ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4088 HIS A4629 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3269 ASN ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3850 HIS ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B4088 HIS B4629 GLN ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1978 ASN ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3850 HIS ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C4088 HIS C4629 GLN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN D1978 ASN ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3850 HIS ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4088 HIS D4629 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 141720 Z= 0.217 Angle : 0.555 15.575 191484 Z= 0.283 Chirality : 0.039 0.219 20988 Planarity : 0.004 0.135 24600 Dihedral : 7.703 158.171 19128 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 0.46 % Allowed : 5.80 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.07), residues: 17212 helix: 1.80 (0.06), residues: 9144 sheet: -0.22 (0.12), residues: 1772 loop : -0.48 (0.08), residues: 6296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.001 TRP A 893 HIS 0.009 0.001 HIS C2729 PHE 0.025 0.001 PHE A3170 TYR 0.030 0.001 TYR A1703 ARG 0.007 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 658 time to evaluate : 11.614 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: E 50 ARG cc_start: 0.8594 (mtp180) cc_final: 0.8313 (mtm-85) REVERT: F 50 ARG cc_start: 0.8609 (mtp180) cc_final: 0.8331 (mtm-85) REVERT: G 50 ARG cc_start: 0.8613 (mtp180) cc_final: 0.8317 (mtm-85) REVERT: A 241 MET cc_start: 0.7719 (pmm) cc_final: 0.7507 (pmm) REVERT: A 393 MET cc_start: 0.7652 (tpt) cc_final: 0.7132 (mmm) REVERT: A 655 MET cc_start: 0.8696 (mmm) cc_final: 0.8401 (mmm) REVERT: A 933 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8254 (mt) REVERT: A 935 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8831 (ptp) REVERT: A 1975 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7779 (pmm) REVERT: A 2442 MET cc_start: 0.8738 (mmp) cc_final: 0.8421 (mmm) REVERT: A 2724 TYR cc_start: 0.8978 (t80) cc_final: 0.8617 (t80) REVERT: A 2732 TRP cc_start: 0.9025 (t60) cc_final: 0.8752 (t60) REVERT: A 2840 MET cc_start: 0.8814 (mtt) cc_final: 0.8237 (mtt) REVERT: A 2844 MET cc_start: 0.9192 (ppp) cc_final: 0.8990 (ppp) REVERT: A 2848 TYR cc_start: 0.8878 (m-80) cc_final: 0.8645 (m-10) REVERT: A 2852 TRP cc_start: 0.9320 (t60) cc_final: 0.9096 (t60) REVERT: A 2877 LEU cc_start: 0.8748 (mt) cc_final: 0.8455 (mt) REVERT: A 3046 MET cc_start: 0.8503 (mmm) cc_final: 0.8178 (mmm) REVERT: A 3072 MET cc_start: 0.8914 (mmp) cc_final: 0.8589 (mmm) REVERT: A 3104 MET cc_start: 0.8923 (ptp) cc_final: 0.8466 (ptt) REVERT: A 3315 LEU cc_start: 0.9096 (mt) cc_final: 0.8630 (mm) REVERT: A 3319 PHE cc_start: 0.8449 (m-80) cc_final: 0.7914 (m-80) REVERT: A 3981 MET cc_start: 0.8256 (ttp) cc_final: 0.7589 (ttp) REVERT: A 4279 MET cc_start: 0.7230 (ptt) cc_final: 0.6946 (mtm) REVERT: A 4707 MET cc_start: 0.8275 (ttm) cc_final: 0.8032 (ttp) REVERT: B 393 MET cc_start: 0.7642 (tpt) cc_final: 0.7059 (mmm) REVERT: B 655 MET cc_start: 0.8336 (mmm) cc_final: 0.8076 (mmp) REVERT: B 933 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 1564 MET cc_start: 0.8664 (tpp) cc_final: 0.8421 (mmm) REVERT: B 1721 MET cc_start: 0.7810 (mmm) cc_final: 0.7603 (mmm) REVERT: B 1975 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7703 (pmm) REVERT: B 2192 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: B 2456 MET cc_start: 0.8798 (tpp) cc_final: 0.8201 (tpt) REVERT: B 2724 TYR cc_start: 0.8966 (t80) cc_final: 0.8706 (t80) REVERT: B 2840 MET cc_start: 0.9064 (mtt) cc_final: 0.8541 (mtt) REVERT: B 2852 TRP cc_start: 0.9068 (t60) cc_final: 0.8740 (t60) REVERT: B 3072 MET cc_start: 0.8975 (mmp) cc_final: 0.8609 (mmm) REVERT: B 3104 MET cc_start: 0.9044 (ptp) cc_final: 0.8656 (ptt) REVERT: B 3109 PHE cc_start: 0.8944 (m-80) cc_final: 0.8366 (m-80) REVERT: B 3981 MET cc_start: 0.8516 (tmm) cc_final: 0.8295 (ttp) REVERT: B 4279 MET cc_start: 0.7285 (ptt) cc_final: 0.7011 (mtm) REVERT: B 4707 MET cc_start: 0.8283 (ttm) cc_final: 0.8042 (ttp) REVERT: C 393 MET cc_start: 0.7630 (tpt) cc_final: 0.7038 (mmm) REVERT: C 933 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8125 (mt) REVERT: C 1564 MET cc_start: 0.8663 (tpp) cc_final: 0.8420 (mmm) REVERT: C 1975 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7687 (pmm) REVERT: C 2192 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: C 2456 MET cc_start: 0.8794 (tpp) cc_final: 0.8021 (tpt) REVERT: C 2512 MET cc_start: 0.8648 (tpp) cc_final: 0.8429 (tpp) REVERT: C 2724 TYR cc_start: 0.8967 (t80) cc_final: 0.8701 (t80) REVERT: C 2840 MET cc_start: 0.9069 (mtt) cc_final: 0.8545 (mtt) REVERT: C 2852 TRP cc_start: 0.9056 (t60) cc_final: 0.8725 (t60) REVERT: C 3072 MET cc_start: 0.8989 (mmp) cc_final: 0.8629 (mmm) REVERT: C 3104 MET cc_start: 0.9051 (ptp) cc_final: 0.8656 (ptt) REVERT: C 3109 PHE cc_start: 0.8964 (m-80) cc_final: 0.8378 (m-80) REVERT: C 3981 MET cc_start: 0.8514 (tmm) cc_final: 0.8293 (ttp) REVERT: C 4279 MET cc_start: 0.7272 (ptt) cc_final: 0.6991 (mtm) REVERT: C 4707 MET cc_start: 0.8293 (ttm) cc_final: 0.8044 (ttp) REVERT: D 393 MET cc_start: 0.7647 (tpt) cc_final: 0.7067 (mmm) REVERT: D 655 MET cc_start: 0.8316 (mmm) cc_final: 0.8051 (mmp) REVERT: D 933 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8128 (mt) REVERT: D 1564 MET cc_start: 0.8667 (tpp) cc_final: 0.8421 (mmm) REVERT: D 1721 MET cc_start: 0.7816 (mmm) cc_final: 0.7606 (mmm) REVERT: D 1975 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7696 (pmm) REVERT: D 2456 MET cc_start: 0.8775 (tpp) cc_final: 0.8171 (tpt) REVERT: D 2724 TYR cc_start: 0.8960 (t80) cc_final: 0.8702 (t80) REVERT: D 2798 MET cc_start: 0.7154 (mmp) cc_final: 0.6932 (mmp) REVERT: D 2840 MET cc_start: 0.9062 (mtt) cc_final: 0.8540 (mtt) REVERT: D 2852 TRP cc_start: 0.9068 (t60) cc_final: 0.8741 (t60) REVERT: D 3072 MET cc_start: 0.8978 (mmp) cc_final: 0.8610 (mmm) REVERT: D 3104 MET cc_start: 0.9042 (ptp) cc_final: 0.8654 (ptt) REVERT: D 3109 PHE cc_start: 0.8938 (m-80) cc_final: 0.8366 (m-80) REVERT: D 3972 MET cc_start: 0.8110 (mtp) cc_final: 0.7821 (mtp) REVERT: D 3981 MET cc_start: 0.8513 (tmm) cc_final: 0.8289 (ttp) REVERT: D 4279 MET cc_start: 0.7235 (ptt) cc_final: 0.6956 (mtm) REVERT: D 4707 MET cc_start: 0.8283 (ttm) cc_final: 0.8027 (ttp) outliers start: 70 outliers final: 39 residues processed: 688 average time/residue: 1.1431 time to fit residues: 1407.1590 Evaluate side-chains 699 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 649 time to evaluate : 10.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 3296 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 20.0000 chunk 948 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 1243 optimal weight: 9.9990 chunk 689 optimal weight: 30.0000 chunk 1425 optimal weight: 9.9990 chunk 1154 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 852 optimal weight: 10.0000 chunk 1499 optimal weight: 9.9990 chunk 421 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 106 ASN ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3905 ASN A4629 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 141720 Z= 0.335 Angle : 0.582 14.461 191484 Z= 0.299 Chirality : 0.040 0.224 20988 Planarity : 0.005 0.132 24600 Dihedral : 7.617 158.498 19124 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 0.57 % Allowed : 6.83 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.06), residues: 17212 helix: 1.77 (0.06), residues: 9172 sheet: -0.26 (0.12), residues: 1768 loop : -0.50 (0.08), residues: 6272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 893 HIS 0.008 0.001 HIS A 395 PHE 0.029 0.002 PHE B3854 TYR 0.030 0.002 TYR C1703 ARG 0.007 0.000 ARG C2127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 668 time to evaluate : 10.574 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: A 393 MET cc_start: 0.7655 (tpt) cc_final: 0.7109 (mmm) REVERT: A 933 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 935 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8905 (ptp) REVERT: A 995 MET cc_start: 0.9129 (ttp) cc_final: 0.7849 (tmm) REVERT: A 1174 MET cc_start: 0.7645 (ptm) cc_final: 0.7161 (ptm) REVERT: A 1975 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7790 (pmm) REVERT: A 2681 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8306 (tpp) REVERT: A 2724 TYR cc_start: 0.8959 (t80) cc_final: 0.8581 (t80) REVERT: A 2732 TRP cc_start: 0.9071 (t60) cc_final: 0.8776 (t60) REVERT: A 2798 MET cc_start: 0.6967 (mmp) cc_final: 0.6543 (mmm) REVERT: A 2840 MET cc_start: 0.8851 (mtt) cc_final: 0.8274 (mtt) REVERT: A 2844 MET cc_start: 0.9203 (ppp) cc_final: 0.8989 (ppp) REVERT: A 2848 TYR cc_start: 0.8895 (m-80) cc_final: 0.8669 (m-10) REVERT: A 2852 TRP cc_start: 0.9327 (t60) cc_final: 0.9106 (t60) REVERT: A 2877 LEU cc_start: 0.8786 (mt) cc_final: 0.8506 (mt) REVERT: A 3003 MET cc_start: 0.9023 (ptm) cc_final: 0.8375 (ppp) REVERT: A 3046 MET cc_start: 0.8583 (mmm) cc_final: 0.8245 (mmm) REVERT: A 3072 MET cc_start: 0.8961 (mmp) cc_final: 0.8655 (mmm) REVERT: A 3104 MET cc_start: 0.8952 (ptp) cc_final: 0.8492 (ptt) REVERT: A 3263 MET cc_start: 0.8889 (tpt) cc_final: 0.8436 (tpp) REVERT: A 3315 LEU cc_start: 0.9118 (mt) cc_final: 0.8872 (mm) REVERT: A 3319 PHE cc_start: 0.8493 (m-80) cc_final: 0.8064 (m-80) REVERT: A 3981 MET cc_start: 0.8257 (ttp) cc_final: 0.7616 (ttp) REVERT: A 4279 MET cc_start: 0.7271 (ptt) cc_final: 0.6987 (mtm) REVERT: A 4629 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: A 4707 MET cc_start: 0.8303 (ttm) cc_final: 0.8058 (ttp) REVERT: B 393 MET cc_start: 0.7649 (tpt) cc_final: 0.7090 (mmm) REVERT: B 933 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8176 (mt) REVERT: B 1564 MET cc_start: 0.8696 (tpp) cc_final: 0.8452 (mmm) REVERT: B 1721 MET cc_start: 0.7812 (mmm) cc_final: 0.7606 (mmm) REVERT: B 1975 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7697 (pmm) REVERT: B 2724 TYR cc_start: 0.8999 (t80) cc_final: 0.8731 (t80) REVERT: B 2798 MET cc_start: 0.7272 (mmp) cc_final: 0.7070 (mmp) REVERT: B 2840 MET cc_start: 0.9100 (mtt) cc_final: 0.8575 (mtt) REVERT: B 2852 TRP cc_start: 0.9069 (t60) cc_final: 0.8754 (t60) REVERT: B 3072 MET cc_start: 0.9009 (mmp) cc_final: 0.8662 (mmm) REVERT: B 3104 MET cc_start: 0.9050 (ptp) cc_final: 0.8664 (ptt) REVERT: B 3109 PHE cc_start: 0.8920 (m-80) cc_final: 0.8373 (m-80) REVERT: B 3159 LEU cc_start: 0.9035 (tp) cc_final: 0.8751 (tp) REVERT: B 3241 MET cc_start: 0.8896 (ppp) cc_final: 0.8622 (ppp) REVERT: B 3250 TRP cc_start: 0.8841 (t60) cc_final: 0.8621 (t60) REVERT: B 3299 LEU cc_start: 0.9375 (mt) cc_final: 0.9137 (mt) REVERT: B 3981 MET cc_start: 0.8514 (tmm) cc_final: 0.8289 (ttp) REVERT: B 4279 MET cc_start: 0.7257 (ptt) cc_final: 0.6980 (mtm) REVERT: B 4707 MET cc_start: 0.8311 (ttm) cc_final: 0.8059 (ttp) REVERT: C 393 MET cc_start: 0.7633 (tpt) cc_final: 0.7071 (mmm) REVERT: C 933 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8170 (mt) REVERT: C 1564 MET cc_start: 0.8691 (tpp) cc_final: 0.8448 (mmm) REVERT: C 1975 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7698 (pmm) REVERT: C 2192 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8028 (tmm) REVERT: C 2456 MET cc_start: 0.8795 (tpp) cc_final: 0.8254 (tpt) REVERT: C 2724 TYR cc_start: 0.8997 (t80) cc_final: 0.8716 (t80) REVERT: C 2840 MET cc_start: 0.9112 (mtt) cc_final: 0.8589 (mtt) REVERT: C 2852 TRP cc_start: 0.9055 (t60) cc_final: 0.8724 (t60) REVERT: C 3072 MET cc_start: 0.9010 (mmp) cc_final: 0.8667 (mmm) REVERT: C 3104 MET cc_start: 0.9057 (ptp) cc_final: 0.8660 (ptt) REVERT: C 3109 PHE cc_start: 0.8941 (m-80) cc_final: 0.8398 (m-80) REVERT: C 3159 LEU cc_start: 0.9039 (tp) cc_final: 0.8746 (tp) REVERT: C 3241 MET cc_start: 0.8902 (ppp) cc_final: 0.8629 (ppp) REVERT: C 3250 TRP cc_start: 0.8838 (t60) cc_final: 0.8619 (t60) REVERT: C 3299 LEU cc_start: 0.9391 (mt) cc_final: 0.9140 (mt) REVERT: C 3981 MET cc_start: 0.8513 (tmm) cc_final: 0.8294 (ttp) REVERT: C 4279 MET cc_start: 0.7254 (ptt) cc_final: 0.6971 (mtm) REVERT: C 4707 MET cc_start: 0.8318 (ttm) cc_final: 0.8078 (ttp) REVERT: D 393 MET cc_start: 0.7649 (tpt) cc_final: 0.7093 (mmm) REVERT: D 933 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8189 (mt) REVERT: D 1564 MET cc_start: 0.8692 (tpp) cc_final: 0.8445 (mmm) REVERT: D 1975 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7687 (pmm) REVERT: D 2724 TYR cc_start: 0.8987 (t80) cc_final: 0.8724 (t80) REVERT: D 2840 MET cc_start: 0.9110 (mtt) cc_final: 0.8587 (mtt) REVERT: D 2852 TRP cc_start: 0.9057 (t60) cc_final: 0.8742 (t60) REVERT: D 3072 MET cc_start: 0.9011 (mmp) cc_final: 0.8662 (mmm) REVERT: D 3104 MET cc_start: 0.9045 (ptp) cc_final: 0.8657 (ptt) REVERT: D 3109 PHE cc_start: 0.8919 (m-80) cc_final: 0.8420 (m-80) REVERT: D 3159 LEU cc_start: 0.9032 (tp) cc_final: 0.8751 (tp) REVERT: D 3241 MET cc_start: 0.8892 (ppp) cc_final: 0.8620 (ppp) REVERT: D 3250 TRP cc_start: 0.8837 (t60) cc_final: 0.8618 (t60) REVERT: D 3299 LEU cc_start: 0.9375 (mt) cc_final: 0.9135 (mt) REVERT: D 3972 MET cc_start: 0.8154 (mtp) cc_final: 0.7871 (mtp) REVERT: D 3981 MET cc_start: 0.8509 (tmm) cc_final: 0.8284 (ttp) REVERT: D 4279 MET cc_start: 0.7279 (ptt) cc_final: 0.6997 (mtm) REVERT: D 4707 MET cc_start: 0.8305 (ttm) cc_final: 0.8065 (ttp) outliers start: 87 outliers final: 44 residues processed: 717 average time/residue: 1.1474 time to fit residues: 1471.1157 Evaluate side-chains 713 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 657 time to evaluate : 10.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 931 TYR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4629 GLN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1173 MET Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1173 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 3296 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 20.0000 chunk 1504 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 980 optimal weight: 7.9990 chunk 412 optimal weight: 2.9990 chunk 1671 optimal weight: 7.9990 chunk 1387 optimal weight: 6.9990 chunk 774 optimal weight: 0.4980 chunk 139 optimal weight: 20.0000 chunk 553 optimal weight: 50.0000 chunk 877 optimal weight: 4.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4629 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 141720 Z= 0.268 Angle : 0.563 13.706 191484 Z= 0.288 Chirality : 0.039 0.202 20988 Planarity : 0.004 0.129 24600 Dihedral : 7.552 158.688 19124 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 0.61 % Allowed : 7.21 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.07), residues: 17212 helix: 1.82 (0.06), residues: 9164 sheet: -0.20 (0.13), residues: 1732 loop : -0.47 (0.08), residues: 6316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP A 893 HIS 0.007 0.001 HIS A 395 PHE 0.021 0.001 PHE A3170 TYR 0.025 0.001 TYR C1703 ARG 0.006 0.000 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 653 time to evaluate : 11.619 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: A 393 MET cc_start: 0.7635 (tpt) cc_final: 0.7077 (mmm) REVERT: A 933 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8187 (mt) REVERT: A 935 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8901 (ptp) REVERT: A 995 MET cc_start: 0.9111 (ttp) cc_final: 0.7847 (tmm) REVERT: A 1174 MET cc_start: 0.7661 (ptm) cc_final: 0.7174 (ptm) REVERT: A 1975 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7648 (pmm) REVERT: A 2397 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7914 (t0) REVERT: A 2605 MET cc_start: 0.8717 (ppp) cc_final: 0.8388 (ppp) REVERT: A 2681 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8294 (tpp) REVERT: A 2688 MET cc_start: 0.8571 (mpp) cc_final: 0.8309 (mpp) REVERT: A 2724 TYR cc_start: 0.8969 (t80) cc_final: 0.8590 (t80) REVERT: A 2732 TRP cc_start: 0.9078 (t60) cc_final: 0.8763 (t60) REVERT: A 2840 MET cc_start: 0.8856 (mtt) cc_final: 0.8278 (mtt) REVERT: A 2844 MET cc_start: 0.9219 (ppp) cc_final: 0.8996 (ppp) REVERT: A 2848 TYR cc_start: 0.8878 (m-80) cc_final: 0.8671 (m-10) REVERT: A 2852 TRP cc_start: 0.9322 (t60) cc_final: 0.9100 (t60) REVERT: A 2877 LEU cc_start: 0.8791 (mt) cc_final: 0.8509 (mt) REVERT: A 2886 ARG cc_start: 0.9504 (ttm110) cc_final: 0.9246 (ttm110) REVERT: A 3003 MET cc_start: 0.9020 (ptm) cc_final: 0.8298 (ppp) REVERT: A 3046 MET cc_start: 0.8561 (mmm) cc_final: 0.8209 (mmm) REVERT: A 3072 MET cc_start: 0.8987 (mmp) cc_final: 0.8646 (mmp) REVERT: A 3104 MET cc_start: 0.8945 (ptp) cc_final: 0.8009 (tmm) REVERT: A 3263 MET cc_start: 0.8865 (tpt) cc_final: 0.8359 (tpp) REVERT: A 3315 LEU cc_start: 0.9116 (mt) cc_final: 0.8855 (mm) REVERT: A 3319 PHE cc_start: 0.8498 (m-80) cc_final: 0.8070 (m-80) REVERT: A 3605 MET cc_start: 0.5837 (ptm) cc_final: 0.5141 (mmm) REVERT: A 3981 MET cc_start: 0.8224 (ttp) cc_final: 0.7595 (ttp) REVERT: A 4161 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: A 4279 MET cc_start: 0.7318 (ptt) cc_final: 0.7041 (mtm) REVERT: A 4707 MET cc_start: 0.8291 (ttm) cc_final: 0.8042 (ttp) REVERT: B 393 MET cc_start: 0.7688 (tpt) cc_final: 0.7086 (mmm) REVERT: B 933 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8162 (mt) REVERT: B 1564 MET cc_start: 0.8685 (tpp) cc_final: 0.8416 (mmm) REVERT: B 1721 MET cc_start: 0.7788 (mmm) cc_final: 0.7575 (mmm) REVERT: B 1975 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7705 (pmm) REVERT: B 2456 MET cc_start: 0.8802 (tpp) cc_final: 0.7876 (tpt) REVERT: B 2512 MET cc_start: 0.8643 (tpp) cc_final: 0.8399 (tpp) REVERT: B 2724 TYR cc_start: 0.8993 (t80) cc_final: 0.8693 (t80) REVERT: B 2798 MET cc_start: 0.7286 (mmp) cc_final: 0.7076 (mmp) REVERT: B 2840 MET cc_start: 0.9104 (mtt) cc_final: 0.8555 (mtt) REVERT: B 2852 TRP cc_start: 0.9052 (t60) cc_final: 0.8712 (t60) REVERT: B 2858 MET cc_start: 0.9263 (pmm) cc_final: 0.8991 (pmm) REVERT: B 3003 MET cc_start: 0.9099 (ptm) cc_final: 0.8565 (ppp) REVERT: B 3072 MET cc_start: 0.9021 (mmp) cc_final: 0.8656 (mmp) REVERT: B 3104 MET cc_start: 0.9040 (ptp) cc_final: 0.8654 (ptt) REVERT: B 3109 PHE cc_start: 0.8928 (m-80) cc_final: 0.8378 (m-80) REVERT: B 3140 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8680 (mt) REVERT: B 3250 TRP cc_start: 0.8825 (t60) cc_final: 0.8600 (t60) REVERT: B 3260 ARG cc_start: 0.7969 (tmt170) cc_final: 0.7532 (ttt90) REVERT: B 3299 LEU cc_start: 0.9379 (mt) cc_final: 0.9142 (mt) REVERT: B 3981 MET cc_start: 0.8503 (tmm) cc_final: 0.8285 (ttp) REVERT: B 4161 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 4279 MET cc_start: 0.7293 (ptt) cc_final: 0.7025 (mtm) REVERT: B 4707 MET cc_start: 0.8304 (ttm) cc_final: 0.8057 (ttp) REVERT: C 393 MET cc_start: 0.7679 (tpt) cc_final: 0.7071 (mmm) REVERT: C 655 MET cc_start: 0.8562 (mmm) cc_final: 0.8194 (mmp) REVERT: C 933 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8131 (mt) REVERT: C 1564 MET cc_start: 0.8666 (tpp) cc_final: 0.8404 (mmm) REVERT: C 1975 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7662 (pmm) REVERT: C 2456 MET cc_start: 0.8709 (tpp) cc_final: 0.8280 (tpt) REVERT: C 2724 TYR cc_start: 0.8977 (t80) cc_final: 0.8674 (t80) REVERT: C 2840 MET cc_start: 0.9109 (mtt) cc_final: 0.8562 (mtt) REVERT: C 2852 TRP cc_start: 0.9051 (t60) cc_final: 0.8712 (t60) REVERT: C 2858 MET cc_start: 0.9267 (pmm) cc_final: 0.9001 (pmm) REVERT: C 3003 MET cc_start: 0.9083 (ptm) cc_final: 0.8576 (ppp) REVERT: C 3072 MET cc_start: 0.9025 (mmp) cc_final: 0.8647 (mmp) REVERT: C 3104 MET cc_start: 0.9044 (ptp) cc_final: 0.8649 (ptt) REVERT: C 3109 PHE cc_start: 0.8931 (m-80) cc_final: 0.8374 (m-80) REVERT: C 3140 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8681 (mt) REVERT: C 3250 TRP cc_start: 0.8811 (t60) cc_final: 0.8579 (t60) REVERT: C 3299 LEU cc_start: 0.9364 (mt) cc_final: 0.9116 (mt) REVERT: C 3981 MET cc_start: 0.8506 (tmm) cc_final: 0.8290 (ttp) REVERT: C 4161 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: C 4279 MET cc_start: 0.7341 (ptt) cc_final: 0.7064 (mtm) REVERT: C 4707 MET cc_start: 0.8310 (ttm) cc_final: 0.8069 (ttp) REVERT: D 393 MET cc_start: 0.7681 (tpt) cc_final: 0.7086 (mmm) REVERT: D 933 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8149 (mt) REVERT: D 1564 MET cc_start: 0.8682 (tpp) cc_final: 0.8415 (mmm) REVERT: D 1975 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7680 (pmm) REVERT: D 2456 MET cc_start: 0.8799 (tpp) cc_final: 0.7876 (tpt) REVERT: D 2512 MET cc_start: 0.8644 (tpp) cc_final: 0.8399 (tpp) REVERT: D 2724 TYR cc_start: 0.8981 (t80) cc_final: 0.8688 (t80) REVERT: D 2798 MET cc_start: 0.7181 (mmp) cc_final: 0.6964 (mmp) REVERT: D 2840 MET cc_start: 0.9105 (mtt) cc_final: 0.8556 (mtt) REVERT: D 2852 TRP cc_start: 0.9050 (t60) cc_final: 0.8711 (t60) REVERT: D 2858 MET cc_start: 0.9271 (pmm) cc_final: 0.9004 (pmm) REVERT: D 3003 MET cc_start: 0.9096 (ptm) cc_final: 0.8557 (ppp) REVERT: D 3072 MET cc_start: 0.9023 (mmp) cc_final: 0.8652 (mmp) REVERT: D 3104 MET cc_start: 0.9035 (ptp) cc_final: 0.8648 (ptt) REVERT: D 3109 PHE cc_start: 0.8923 (m-80) cc_final: 0.8406 (m-80) REVERT: D 3140 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8680 (mt) REVERT: D 3250 TRP cc_start: 0.8821 (t60) cc_final: 0.8595 (t60) REVERT: D 3299 LEU cc_start: 0.9377 (mt) cc_final: 0.9151 (mt) REVERT: D 3972 MET cc_start: 0.8132 (mtp) cc_final: 0.7857 (mtp) REVERT: D 3981 MET cc_start: 0.8501 (tmm) cc_final: 0.8277 (ttp) REVERT: D 4161 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: D 4279 MET cc_start: 0.7306 (ptt) cc_final: 0.7035 (mtm) REVERT: D 4707 MET cc_start: 0.8301 (ttm) cc_final: 0.8055 (ttp) outliers start: 92 outliers final: 59 residues processed: 709 average time/residue: 1.1576 time to fit residues: 1472.9560 Evaluate side-chains 728 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 651 time to evaluate : 11.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 931 TYR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2397 ASP Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4629 GLN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3140 LEU Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2384 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3140 LEU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4161 GLU Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3140 LEU Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 4161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 952 optimal weight: 10.0000 chunk 1220 optimal weight: 1.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 30.0000 chunk 933 optimal weight: 6.9990 chunk 1665 optimal weight: 7.9990 chunk 1042 optimal weight: 7.9990 chunk 1015 optimal weight: 9.9990 chunk 768 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4629 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3905 ASN ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 141720 Z= 0.351 Angle : 0.587 13.151 191484 Z= 0.302 Chirality : 0.040 0.193 20988 Planarity : 0.004 0.127 24600 Dihedral : 7.530 159.374 19124 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 0.61 % Allowed : 7.46 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.07), residues: 17212 helix: 1.79 (0.06), residues: 9160 sheet: -0.21 (0.13), residues: 1732 loop : -0.48 (0.08), residues: 6320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 893 HIS 0.008 0.001 HIS A 395 PHE 0.025 0.001 PHE D3854 TYR 0.026 0.002 TYR B1703 ARG 0.007 0.000 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 662 time to evaluate : 11.737 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: A 393 MET cc_start: 0.7624 (tpt) cc_final: 0.7008 (mmm) REVERT: A 655 MET cc_start: 0.8555 (mmm) cc_final: 0.8153 (mmp) REVERT: A 933 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8174 (mt) REVERT: A 935 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8927 (ptp) REVERT: A 995 MET cc_start: 0.9103 (ttp) cc_final: 0.7842 (tmm) REVERT: A 1831 MET cc_start: 0.9103 (mtp) cc_final: 0.8850 (mtm) REVERT: A 1975 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7636 (pmm) REVERT: A 2397 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7883 (t0) REVERT: A 2605 MET cc_start: 0.8786 (ppp) cc_final: 0.8509 (ppp) REVERT: A 2681 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8304 (tpp) REVERT: A 2688 MET cc_start: 0.8576 (mpp) cc_final: 0.8333 (mpp) REVERT: A 2724 TYR cc_start: 0.9000 (t80) cc_final: 0.8567 (t80) REVERT: A 2732 TRP cc_start: 0.9098 (t60) cc_final: 0.8763 (t60) REVERT: A 2840 MET cc_start: 0.8847 (mtt) cc_final: 0.8268 (mtt) REVERT: A 2844 MET cc_start: 0.9221 (ppp) cc_final: 0.9004 (ppp) REVERT: A 2877 LEU cc_start: 0.8823 (mt) cc_final: 0.8563 (mt) REVERT: A 3003 MET cc_start: 0.9029 (ptm) cc_final: 0.8456 (ppp) REVERT: A 3046 MET cc_start: 0.8613 (mmm) cc_final: 0.8240 (mmm) REVERT: A 3072 MET cc_start: 0.9026 (mmp) cc_final: 0.8701 (mmp) REVERT: A 3104 MET cc_start: 0.8964 (ptp) cc_final: 0.8034 (tmm) REVERT: A 3109 PHE cc_start: 0.9037 (m-80) cc_final: 0.8470 (m-80) REVERT: A 3221 LEU cc_start: 0.9163 (mt) cc_final: 0.8951 (mt) REVERT: A 3315 LEU cc_start: 0.9121 (mt) cc_final: 0.8877 (mm) REVERT: A 3319 PHE cc_start: 0.8510 (m-80) cc_final: 0.8086 (m-80) REVERT: A 3981 MET cc_start: 0.8229 (ttp) cc_final: 0.7604 (ttp) REVERT: A 4279 MET cc_start: 0.7360 (ptt) cc_final: 0.6979 (mtm) REVERT: A 4629 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: A 4707 MET cc_start: 0.8301 (ttm) cc_final: 0.8051 (ttp) REVERT: B 393 MET cc_start: 0.7702 (tpt) cc_final: 0.7094 (mmm) REVERT: B 933 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8161 (mt) REVERT: B 1564 MET cc_start: 0.8714 (tpp) cc_final: 0.8467 (mmm) REVERT: B 1831 MET cc_start: 0.9096 (mtp) cc_final: 0.8841 (mtm) REVERT: B 1975 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7707 (pmm) REVERT: B 2442 MET cc_start: 0.9008 (mmp) cc_final: 0.8730 (mmm) REVERT: B 2456 MET cc_start: 0.8828 (tpp) cc_final: 0.8561 (tpt) REVERT: B 2724 TYR cc_start: 0.8993 (t80) cc_final: 0.8681 (t80) REVERT: B 2798 MET cc_start: 0.7327 (mmp) cc_final: 0.7112 (mmp) REVERT: B 2840 MET cc_start: 0.9100 (mtt) cc_final: 0.8567 (mtt) REVERT: B 2852 TRP cc_start: 0.9046 (t60) cc_final: 0.8715 (t60) REVERT: B 3072 MET cc_start: 0.9009 (mmp) cc_final: 0.8689 (mmp) REVERT: B 3104 MET cc_start: 0.9042 (ptp) cc_final: 0.8659 (ptt) REVERT: B 3109 PHE cc_start: 0.8944 (m-80) cc_final: 0.8431 (m-80) REVERT: B 3140 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8725 (mt) REVERT: B 3250 TRP cc_start: 0.8838 (t60) cc_final: 0.8596 (t60) REVERT: B 3299 LEU cc_start: 0.9381 (mt) cc_final: 0.9141 (mt) REVERT: B 3981 MET cc_start: 0.8505 (tmm) cc_final: 0.8282 (ttp) REVERT: B 4279 MET cc_start: 0.7335 (ptt) cc_final: 0.7062 (mtm) REVERT: B 4641 PRO cc_start: 0.8516 (OUTLIER) cc_final: 0.8117 (Cg_endo) REVERT: B 4707 MET cc_start: 0.8303 (ttm) cc_final: 0.8054 (ttp) REVERT: C 393 MET cc_start: 0.7680 (tpt) cc_final: 0.7060 (mmm) REVERT: C 655 MET cc_start: 0.8677 (mmm) cc_final: 0.8454 (mmp) REVERT: C 933 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8139 (mt) REVERT: C 1564 MET cc_start: 0.8710 (tpp) cc_final: 0.8461 (mmm) REVERT: C 1831 MET cc_start: 0.9100 (mtp) cc_final: 0.8851 (mtm) REVERT: C 1975 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7674 (pmm) REVERT: C 2724 TYR cc_start: 0.8978 (t80) cc_final: 0.8662 (t80) REVERT: C 2840 MET cc_start: 0.9107 (mtt) cc_final: 0.8564 (mtt) REVERT: C 2852 TRP cc_start: 0.9045 (t60) cc_final: 0.8679 (t60) REVERT: C 3072 MET cc_start: 0.9036 (mmp) cc_final: 0.8750 (mmp) REVERT: C 3104 MET cc_start: 0.9048 (ptp) cc_final: 0.8656 (ptt) REVERT: C 3109 PHE cc_start: 0.8952 (m-80) cc_final: 0.8394 (m-80) REVERT: C 3140 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8721 (mt) REVERT: C 3241 MET cc_start: 0.8844 (ppp) cc_final: 0.8430 (ppp) REVERT: C 3250 TRP cc_start: 0.8838 (t60) cc_final: 0.8608 (t60) REVERT: C 3299 LEU cc_start: 0.9379 (mt) cc_final: 0.9143 (mt) REVERT: C 3981 MET cc_start: 0.8498 (tmm) cc_final: 0.8295 (ttp) REVERT: C 4279 MET cc_start: 0.7311 (ptt) cc_final: 0.6939 (mtm) REVERT: C 4641 PRO cc_start: 0.8515 (OUTLIER) cc_final: 0.8115 (Cg_endo) REVERT: C 4707 MET cc_start: 0.8311 (ttm) cc_final: 0.8057 (ttp) REVERT: D 393 MET cc_start: 0.7689 (tpt) cc_final: 0.7092 (mmm) REVERT: D 933 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8146 (mt) REVERT: D 1564 MET cc_start: 0.8716 (tpp) cc_final: 0.8470 (mmm) REVERT: D 1975 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7714 (pmm) REVERT: D 2442 MET cc_start: 0.9000 (mmp) cc_final: 0.8728 (mmm) REVERT: D 2456 MET cc_start: 0.8831 (tpp) cc_final: 0.8560 (tpt) REVERT: D 2724 TYR cc_start: 0.8993 (t80) cc_final: 0.8681 (t80) REVERT: D 2798 MET cc_start: 0.7314 (mmp) cc_final: 0.7099 (mmp) REVERT: D 2840 MET cc_start: 0.9098 (mtt) cc_final: 0.8562 (mtt) REVERT: D 2852 TRP cc_start: 0.9037 (t60) cc_final: 0.8700 (t60) REVERT: D 3072 MET cc_start: 0.9030 (mmp) cc_final: 0.8700 (mmp) REVERT: D 3104 MET cc_start: 0.9039 (ptp) cc_final: 0.8658 (ptt) REVERT: D 3109 PHE cc_start: 0.8936 (m-80) cc_final: 0.8430 (m-80) REVERT: D 3140 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8725 (mt) REVERT: D 3250 TRP cc_start: 0.8839 (t60) cc_final: 0.8615 (t60) REVERT: D 3299 LEU cc_start: 0.9382 (mt) cc_final: 0.9146 (mt) REVERT: D 3981 MET cc_start: 0.8501 (tmm) cc_final: 0.8283 (ttp) REVERT: D 4279 MET cc_start: 0.7347 (ptt) cc_final: 0.6969 (mtm) REVERT: D 4641 PRO cc_start: 0.8531 (OUTLIER) cc_final: 0.8132 (Cg_endo) REVERT: D 4707 MET cc_start: 0.8299 (ttm) cc_final: 0.8053 (ttp) outliers start: 92 outliers final: 52 residues processed: 720 average time/residue: 1.1767 time to fit residues: 1527.6187 Evaluate side-chains 722 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 652 time to evaluate : 11.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 931 TYR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2397 ASP Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4629 GLN Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3140 LEU Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain B residue 4641 PRO Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2384 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3140 LEU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1173 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3140 LEU Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 0.7980 chunk 665 optimal weight: 6.9990 chunk 994 optimal weight: 8.9990 chunk 501 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 322 optimal weight: 50.0000 chunk 1058 optimal weight: 7.9990 chunk 1134 optimal weight: 20.0000 chunk 823 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 1309 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4629 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 141720 Z= 0.271 Angle : 0.569 12.960 191484 Z= 0.290 Chirality : 0.039 0.198 20988 Planarity : 0.004 0.126 24600 Dihedral : 7.446 159.701 19112 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.72 % Rotamer: Outliers : 0.57 % Allowed : 7.59 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.07), residues: 17212 helix: 1.83 (0.06), residues: 9156 sheet: -0.21 (0.13), residues: 1700 loop : -0.47 (0.08), residues: 6356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP D 893 HIS 0.008 0.001 HIS C2729 PHE 0.018 0.001 PHE A3170 TYR 0.022 0.001 TYR D1703 ARG 0.006 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 657 time to evaluate : 11.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.7622 (tpt) cc_final: 0.7187 (mmm) REVERT: A 655 MET cc_start: 0.8573 (mmm) cc_final: 0.8256 (mmp) REVERT: A 933 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 935 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8932 (ptp) REVERT: A 995 MET cc_start: 0.9083 (ttp) cc_final: 0.7840 (tmm) REVERT: A 1831 MET cc_start: 0.9089 (mtp) cc_final: 0.8829 (mtm) REVERT: A 1975 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7634 (pmm) REVERT: A 2142 MET cc_start: 0.8043 (tmm) cc_final: 0.7819 (tmm) REVERT: A 2397 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7881 (t0) REVERT: A 2605 MET cc_start: 0.8786 (ppp) cc_final: 0.8491 (ppp) REVERT: A 2681 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8271 (tpp) REVERT: A 2688 MET cc_start: 0.8550 (mpp) cc_final: 0.8317 (mpp) REVERT: A 2724 TYR cc_start: 0.9008 (t80) cc_final: 0.8571 (t80) REVERT: A 2732 TRP cc_start: 0.9076 (t60) cc_final: 0.8721 (t60) REVERT: A 2840 MET cc_start: 0.8877 (mtt) cc_final: 0.8364 (mtt) REVERT: A 2877 LEU cc_start: 0.8830 (mt) cc_final: 0.8621 (mt) REVERT: A 3046 MET cc_start: 0.8613 (mmm) cc_final: 0.8251 (mmm) REVERT: A 3072 MET cc_start: 0.9048 (mmp) cc_final: 0.8683 (mmp) REVERT: A 3104 MET cc_start: 0.8959 (ptp) cc_final: 0.8032 (tmm) REVERT: A 3109 PHE cc_start: 0.9012 (m-80) cc_final: 0.8436 (m-80) REVERT: A 3263 MET cc_start: 0.8817 (tpt) cc_final: 0.8325 (tpp) REVERT: A 3315 LEU cc_start: 0.9131 (mt) cc_final: 0.8878 (mm) REVERT: A 3319 PHE cc_start: 0.8483 (m-80) cc_final: 0.8048 (m-80) REVERT: A 3981 MET cc_start: 0.8227 (ttp) cc_final: 0.7603 (ttp) REVERT: A 4279 MET cc_start: 0.7367 (ptt) cc_final: 0.7095 (mtm) REVERT: A 4641 PRO cc_start: 0.8527 (OUTLIER) cc_final: 0.8133 (Cg_endo) REVERT: A 4707 MET cc_start: 0.8290 (ttm) cc_final: 0.8036 (ttp) REVERT: B 393 MET cc_start: 0.7694 (tpt) cc_final: 0.7276 (mmm) REVERT: B 933 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8140 (mt) REVERT: B 1564 MET cc_start: 0.8701 (tpp) cc_final: 0.8431 (mmm) REVERT: B 1831 MET cc_start: 0.9075 (mtp) cc_final: 0.8818 (mtm) REVERT: B 1975 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7701 (pmm) REVERT: B 2456 MET cc_start: 0.8821 (tpp) cc_final: 0.8162 (tpt) REVERT: B 2724 TYR cc_start: 0.8977 (t80) cc_final: 0.8670 (t80) REVERT: B 2773 TRP cc_start: 0.9057 (t60) cc_final: 0.8827 (t60) REVERT: B 2798 MET cc_start: 0.7282 (mmp) cc_final: 0.7067 (mmp) REVERT: B 2840 MET cc_start: 0.9095 (mtt) cc_final: 0.8543 (mtt) REVERT: B 2852 TRP cc_start: 0.9035 (t60) cc_final: 0.8648 (t60) REVERT: B 3003 MET cc_start: 0.9053 (ptm) cc_final: 0.8535 (ppp) REVERT: B 3072 MET cc_start: 0.9044 (mmp) cc_final: 0.8719 (mmp) REVERT: B 3104 MET cc_start: 0.9037 (ptp) cc_final: 0.8650 (ptt) REVERT: B 3109 PHE cc_start: 0.8940 (m-80) cc_final: 0.8388 (m-80) REVERT: B 3140 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 3250 TRP cc_start: 0.8825 (t60) cc_final: 0.8593 (t60) REVERT: B 3299 LEU cc_start: 0.9357 (mt) cc_final: 0.9136 (mt) REVERT: B 3605 MET cc_start: 0.6350 (ttp) cc_final: 0.5318 (mmm) REVERT: B 3981 MET cc_start: 0.8486 (tmm) cc_final: 0.8281 (ttp) REVERT: B 4279 MET cc_start: 0.7343 (ptt) cc_final: 0.7062 (mtm) REVERT: B 4641 PRO cc_start: 0.8510 (OUTLIER) cc_final: 0.8105 (Cg_endo) REVERT: B 4707 MET cc_start: 0.8297 (ttm) cc_final: 0.8046 (ttp) REVERT: C 393 MET cc_start: 0.7683 (tpt) cc_final: 0.7262 (mmm) REVERT: C 933 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8159 (mt) REVERT: C 1564 MET cc_start: 0.8676 (tpp) cc_final: 0.8415 (mmm) REVERT: C 1831 MET cc_start: 0.9082 (mtp) cc_final: 0.8826 (mtm) REVERT: C 1975 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7711 (pmm) REVERT: C 2724 TYR cc_start: 0.8961 (t80) cc_final: 0.8650 (t80) REVERT: C 2840 MET cc_start: 0.9105 (mtt) cc_final: 0.8555 (mtt) REVERT: C 2852 TRP cc_start: 0.9029 (t60) cc_final: 0.8639 (t60) REVERT: C 3003 MET cc_start: 0.9061 (ptm) cc_final: 0.8561 (ppp) REVERT: C 3072 MET cc_start: 0.9034 (mmp) cc_final: 0.8713 (mmp) REVERT: C 3104 MET cc_start: 0.9039 (ptp) cc_final: 0.8638 (ptt) REVERT: C 3109 PHE cc_start: 0.8955 (m-80) cc_final: 0.8390 (m-80) REVERT: C 3140 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 3241 MET cc_start: 0.8885 (ppp) cc_final: 0.8628 (ppp) REVERT: C 3250 TRP cc_start: 0.8806 (t60) cc_final: 0.8573 (t60) REVERT: C 3299 LEU cc_start: 0.9354 (mt) cc_final: 0.9145 (mt) REVERT: C 3605 MET cc_start: 0.6259 (ttp) cc_final: 0.5222 (mmm) REVERT: C 4279 MET cc_start: 0.7381 (ptt) cc_final: 0.7031 (mtm) REVERT: C 4641 PRO cc_start: 0.8509 (OUTLIER) cc_final: 0.8103 (Cg_endo) REVERT: C 4707 MET cc_start: 0.8301 (ttm) cc_final: 0.8043 (ttp) REVERT: D 128 MET cc_start: 0.8965 (mtm) cc_final: 0.8700 (mtm) REVERT: D 393 MET cc_start: 0.7691 (tpt) cc_final: 0.7283 (mmm) REVERT: D 933 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8153 (mt) REVERT: D 1564 MET cc_start: 0.8698 (tpp) cc_final: 0.8432 (mmm) REVERT: D 1975 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7702 (pmm) REVERT: D 2456 MET cc_start: 0.8816 (tpp) cc_final: 0.8159 (tpt) REVERT: D 2585 MET cc_start: 0.7882 (ptt) cc_final: 0.7414 (ppp) REVERT: D 2724 TYR cc_start: 0.8965 (t80) cc_final: 0.8662 (t80) REVERT: D 2773 TRP cc_start: 0.9056 (t60) cc_final: 0.8829 (t60) REVERT: D 2798 MET cc_start: 0.7271 (mmp) cc_final: 0.7064 (mmp) REVERT: D 2840 MET cc_start: 0.9090 (mtt) cc_final: 0.8538 (mtt) REVERT: D 2852 TRP cc_start: 0.9030 (t60) cc_final: 0.8644 (t60) REVERT: D 3003 MET cc_start: 0.9049 (ptm) cc_final: 0.8531 (ppp) REVERT: D 3072 MET cc_start: 0.9048 (mmp) cc_final: 0.8719 (mmp) REVERT: D 3104 MET cc_start: 0.9028 (ptp) cc_final: 0.8638 (ptt) REVERT: D 3109 PHE cc_start: 0.8938 (m-80) cc_final: 0.8380 (m-80) REVERT: D 3140 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8692 (mt) REVERT: D 3250 TRP cc_start: 0.8818 (t60) cc_final: 0.8571 (t60) REVERT: D 3299 LEU cc_start: 0.9360 (mt) cc_final: 0.9139 (mt) REVERT: D 3605 MET cc_start: 0.5798 (ptt) cc_final: 0.5282 (mmm) REVERT: D 3981 MET cc_start: 0.8483 (tmm) cc_final: 0.8260 (ttp) REVERT: D 4279 MET cc_start: 0.7368 (ptt) cc_final: 0.7086 (mtm) REVERT: D 4641 PRO cc_start: 0.8496 (OUTLIER) cc_final: 0.8089 (Cg_endo) REVERT: D 4707 MET cc_start: 0.8290 (ttm) cc_final: 0.8042 (ttp) outliers start: 86 outliers final: 51 residues processed: 710 average time/residue: 1.1919 time to fit residues: 1526.6788 Evaluate side-chains 718 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 649 time to evaluate : 11.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 931 TYR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2397 ASP Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4629 GLN Chi-restraints excluded: chain A residue 4641 PRO Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 2858 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3140 LEU Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain B residue 4641 PRO Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2858 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3140 LEU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3140 LEU Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 5.9990 chunk 1595 optimal weight: 4.9990 chunk 1455 optimal weight: 4.9990 chunk 1552 optimal weight: 40.0000 chunk 934 optimal weight: 9.9990 chunk 676 optimal weight: 7.9990 chunk 1218 optimal weight: 10.0000 chunk 476 optimal weight: 30.0000 chunk 1402 optimal weight: 5.9990 chunk 1467 optimal weight: 20.0000 chunk 1546 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 HIS ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3905 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 141720 Z= 0.332 Angle : 0.590 16.768 191484 Z= 0.302 Chirality : 0.040 0.201 20988 Planarity : 0.004 0.126 24600 Dihedral : 7.440 160.561 19112 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 0.52 % Allowed : 7.82 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.07), residues: 17212 helix: 1.80 (0.06), residues: 9156 sheet: -0.22 (0.13), residues: 1692 loop : -0.48 (0.08), residues: 6364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP C 893 HIS 0.008 0.001 HIS C2729 PHE 0.024 0.001 PHE C3854 TYR 0.061 0.001 TYR A2874 ARG 0.006 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 653 time to evaluate : 11.639 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: A 393 MET cc_start: 0.7623 (tpt) cc_final: 0.7181 (mmm) REVERT: A 655 MET cc_start: 0.8658 (mmm) cc_final: 0.8416 (mmp) REVERT: A 933 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8214 (mt) REVERT: A 935 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8934 (ptp) REVERT: A 995 MET cc_start: 0.9062 (ttp) cc_final: 0.7828 (tmm) REVERT: A 1831 MET cc_start: 0.9108 (mtp) cc_final: 0.8856 (mtm) REVERT: A 1975 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7600 (pmm) REVERT: A 2142 MET cc_start: 0.8044 (tmm) cc_final: 0.7818 (tmm) REVERT: A 2397 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7869 (t0) REVERT: A 2605 MET cc_start: 0.8838 (ppp) cc_final: 0.8612 (ppp) REVERT: A 2681 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8302 (tpp) REVERT: A 2688 MET cc_start: 0.8523 (mpp) cc_final: 0.8276 (mpp) REVERT: A 2724 TYR cc_start: 0.9011 (t80) cc_final: 0.8570 (t80) REVERT: A 2732 TRP cc_start: 0.9095 (t60) cc_final: 0.8723 (t60) REVERT: A 2840 MET cc_start: 0.8917 (mtt) cc_final: 0.8410 (mtt) REVERT: A 2877 LEU cc_start: 0.8872 (mt) cc_final: 0.8652 (mt) REVERT: A 3046 MET cc_start: 0.8639 (mmm) cc_final: 0.8223 (mmm) REVERT: A 3072 MET cc_start: 0.9058 (mmp) cc_final: 0.8708 (mmp) REVERT: A 3104 MET cc_start: 0.8975 (ptp) cc_final: 0.8049 (tmm) REVERT: A 3109 PHE cc_start: 0.9014 (m-80) cc_final: 0.8429 (m-80) REVERT: A 3221 LEU cc_start: 0.9326 (tp) cc_final: 0.9054 (mt) REVERT: A 3263 MET cc_start: 0.8783 (tpt) cc_final: 0.8251 (tpp) REVERT: A 3319 PHE cc_start: 0.8479 (m-80) cc_final: 0.8180 (m-80) REVERT: A 3981 MET cc_start: 0.8222 (ttp) cc_final: 0.7609 (ttp) REVERT: A 4279 MET cc_start: 0.7379 (ptt) cc_final: 0.7014 (mtm) REVERT: A 4629 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: A 4641 PRO cc_start: 0.8566 (OUTLIER) cc_final: 0.8184 (Cg_endo) REVERT: A 4707 MET cc_start: 0.8291 (ttm) cc_final: 0.8039 (ttp) REVERT: B 309 MET cc_start: 0.7314 (mmm) cc_final: 0.7066 (mmm) REVERT: B 393 MET cc_start: 0.7714 (tpt) cc_final: 0.7300 (mmm) REVERT: B 933 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8180 (mt) REVERT: B 995 MET cc_start: 0.8703 (ptm) cc_final: 0.7872 (tmm) REVERT: B 1564 MET cc_start: 0.8708 (tpp) cc_final: 0.8460 (mmm) REVERT: B 1831 MET cc_start: 0.9096 (mtp) cc_final: 0.8847 (mtm) REVERT: B 1975 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7698 (pmm) REVERT: B 2134 MET cc_start: 0.8291 (mmm) cc_final: 0.8000 (mmm) REVERT: B 2442 MET cc_start: 0.9015 (mmp) cc_final: 0.8812 (mmm) REVERT: B 2512 MET cc_start: 0.8652 (tpp) cc_final: 0.8419 (tpp) REVERT: B 2724 TYR cc_start: 0.8987 (t80) cc_final: 0.8675 (t80) REVERT: B 2773 TRP cc_start: 0.9069 (t60) cc_final: 0.8840 (t60) REVERT: B 2840 MET cc_start: 0.9091 (mtt) cc_final: 0.8532 (mtt) REVERT: B 2852 TRP cc_start: 0.9035 (t60) cc_final: 0.8647 (t60) REVERT: B 3003 MET cc_start: 0.9044 (ptm) cc_final: 0.8532 (ppp) REVERT: B 3072 MET cc_start: 0.9049 (mmp) cc_final: 0.8770 (mmm) REVERT: B 3104 MET cc_start: 0.9048 (ptp) cc_final: 0.8646 (ptt) REVERT: B 3109 PHE cc_start: 0.8963 (m-80) cc_final: 0.8416 (m-80) REVERT: B 3140 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8725 (mt) REVERT: B 3250 TRP cc_start: 0.8827 (t60) cc_final: 0.8572 (t60) REVERT: B 3299 LEU cc_start: 0.9360 (mt) cc_final: 0.9145 (mt) REVERT: B 3605 MET cc_start: 0.6427 (ttp) cc_final: 0.5481 (mmm) REVERT: B 4279 MET cc_start: 0.7372 (ptt) cc_final: 0.6988 (mtm) REVERT: B 4641 PRO cc_start: 0.8539 (OUTLIER) cc_final: 0.8151 (Cg_endo) REVERT: B 4707 MET cc_start: 0.8293 (ttm) cc_final: 0.8044 (ttp) REVERT: C 309 MET cc_start: 0.7318 (mmm) cc_final: 0.7034 (mmm) REVERT: C 393 MET cc_start: 0.7683 (tpt) cc_final: 0.7257 (mmm) REVERT: C 933 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8171 (mt) REVERT: C 995 MET cc_start: 0.8687 (ptm) cc_final: 0.7845 (tmm) REVERT: C 1564 MET cc_start: 0.8689 (tpp) cc_final: 0.8451 (mmm) REVERT: C 1831 MET cc_start: 0.9097 (mtp) cc_final: 0.8841 (mtm) REVERT: C 1975 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7719 (pmm) REVERT: C 2456 MET cc_start: 0.8842 (tpp) cc_final: 0.8457 (tpt) REVERT: C 2724 TYR cc_start: 0.8977 (t80) cc_final: 0.8665 (t80) REVERT: C 2840 MET cc_start: 0.9126 (mtt) cc_final: 0.8579 (mtt) REVERT: C 2852 TRP cc_start: 0.9048 (t60) cc_final: 0.8668 (t60) REVERT: C 3003 MET cc_start: 0.9045 (ptm) cc_final: 0.8533 (ppp) REVERT: C 3072 MET cc_start: 0.9044 (mmp) cc_final: 0.8750 (mmm) REVERT: C 3104 MET cc_start: 0.9044 (ptp) cc_final: 0.8644 (ptt) REVERT: C 3109 PHE cc_start: 0.8970 (m-80) cc_final: 0.8405 (m-80) REVERT: C 3140 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8725 (mt) REVERT: C 3241 MET cc_start: 0.8882 (ppp) cc_final: 0.8583 (ppp) REVERT: C 3250 TRP cc_start: 0.8819 (t60) cc_final: 0.8581 (t60) REVERT: C 3299 LEU cc_start: 0.9349 (mt) cc_final: 0.9133 (mt) REVERT: C 3605 MET cc_start: 0.6329 (ttp) cc_final: 0.5310 (mmm) REVERT: C 4279 MET cc_start: 0.7426 (ptt) cc_final: 0.7062 (mtm) REVERT: C 4641 PRO cc_start: 0.8539 (OUTLIER) cc_final: 0.8151 (Cg_endo) REVERT: C 4707 MET cc_start: 0.8299 (ttm) cc_final: 0.8047 (ttp) REVERT: D 309 MET cc_start: 0.7325 (mmm) cc_final: 0.7073 (mmm) REVERT: D 393 MET cc_start: 0.7662 (tpt) cc_final: 0.7255 (mmm) REVERT: D 933 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8183 (mt) REVERT: D 995 MET cc_start: 0.8698 (ptm) cc_final: 0.7859 (tmm) REVERT: D 1564 MET cc_start: 0.8711 (tpp) cc_final: 0.8462 (mmm) REVERT: D 1975 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7711 (pmm) REVERT: D 2134 MET cc_start: 0.8257 (mmm) cc_final: 0.8045 (mmm) REVERT: D 2142 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7804 (tmm) REVERT: D 2512 MET cc_start: 0.8649 (tpp) cc_final: 0.8416 (tpp) REVERT: D 2585 MET cc_start: 0.7807 (ptt) cc_final: 0.7464 (ppp) REVERT: D 2724 TYR cc_start: 0.8989 (t80) cc_final: 0.8674 (t80) REVERT: D 2773 TRP cc_start: 0.9069 (t60) cc_final: 0.8841 (t60) REVERT: D 2798 MET cc_start: 0.7278 (mmp) cc_final: 0.7071 (mmp) REVERT: D 2840 MET cc_start: 0.9096 (mtt) cc_final: 0.8537 (mtt) REVERT: D 2852 TRP cc_start: 0.9031 (t60) cc_final: 0.8644 (t60) REVERT: D 3003 MET cc_start: 0.9039 (ptm) cc_final: 0.8531 (ppp) REVERT: D 3072 MET cc_start: 0.9049 (mmp) cc_final: 0.8753 (mmm) REVERT: D 3104 MET cc_start: 0.9049 (ptp) cc_final: 0.8649 (ptt) REVERT: D 3109 PHE cc_start: 0.8947 (m-80) cc_final: 0.8400 (m-80) REVERT: D 3140 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8747 (mt) REVERT: D 3250 TRP cc_start: 0.8830 (t60) cc_final: 0.8580 (t60) REVERT: D 3299 LEU cc_start: 0.9359 (mt) cc_final: 0.9145 (mt) REVERT: D 3605 MET cc_start: 0.5882 (ptt) cc_final: 0.5298 (mmm) REVERT: D 3981 MET cc_start: 0.8486 (tmm) cc_final: 0.8283 (ttp) REVERT: D 4279 MET cc_start: 0.7382 (ptt) cc_final: 0.6996 (mtm) REVERT: D 4641 PRO cc_start: 0.8541 (OUTLIER) cc_final: 0.8154 (Cg_endo) REVERT: D 4707 MET cc_start: 0.8288 (ttm) cc_final: 0.8035 (ttp) outliers start: 79 outliers final: 45 residues processed: 702 average time/residue: 1.1562 time to fit residues: 1462.4305 Evaluate side-chains 715 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 650 time to evaluate : 10.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 931 TYR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2397 ASP Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4629 GLN Chi-restraints excluded: chain A residue 4641 PRO Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 2858 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3140 LEU Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain B residue 4641 PRO Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2858 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3140 LEU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3140 LEU Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 7.9990 chunk 1641 optimal weight: 2.9990 chunk 1001 optimal weight: 6.9990 chunk 778 optimal weight: 9.9990 chunk 1140 optimal weight: 6.9990 chunk 1721 optimal weight: 10.0000 chunk 1584 optimal weight: 0.5980 chunk 1370 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 1058 optimal weight: 7.9990 chunk 840 optimal weight: 0.6980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 GLN ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4629 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2091 GLN ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4579 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3269 ASN ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2091 GLN ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 141720 Z= 0.179 Angle : 0.557 13.937 191484 Z= 0.282 Chirality : 0.038 0.227 20988 Planarity : 0.004 0.124 24600 Dihedral : 7.352 161.064 19112 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 0.47 % Allowed : 7.94 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.07), residues: 17212 helix: 1.91 (0.06), residues: 9124 sheet: -0.29 (0.12), residues: 1744 loop : -0.41 (0.08), residues: 6344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.001 TRP D 893 HIS 0.007 0.001 HIS A3732 PHE 0.018 0.001 PHE A3170 TYR 0.046 0.001 TYR A2874 ARG 0.006 0.000 ARG E 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 659 time to evaluate : 11.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.7654 (tpt) cc_final: 0.7193 (mmm) REVERT: A 655 MET cc_start: 0.8601 (mmm) cc_final: 0.8362 (mmp) REVERT: A 933 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 935 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8919 (ptp) REVERT: A 995 MET cc_start: 0.9033 (ttp) cc_final: 0.7816 (tmm) REVERT: A 1975 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7613 (pmm) REVERT: A 2142 MET cc_start: 0.7998 (tmm) cc_final: 0.7797 (tmm) REVERT: A 2605 MET cc_start: 0.8811 (ppp) cc_final: 0.8578 (ppp) REVERT: A 2681 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8190 (tpp) REVERT: A 2688 MET cc_start: 0.8522 (mpp) cc_final: 0.8296 (mpp) REVERT: A 2724 TYR cc_start: 0.8966 (t80) cc_final: 0.8528 (t80) REVERT: A 2732 TRP cc_start: 0.9005 (t60) cc_final: 0.8705 (t60) REVERT: A 2840 MET cc_start: 0.8868 (mtt) cc_final: 0.8309 (mtt) REVERT: A 2852 TRP cc_start: 0.9292 (t60) cc_final: 0.9077 (t60) REVERT: A 2877 LEU cc_start: 0.8859 (mt) cc_final: 0.8638 (mt) REVERT: A 3046 MET cc_start: 0.8563 (mmm) cc_final: 0.8202 (mmm) REVERT: A 3072 MET cc_start: 0.9036 (mmp) cc_final: 0.8699 (mmp) REVERT: A 3104 MET cc_start: 0.8941 (ptp) cc_final: 0.8000 (tmm) REVERT: A 3109 PHE cc_start: 0.8998 (m-80) cc_final: 0.8406 (m-80) REVERT: A 3263 MET cc_start: 0.8758 (tpt) cc_final: 0.8214 (tpp) REVERT: A 3315 LEU cc_start: 0.9117 (mt) cc_final: 0.8875 (pp) REVERT: A 3319 PHE cc_start: 0.8500 (m-80) cc_final: 0.8155 (m-80) REVERT: A 3981 MET cc_start: 0.8197 (ttp) cc_final: 0.7567 (ttp) REVERT: A 4279 MET cc_start: 0.7394 (ptt) cc_final: 0.7140 (mtm) REVERT: A 4641 PRO cc_start: 0.8487 (OUTLIER) cc_final: 0.8103 (Cg_endo) REVERT: A 4707 MET cc_start: 0.8275 (ttm) cc_final: 0.8023 (ttp) REVERT: A 4726 MET cc_start: 0.7971 (tpp) cc_final: 0.7654 (tpp) REVERT: B 393 MET cc_start: 0.7712 (tpt) cc_final: 0.7285 (mmm) REVERT: B 933 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 995 MET cc_start: 0.8648 (ptm) cc_final: 0.7854 (tmm) REVERT: B 1975 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7659 (pmm) REVERT: B 2134 MET cc_start: 0.8228 (mmm) cc_final: 0.8014 (mmm) REVERT: B 2142 MET cc_start: 0.7979 (tmm) cc_final: 0.7758 (tmm) REVERT: B 2724 TYR cc_start: 0.8940 (t80) cc_final: 0.8644 (t80) REVERT: B 2773 TRP cc_start: 0.9029 (t60) cc_final: 0.8793 (t60) REVERT: B 2798 MET cc_start: 0.7172 (mmp) cc_final: 0.6970 (mmp) REVERT: B 2840 MET cc_start: 0.9114 (mtt) cc_final: 0.8575 (mtt) REVERT: B 2852 TRP cc_start: 0.9015 (t60) cc_final: 0.8638 (t60) REVERT: B 3003 MET cc_start: 0.9023 (ptm) cc_final: 0.8517 (ppp) REVERT: B 3072 MET cc_start: 0.9038 (mmp) cc_final: 0.8757 (mmm) REVERT: B 3104 MET cc_start: 0.9013 (ptp) cc_final: 0.8620 (ptt) REVERT: B 3109 PHE cc_start: 0.8947 (m-80) cc_final: 0.8379 (m-80) REVERT: B 3299 LEU cc_start: 0.9346 (mt) cc_final: 0.9121 (mt) REVERT: B 3605 MET cc_start: 0.6298 (ttp) cc_final: 0.5461 (mmm) REVERT: B 4279 MET cc_start: 0.7407 (ptt) cc_final: 0.7155 (mtm) REVERT: B 4292 MET cc_start: 0.8138 (mmm) cc_final: 0.7891 (mmm) REVERT: B 4641 PRO cc_start: 0.8452 (OUTLIER) cc_final: 0.8065 (Cg_endo) REVERT: B 4707 MET cc_start: 0.8290 (ttm) cc_final: 0.8040 (ttp) REVERT: B 4726 MET cc_start: 0.7981 (tpp) cc_final: 0.7652 (tpp) REVERT: C 393 MET cc_start: 0.7677 (tpt) cc_final: 0.7259 (mmm) REVERT: C 933 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 995 MET cc_start: 0.8645 (ptm) cc_final: 0.7842 (tmm) REVERT: C 1975 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7664 (pmm) REVERT: C 2456 MET cc_start: 0.8822 (tpp) cc_final: 0.8553 (tpt) REVERT: C 2724 TYR cc_start: 0.8958 (t80) cc_final: 0.8650 (t80) REVERT: C 2773 TRP cc_start: 0.9060 (t60) cc_final: 0.8792 (t60) REVERT: C 2840 MET cc_start: 0.9116 (mtt) cc_final: 0.8557 (mtt) REVERT: C 2852 TRP cc_start: 0.9021 (t60) cc_final: 0.8652 (t60) REVERT: C 3003 MET cc_start: 0.9022 (ptm) cc_final: 0.8507 (ppp) REVERT: C 3072 MET cc_start: 0.9021 (mmp) cc_final: 0.8758 (mmm) REVERT: C 3104 MET cc_start: 0.9034 (ptp) cc_final: 0.8611 (ptt) REVERT: C 3109 PHE cc_start: 0.8935 (m-80) cc_final: 0.8377 (m-80) REVERT: C 3241 MET cc_start: 0.8820 (ppp) cc_final: 0.8538 (ppp) REVERT: C 3250 TRP cc_start: 0.8762 (t60) cc_final: 0.8532 (t60) REVERT: C 3299 LEU cc_start: 0.9345 (mt) cc_final: 0.9114 (mt) REVERT: C 3605 MET cc_start: 0.6136 (ttp) cc_final: 0.5244 (mmm) REVERT: C 4279 MET cc_start: 0.7363 (ptt) cc_final: 0.7122 (mtm) REVERT: C 4292 MET cc_start: 0.8135 (mmm) cc_final: 0.7891 (mmm) REVERT: C 4641 PRO cc_start: 0.8452 (OUTLIER) cc_final: 0.8068 (Cg_endo) REVERT: C 4707 MET cc_start: 0.8292 (ttm) cc_final: 0.8042 (ttp) REVERT: C 4726 MET cc_start: 0.7974 (tpp) cc_final: 0.7649 (tpp) REVERT: D 393 MET cc_start: 0.7710 (tpt) cc_final: 0.7286 (mmm) REVERT: D 933 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8147 (mt) REVERT: D 995 MET cc_start: 0.8651 (ptm) cc_final: 0.7851 (tmm) REVERT: D 1975 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7653 (pmm) REVERT: D 2134 MET cc_start: 0.8233 (mmm) cc_final: 0.8022 (mmm) REVERT: D 2142 MET cc_start: 0.7964 (tmm) cc_final: 0.7749 (tmm) REVERT: D 2585 MET cc_start: 0.7729 (ptt) cc_final: 0.7425 (ppp) REVERT: D 2724 TYR cc_start: 0.8941 (t80) cc_final: 0.8641 (t80) REVERT: D 2773 TRP cc_start: 0.9029 (t60) cc_final: 0.8795 (t60) REVERT: D 2840 MET cc_start: 0.9112 (mtt) cc_final: 0.8561 (mtt) REVERT: D 2852 TRP cc_start: 0.9012 (t60) cc_final: 0.8631 (t60) REVERT: D 3003 MET cc_start: 0.9023 (ptm) cc_final: 0.8525 (ppp) REVERT: D 3072 MET cc_start: 0.9043 (mmp) cc_final: 0.8756 (mmm) REVERT: D 3104 MET cc_start: 0.9012 (ptp) cc_final: 0.8619 (ptt) REVERT: D 3109 PHE cc_start: 0.8939 (m-80) cc_final: 0.8373 (m-80) REVERT: D 3250 TRP cc_start: 0.8779 (t60) cc_final: 0.8536 (t60) REVERT: D 3299 LEU cc_start: 0.9356 (mt) cc_final: 0.9132 (mt) REVERT: D 3605 MET cc_start: 0.5947 (ptt) cc_final: 0.5440 (mmm) REVERT: D 3981 MET cc_start: 0.8481 (tmm) cc_final: 0.8263 (ttp) REVERT: D 4279 MET cc_start: 0.7413 (ptt) cc_final: 0.7159 (mtm) REVERT: D 4641 PRO cc_start: 0.8455 (OUTLIER) cc_final: 0.8067 (Cg_endo) REVERT: D 4707 MET cc_start: 0.8287 (ttm) cc_final: 0.8037 (ttp) REVERT: D 4726 MET cc_start: 0.7819 (tpp) cc_final: 0.7502 (tpp) outliers start: 71 outliers final: 49 residues processed: 704 average time/residue: 1.1763 time to fit residues: 1495.2559 Evaluate side-chains 714 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 651 time to evaluate : 11.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 931 TYR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2681 MET Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4641 PRO Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2396 ILE Chi-restraints excluded: chain B residue 2858 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain B residue 4641 PRO Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2858 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4641 PRO Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 931 TYR Chi-restraints excluded: chain D residue 933 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 4186 MET Chi-restraints excluded: chain D residue 4641 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 4.9990 chunk 1460 optimal weight: 1.9990 chunk 419 optimal weight: 10.0000 chunk 1264 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 380 optimal weight: 5.9990 chunk 1373 optimal weight: 0.9980 chunk 574 optimal weight: 8.9990 chunk 1409 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 252 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 GLN ** A2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4579 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2091 GLN ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2091 GLN ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3905 ASN C4579 HIS ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2091 GLN ** D2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4579 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.035647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.026732 restraints weight = 1945073.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.027868 restraints weight = 812028.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.028194 restraints weight = 424905.055| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 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 = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 141720 Z= 0.154 Angle : 0.552 22.989 191484 Z= 0.277 Chirality : 0.038 0.204 20988 Planarity : 0.004 0.125 24600 Dihedral : 7.261 161.128 19112 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.89 % Rotamer: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.07), residues: 17212 helix: 1.97 (0.06), residues: 9116 sheet: -0.27 (0.12), residues: 1800 loop : -0.37 (0.08), residues: 6296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.001 TRP D 893 HIS 0.007 0.001 HIS A3732 PHE 0.029 0.001 PHE A2943 TYR 0.045 0.001 TYR A2874 ARG 0.006 0.000 ARG A2581 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29041.81 seconds wall clock time: 513 minutes 29.57 seconds (30809.57 seconds total)