Starting phenix.real_space_refine on Tue Mar 19 03:03:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxg_42763/03_2024/8uxg_42763_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxg_42763/03_2024/8uxg_42763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxg_42763/03_2024/8uxg_42763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxg_42763/03_2024/8uxg_42763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxg_42763/03_2024/8uxg_42763_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxg_42763/03_2024/8uxg_42763_neut_updated.pdb" } resolution = 3.08 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= 0.011 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 940 5.16 5 C 88300 2.51 5 N 23592 2.21 5 O 25852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1732": "OE1" <-> "OE2" Residue "A GLU 2355": "OE1" <-> "OE2" Residue "A ASP 2360": "OD1" <-> "OD2" Residue "A GLU 2378": "OE1" <-> "OE2" Residue "A GLU 2453": "OE1" <-> "OE2" Residue "A PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2546": "OD1" <-> "OD2" Residue "A PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3062": "OD1" <-> "OD2" Residue "A PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3255": "OE1" <-> "OE2" Residue "A GLU 3710": "OE1" <-> "OE2" Residue "A PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4151": "OE1" <-> "OE2" Residue "A GLU 4182": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4681": "OD1" <-> "OD2" Residue "A GLU 4797": "OE1" <-> "OE2" Residue "A ASP 4833": "OD1" <-> "OD2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 721": "OD1" <-> "OD2" Residue "B ARG 880": "NH1" <-> "NH2" Residue "B ASP 910": "OD1" <-> "OD2" Residue "B TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 958": "OE1" <-> "OE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1732": "OE1" <-> "OE2" Residue "B GLU 2355": "OE1" <-> "OE2" Residue "B ASP 2360": "OD1" <-> "OD2" Residue "B GLU 2378": "OE1" <-> "OE2" Residue "B GLU 2453": "OE1" <-> "OE2" Residue "B PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2546": "OD1" <-> "OD2" Residue "B PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3062": "OD1" <-> "OD2" Residue "B PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3255": "OE1" <-> "OE2" Residue "B GLU 3710": "OE1" <-> "OE2" Residue "B PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4151": "OE1" <-> "OE2" Residue "B GLU 4182": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4681": "OD1" <-> "OD2" Residue "B GLU 4797": "OE1" <-> "OE2" Residue "B ASP 4833": "OD1" <-> "OD2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 721": "OD1" <-> "OD2" Residue "C ARG 880": "NH1" <-> "NH2" Residue "C ASP 910": "OD1" <-> "OD2" Residue "C TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 958": "OE1" <-> "OE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1732": "OE1" <-> "OE2" Residue "C GLU 2355": "OE1" <-> "OE2" Residue "C ASP 2360": "OD1" <-> "OD2" Residue "C GLU 2378": "OE1" <-> "OE2" Residue "C GLU 2453": "OE1" <-> "OE2" Residue "C PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2546": "OD1" <-> "OD2" Residue "C PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3062": "OD1" <-> "OD2" Residue "C PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3255": "OE1" <-> "OE2" Residue "C GLU 3710": "OE1" <-> "OE2" Residue "C PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4151": "OE1" <-> "OE2" Residue "C GLU 4182": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4681": "OD1" <-> "OD2" Residue "C GLU 4797": "OE1" <-> "OE2" Residue "C ASP 4833": "OD1" <-> "OD2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 721": "OD1" <-> "OD2" Residue "D ARG 880": "NH1" <-> "NH2" Residue "D ASP 910": "OD1" <-> "OD2" Residue "D TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 958": "OE1" <-> "OE2" Residue "D PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1732": "OE1" <-> "OE2" Residue "D GLU 2355": "OE1" <-> "OE2" Residue "D ASP 2360": "OD1" <-> "OD2" Residue "D GLU 2378": "OE1" <-> "OE2" Residue "D GLU 2453": "OE1" <-> "OE2" Residue "D PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2546": "OD1" <-> "OD2" Residue "D PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3062": "OD1" <-> "OD2" Residue "D PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3255": "OE1" <-> "OE2" Residue "D GLU 3710": "OE1" <-> "OE2" Residue "D PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4151": "OE1" <-> "OE2" Residue "D GLU 4182": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4681": "OD1" <-> "OD2" Residue "D GLU 4797": "OE1" <-> "OE2" Residue "D ASP 4833": "OD1" <-> "OD2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.38s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138712 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 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, 33766 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: 34490 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 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, 33766 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: 34490 Chain: "C" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 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, 33766 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: 34490 Chain: "D" Number of atoms: 33774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33766 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, 33766 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: 34490 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 33095 SG CYS A4888 178.149 203.581 88.477 1.00 93.33 S ATOM 33120 SG CYS A4891 180.574 203.529 91.403 1.00 92.94 S ATOM 70141 SG CYS B4888 176.586 178.118 88.479 1.00 93.33 S ATOM 70166 SG CYS B4891 176.640 180.544 91.404 1.00 92.94 S ATOM A030R SG CYS C4888 202.220 176.402 88.133 1.00 93.33 S ATOM A031G SG CYS C4891 199.782 176.456 91.048 1.00 92.94 S ATOM A0T2X SG CYS D4888 203.527 202.217 88.460 1.00 93.33 S ATOM A0T3M SG CYS D4891 203.470 199.789 91.383 1.00 92.94 S Time building chain proxies: 95.87, per 1000 atoms: 0.69 Number of scatterers: 138712 At special positions: 0 Unit cell: (380.973, 380.973, 212.773, 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 25852 8.00 N 23592 7.00 C 88300 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: 40.37 Conformation dependent library (CDL) restraints added in 34.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS 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 D4888 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " Number of angles added : 4 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32464 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 700 helices and 96 sheets defined 59.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 45.27 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.151A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.628A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' 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: 4.842A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.816A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.528A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.556A pdb=" N VAL A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' 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: 3.739A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.029A 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: 4.704A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.572A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.507A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.023A 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: 4.225A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.527A 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: 3.657A pdb=" N SER A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.624A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.686A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.564A 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 879 through 901 removed outlier: 3.866A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 Proline residue: A 925 - end of helix Processing helix chain 'A' and resid 926 through 947 removed outlier: 4.005A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 4.911A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 4.775A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.109A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.306A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A1235 " --> pdb=" O GLY A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1230 through 1235' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.882A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.135A 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: 3.955A pdb=" N ASN A1502 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.851A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.345A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.845A 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: 3.704A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.831A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1722 removed outlier: 3.601A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.633A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 removed outlier: 3.699A pdb=" N LYS A1800 " --> pdb=" O THR A1796 " (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: 4.262A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.935A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1955 removed outlier: 4.043A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1966 removed outlier: 4.079A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 removed outlier: 4.115A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.695A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.834A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2106 Proline residue: A2103 - end of helix removed outlier: 5.566A pdb=" N TYR A2106 " --> pdb=" O LEU A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.902A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A2129 " --> pdb=" O GLN A2125 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 3.520A pdb=" N LYS A2140 " --> pdb=" O LYS A2136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A2141 " --> pdb=" O GLU A2137 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2183 removed outlier: 5.369A pdb=" N MET A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N HIS A2168 " --> pdb=" O ALA A2164 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A2170 " --> pdb=" O GLY A2166 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET A2172 " --> pdb=" O HIS A2168 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.659A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.219A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.288A 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: 3.724A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.956A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 5.366A pdb=" N ILE A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2383 through 2412 Proline residue: A2404 - end of helix removed outlier: 9.077A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2439 removed outlier: 5.825A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.761A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A2467 " --> pdb=" O ASP A2463 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2503 removed outlier: 3.863A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 4.919A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.484A 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 2558 removed outlier: 3.621A pdb=" N LYS A2557 " --> pdb=" O TYR A2553 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 3.642A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.037A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.593A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.192A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.607A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.328A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 4.652A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 3.533A pdb=" N ALA A2799 " --> pdb=" O GLY A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.383A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.611A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2921 removed outlier: 4.388A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE A2921 " --> pdb=" O ILE A2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2916 through 2921' Processing helix chain 'A' and resid 2922 through 2947 Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.594A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 3.784A pdb=" N PHE A3022 " --> pdb=" O ARG A3018 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3018 through 3023' Processing helix chain 'A' and resid 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3077 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.865A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3117 through 3122 Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.149A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 4.310A pdb=" N GLU A3149 " --> pdb=" O SER A3145 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3175 through 3180 removed outlier: 4.065A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.442A 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 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.772A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3205 removed outlier: 5.070A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 4.020A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3250 removed outlier: 5.158A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix Processing helix chain 'A' and resid 3253 through 3258 removed outlier: 3.582A pdb=" N ASN A3257 " --> pdb=" O GLY A3253 " (cutoff:3.500A) Proline residue: A3258 - end of helix No H-bonds generated for 'chain 'A' and resid 3253 through 3258' Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 4.646A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.599A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.250A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3318 removed outlier: 5.209A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3330 removed outlier: 5.345A pdb=" N ALA A3330 " --> pdb=" O LEU A3326 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3604 Processing helix chain 'A' and resid 3607 through 3612 Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.977A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 removed outlier: 3.505A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.692A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.850A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.880A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.690A pdb=" N LEU A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 3.877A 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: 4.824A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 removed outlier: 3.808A pdb=" N GLY A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) Processing helix chain 'A' and resid 3826 through 3848 removed outlier: 5.326A pdb=" N LEU A3830 " --> pdb=" O GLY A3826 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A3831 " --> pdb=" O GLU A3827 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP A3832 " --> pdb=" O LYS A3828 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP A3833 " --> pdb=" O VAL A3829 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A3834 " --> pdb=" O LEU A3830 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A3835 " --> pdb=" O GLN A3831 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A3837 " --> pdb=" O ASP A3833 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.535A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.684A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 4.954A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3962 removed outlier: 3.694A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.614A pdb=" N LEU A3986 " --> pdb=" O LEU A3982 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 4.097A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.226A 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: 3.625A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.411A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 5.231A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 3.750A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4184 through 4208 removed outlier: 4.512A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4262 removed outlier: 4.430A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS A4262 " --> pdb=" O MET A4258 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4272 Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.846A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.521A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 4.326A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 3.929A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 4.914A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.862A 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: 3.820A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.786A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4761 removed outlier: 3.904A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.114A 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: 3.545A pdb=" N GLY A4820 " --> pdb=" O HIS A4816 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.228A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.067A 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 1772 through 1778 removed outlier: 4.407A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) 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: 4.151A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 66' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.629A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.741A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.817A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.528A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.555A pdb=" N VAL B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 446' 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: 3.739A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.029A 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: 4.704A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.573A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.508A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.023A 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: 4.225A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.527A 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: 3.657A pdb=" N SER B 596 " --> pdb=" O GLY B 592 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.624A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.686A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.563A 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 879 through 901 removed outlier: 3.866A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 Proline residue: B 925 - end of helix Processing helix chain 'B' and resid 926 through 947 removed outlier: 4.005A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 4.911A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 4.774A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 4.109A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.306A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY B1235 " --> pdb=" O GLY B1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1230 through 1235' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.882A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.136A 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: 3.955A pdb=" N ASN B1502 " --> pdb=" O GLN B1498 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.851A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.346A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.844A 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: 3.703A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B1666 " --> pdb=" O SER B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.832A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1722 removed outlier: 3.600A pdb=" N MET B1721 " --> pdb=" O ALA B1717 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.633A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1802 removed outlier: 3.699A pdb=" N LYS B1800 " --> pdb=" O THR B1796 " (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: 4.262A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.936A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1955 removed outlier: 4.043A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1966 removed outlier: 4.079A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 removed outlier: 4.114A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.695A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.834A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2106 Proline residue: B2103 - end of helix removed outlier: 5.566A pdb=" N TYR B2106 " --> pdb=" O LEU B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.903A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B2129 " --> pdb=" O GLN B2125 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 3.520A pdb=" N LYS B2140 " --> pdb=" O LYS B2136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B2141 " --> pdb=" O GLU B2137 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2183 removed outlier: 5.368A pdb=" N MET B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N HIS B2168 " --> pdb=" O ALA B2164 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B2170 " --> pdb=" O GLY B2166 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET B2172 " --> pdb=" O HIS B2168 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.659A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.220A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.288A 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: 3.724A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.956A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B2298 " --> pdb=" O GLU B2294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B2320 " --> pdb=" O ASN B2316 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2377 through 2382 removed outlier: 5.366A pdb=" N ILE B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2383 through 2412 Proline residue: B2404 - end of helix removed outlier: 9.076A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2439 removed outlier: 5.825A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.761A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B2467 " --> pdb=" O ASP B2463 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2503 removed outlier: 3.863A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 4.919A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.484A 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 2558 removed outlier: 3.621A pdb=" N LYS B2557 " --> pdb=" O TYR B2553 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 3.642A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.036A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.593A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.192A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.607A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.328A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 4.652A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 3.532A pdb=" N ALA B2799 " --> pdb=" O GLY B2795 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.383A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.611A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2921 removed outlier: 4.388A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE B2921 " --> pdb=" O ILE B2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2916 through 2921' Processing helix chain 'B' and resid 2922 through 2947 Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.594A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 3.784A pdb=" N PHE B3022 " --> pdb=" O ARG B3018 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3018 through 3023' Processing helix chain 'B' and resid 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3077 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.866A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3117 through 3122 Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.149A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 4.310A pdb=" N GLU B3149 " --> pdb=" O SER B3145 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3175 through 3180 removed outlier: 4.064A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.442A 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 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.772A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3205 removed outlier: 5.069A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 4.020A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3250 removed outlier: 5.158A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix Processing helix chain 'B' and resid 3253 through 3258 removed outlier: 3.583A pdb=" N ASN B3257 " --> pdb=" O GLY B3253 " (cutoff:3.500A) Proline residue: B3258 - end of helix No H-bonds generated for 'chain 'B' and resid 3253 through 3258' Processing helix chain 'B' and resid 3269 through 3289 removed outlier: 4.645A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.599A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.250A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3318 removed outlier: 5.208A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) Processing helix chain 'B' and resid 3319 through 3330 removed outlier: 5.344A pdb=" N ALA B3330 " --> pdb=" O LEU B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3604 Processing helix chain 'B' and resid 3607 through 3612 Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.977A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 removed outlier: 3.505A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.692A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.849A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.879A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.691A pdb=" N LEU B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) removed outlier: 3.876A 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: 4.824A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 removed outlier: 3.808A pdb=" N GLY B3818 " --> pdb=" O ALA B3814 " (cutoff:3.500A) Processing helix chain 'B' and resid 3826 through 3848 removed outlier: 5.325A pdb=" N LEU B3830 " --> pdb=" O GLY B3826 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN B3831 " --> pdb=" O GLU B3827 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B3832 " --> pdb=" O LYS B3828 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP B3833 " --> pdb=" O VAL B3829 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU B3834 " --> pdb=" O LEU B3830 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N PHE B3835 " --> pdb=" O GLN B3831 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS B3837 " --> pdb=" O ASP B3833 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.535A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.685A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 4.955A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3962 removed outlier: 3.695A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.614A pdb=" N LEU B3986 " --> pdb=" O LEU B3982 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 4.097A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.226A 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: 3.625A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.411A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 5.232A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 3.750A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4184 through 4208 removed outlier: 4.513A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4262 removed outlier: 4.430A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS B4262 " --> pdb=" O MET B4258 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4272 Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.846A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.521A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 4.326A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 3.928A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 4.914A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.861A 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: 3.820A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.785A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4761 removed outlier: 3.903A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.115A 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: 3.545A pdb=" N GLY B4820 " --> pdb=" O HIS B4816 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.227A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.067A 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 1772 through 1778 removed outlier: 4.406A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) 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: 4.151A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.628A pdb=" N ALA C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 224' 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: 4.843A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.816A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.528A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.556A pdb=" N VAL C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 446' 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: 3.739A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.029A 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: 4.703A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.573A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.508A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.023A 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: 4.226A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 5.527A 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: 3.657A pdb=" N SER C 596 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.625A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.686A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.564A 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 879 through 901 removed outlier: 3.865A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 Proline residue: C 925 - end of helix Processing helix chain 'C' and resid 926 through 947 removed outlier: 4.005A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 4.911A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 4.774A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 4.109A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.305A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY C1235 " --> pdb=" O GLY C1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1230 through 1235' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.882A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.135A 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: 3.955A pdb=" N ASN C1502 " --> pdb=" O GLN C1498 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.851A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.345A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.845A 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: 3.703A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C1666 " --> pdb=" O SER C1662 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.831A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1722 removed outlier: 3.601A pdb=" N MET C1721 " --> pdb=" O ALA C1717 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.632A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 removed outlier: 3.699A pdb=" N LYS C1800 " --> pdb=" O THR C1796 " (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: 4.262A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.935A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1955 removed outlier: 4.042A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1966 removed outlier: 4.079A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 removed outlier: 4.115A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.694A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.834A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2106 Proline residue: C2103 - end of helix removed outlier: 5.567A pdb=" N TYR C2106 " --> pdb=" O LEU C2102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.902A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C2129 " --> pdb=" O GLN C2125 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 3.520A pdb=" N LYS C2140 " --> pdb=" O LYS C2136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C2141 " --> pdb=" O GLU C2137 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2183 removed outlier: 5.369A pdb=" N MET C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N HIS C2168 " --> pdb=" O ALA C2164 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C2170 " --> pdb=" O GLY C2166 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET C2172 " --> pdb=" O HIS C2168 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.660A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.220A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.288A 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: 3.723A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.955A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C2298 " --> pdb=" O GLU C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.682A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C2320 " --> pdb=" O ASN C2316 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2377 through 2382 removed outlier: 5.365A pdb=" N ILE C2382 " --> pdb=" O GLU C2378 " (cutoff:3.500A) Processing helix chain 'C' and resid 2383 through 2412 Proline residue: C2404 - end of helix removed outlier: 9.077A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2439 removed outlier: 5.825A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.761A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C2467 " --> pdb=" O ASP C2463 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2503 removed outlier: 3.864A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 4.919A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.484A 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 2558 removed outlier: 3.621A pdb=" N LYS C2557 " --> pdb=" O TYR C2553 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 3.641A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.037A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.592A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.191A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.608A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.327A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 4.652A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 3.533A pdb=" N ALA C2799 " --> pdb=" O GLY C2795 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.383A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.611A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2921 removed outlier: 4.388A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE C2921 " --> pdb=" O ILE C2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2916 through 2921' Processing helix chain 'C' and resid 2922 through 2947 Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.594A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 3.784A pdb=" N PHE C3022 " --> pdb=" O ARG C3018 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3018 through 3023' Processing helix chain 'C' and resid 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3077 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.865A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3117 through 3122 Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.148A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 4.309A pdb=" N GLU C3149 " --> pdb=" O SER C3145 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3175 through 3180 removed outlier: 4.065A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.442A 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 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.772A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3205 removed outlier: 5.070A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 4.020A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3250 removed outlier: 5.158A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix Processing helix chain 'C' and resid 3253 through 3258 removed outlier: 3.583A pdb=" N ASN C3257 " --> pdb=" O GLY C3253 " (cutoff:3.500A) Proline residue: C3258 - end of helix No H-bonds generated for 'chain 'C' and resid 3253 through 3258' Processing helix chain 'C' and resid 3269 through 3289 removed outlier: 4.646A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.600A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.250A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3318 removed outlier: 5.209A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) Processing helix chain 'C' and resid 3319 through 3330 removed outlier: 5.344A pdb=" N ALA C3330 " --> pdb=" O LEU C3326 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3604 Processing helix chain 'C' and resid 3607 through 3612 Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.977A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 removed outlier: 3.505A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.692A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.850A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.880A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.691A pdb=" N LEU C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) removed outlier: 3.877A 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: 4.824A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 removed outlier: 3.807A pdb=" N GLY C3818 " --> pdb=" O ALA C3814 " (cutoff:3.500A) Processing helix chain 'C' and resid 3826 through 3848 removed outlier: 5.325A pdb=" N LEU C3830 " --> pdb=" O GLY C3826 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN C3831 " --> pdb=" O GLU C3827 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP C3832 " --> pdb=" O LYS C3828 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP C3833 " --> pdb=" O VAL C3829 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU C3834 " --> pdb=" O LEU C3830 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE C3835 " --> pdb=" O GLN C3831 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS C3837 " --> pdb=" O ASP C3833 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.535A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.683A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 4.954A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3962 removed outlier: 3.693A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.615A pdb=" N LEU C3986 " --> pdb=" O LEU C3982 " (cutoff:3.500A) Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 4.097A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.226A 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: 3.625A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.411A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 5.231A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 3.751A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4184 through 4208 removed outlier: 4.512A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4262 removed outlier: 4.430A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS C4262 " --> pdb=" O MET C4258 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4272 Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.846A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.521A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 4.326A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 3.929A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 4.915A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.861A 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: 3.820A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.786A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4761 removed outlier: 3.904A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.114A 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: 3.545A pdb=" N GLY C4820 " --> pdb=" O HIS C4816 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.228A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.067A 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 1772 through 1778 removed outlier: 4.407A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) 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: 4.151A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.628A pdb=" N ALA D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 224' Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.741A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.816A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.529A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.556A pdb=" N VAL D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 446' 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: 3.739A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.029A 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: 4.703A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.573A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.507A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.022A 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: 4.225A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 5.528A 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: 3.657A pdb=" N SER D 596 " --> pdb=" O GLY D 592 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.624A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.686A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.564A 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 879 through 901 removed outlier: 3.866A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 925 Proline residue: D 925 - end of helix Processing helix chain 'D' and resid 926 through 947 removed outlier: 4.005A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 4.911A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 4.775A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 4.108A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.305A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D1235 " --> pdb=" O GLY D1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1230 through 1235' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.882A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.135A 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: 3.955A pdb=" N ASN D1502 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.851A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.345A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.845A 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: 3.703A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D1666 " --> pdb=" O SER D1662 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.832A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1722 removed outlier: 3.601A pdb=" N MET D1721 " --> pdb=" O ALA D1717 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.633A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1802 removed outlier: 3.699A pdb=" N LYS D1800 " --> pdb=" O THR D1796 " (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: 4.262A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.935A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1955 removed outlier: 4.043A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1966 removed outlier: 4.079A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 removed outlier: 4.114A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.695A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.834A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2106 Proline residue: D2103 - end of helix removed outlier: 5.567A pdb=" N TYR D2106 " --> pdb=" O LEU D2102 " (cutoff:3.500A) Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.902A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D2129 " --> pdb=" O GLN D2125 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 3.520A pdb=" N LYS D2140 " --> pdb=" O LYS D2136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D2141 " --> pdb=" O GLU D2137 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2183 removed outlier: 5.369A pdb=" N MET D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N HIS D2168 " --> pdb=" O ALA D2164 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D2170 " --> pdb=" O GLY D2166 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET D2172 " --> pdb=" O HIS D2168 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.660A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.220A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.289A 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: 3.723A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.956A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D2298 " --> pdb=" O GLU D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D2320 " --> pdb=" O ASN D2316 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2377 through 2382 removed outlier: 5.366A pdb=" N ILE D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) Processing helix chain 'D' and resid 2383 through 2412 Proline residue: D2404 - end of helix removed outlier: 9.077A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2439 removed outlier: 5.824A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.762A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D2467 " --> pdb=" O ASP D2463 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2503 removed outlier: 3.863A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 4.919A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.484A 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 2558 removed outlier: 3.621A pdb=" N LYS D2557 " --> pdb=" O TYR D2553 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 3.643A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.037A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.593A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.191A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.608A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.328A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 4.651A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 3.533A pdb=" N ALA D2799 " --> pdb=" O GLY D2795 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.383A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.611A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2921 removed outlier: 4.388A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE D2921 " --> pdb=" O ILE D2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2916 through 2921' Processing helix chain 'D' and resid 2922 through 2947 Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.594A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 3.784A pdb=" N PHE D3022 " --> pdb=" O ARG D3018 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3018 through 3023' Processing helix chain 'D' and resid 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3077 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.864A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3117 through 3122 Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.148A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 4.311A pdb=" N GLU D3149 " --> pdb=" O SER D3145 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3175 through 3180 removed outlier: 4.066A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.442A 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 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.772A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3205 removed outlier: 5.069A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 4.020A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3250 removed outlier: 5.158A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix Processing helix chain 'D' and resid 3253 through 3258 removed outlier: 3.582A pdb=" N ASN D3257 " --> pdb=" O GLY D3253 " (cutoff:3.500A) Proline residue: D3258 - end of helix No H-bonds generated for 'chain 'D' and resid 3253 through 3258' Processing helix chain 'D' and resid 3269 through 3289 removed outlier: 4.645A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.599A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.249A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3318 removed outlier: 5.209A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) Processing helix chain 'D' and resid 3319 through 3330 removed outlier: 5.344A pdb=" N ALA D3330 " --> pdb=" O LEU D3326 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3604 Processing helix chain 'D' and resid 3607 through 3612 Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.977A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 removed outlier: 3.505A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.692A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.850A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.880A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.690A pdb=" N LEU D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 3.877A 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: 4.824A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 removed outlier: 3.808A pdb=" N GLY D3818 " --> pdb=" O ALA D3814 " (cutoff:3.500A) Processing helix chain 'D' and resid 3826 through 3848 removed outlier: 5.326A pdb=" N LEU D3830 " --> pdb=" O GLY D3826 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN D3831 " --> pdb=" O GLU D3827 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP D3832 " --> pdb=" O LYS D3828 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP D3833 " --> pdb=" O VAL D3829 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU D3834 " --> pdb=" O LEU D3830 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE D3835 " --> pdb=" O GLN D3831 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS D3837 " --> pdb=" O ASP D3833 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.536A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.684A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 4.955A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3962 removed outlier: 3.694A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.615A pdb=" N LEU D3986 " --> pdb=" O LEU D3982 " (cutoff:3.500A) Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 4.097A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.226A 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: 3.625A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.411A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 5.231A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 3.750A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4184 through 4208 removed outlier: 4.512A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4262 removed outlier: 4.430A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS D4262 " --> pdb=" O MET D4258 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4272 Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.847A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.520A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 4.327A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 3.929A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 4.915A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.862A 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: 3.820A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.785A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4761 removed outlier: 3.904A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.114A 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: 3.545A pdb=" N GLY D4820 " --> pdb=" O HIS D4816 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.228A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.066A 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 1772 through 1778 removed outlier: 4.407A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.807A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.547A pdb=" N GLN E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.902A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.807A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 3.547A pdb=" N GLN F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.903A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.806A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.547A pdb=" N GLN G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.903A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.807A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 3.547A pdb=" N GLN H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.903A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.278A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.226A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.672A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 160 through 164 Processing sheet with id= 4, first strand: chain 'A' and resid 231 through 235 removed outlier: 4.054A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 14.359A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 307 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 243 through 247 Processing sheet with id= 6, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 7, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 8, first strand: chain 'A' and resid 737 through 740 removed outlier: 5.558A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 728 " --> pdb=" O HIS A 731 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.811A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 776 through 780 removed outlier: 5.397A pdb=" N GLN A 776 " --> pdb=" O GLY A1470 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.356A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 948 through 952 Processing sheet with id= 13, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 7.371A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 7.170A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A1115 " --> pdb=" O PHE A1137 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1257 through 1260 removed outlier: 4.698A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.658A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A1505 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 4.401A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2741 through 2744 removed outlier: 3.513A pdb=" N GLY A2744 " --> pdb=" O GLN A2754 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 3.724A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.728A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 4521 through 4524 removed outlier: 3.612A pdb=" N SER A4523 " --> pdb=" O HIS A4558 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A4558 " --> pdb=" O SER A4523 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 4793 through 4796 removed outlier: 7.912A pdb=" N TYR A4793 " --> pdb=" O LYS A4805 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP A4803 " --> pdb=" O LYS A4795 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.278A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.225A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.672A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 160 through 164 Processing sheet with id= 26, first strand: chain 'B' and resid 231 through 235 removed outlier: 4.054A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 14.358A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 307 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 243 through 247 Processing sheet with id= 28, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 29, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 30, first strand: chain 'B' and resid 737 through 740 removed outlier: 5.558A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 728 " --> pdb=" O HIS B 731 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.811A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 776 through 780 removed outlier: 5.397A pdb=" N GLN B 776 " --> pdb=" O GLY B1470 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.357A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 948 through 952 Processing sheet with id= 35, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 7.372A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 7.170A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B1115 " --> pdb=" O PHE B1137 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 1257 through 1260 removed outlier: 4.698A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.658A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B1505 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 4.402A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 2741 through 2744 removed outlier: 3.512A pdb=" N GLY B2744 " --> pdb=" O GLN B2754 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 3.724A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.728A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 4521 through 4524 removed outlier: 3.611A pdb=" N SER B4523 " --> pdb=" O HIS B4558 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B4558 " --> pdb=" O SER B4523 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'B' and resid 4793 through 4796 removed outlier: 7.913A pdb=" N TYR B4793 " --> pdb=" O LYS B4805 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP B4803 " --> pdb=" O LYS B4795 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.278A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.226A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.672A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 160 through 164 Processing sheet with id= 48, first strand: chain 'C' and resid 231 through 235 removed outlier: 4.054A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 14.359A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 307 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 243 through 247 Processing sheet with id= 50, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 51, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 52, first strand: chain 'C' and resid 737 through 740 removed outlier: 5.559A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 728 " --> pdb=" O HIS C 731 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.811A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 776 through 780 removed outlier: 5.398A pdb=" N GLN C 776 " --> pdb=" O GLY C1470 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.355A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 948 through 952 Processing sheet with id= 57, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 7.371A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 7.170A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C1115 " --> pdb=" O PHE C1137 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 1257 through 1260 removed outlier: 4.698A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.658A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C1505 " --> pdb=" O ILE C1432 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 4.401A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 2741 through 2744 removed outlier: 3.513A pdb=" N GLY C2744 " --> pdb=" O GLN C2754 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 3.725A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.728A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'C' and resid 4521 through 4524 removed outlier: 3.612A pdb=" N SER C4523 " --> pdb=" O HIS C4558 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS C4558 " --> pdb=" O SER C4523 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'C' and resid 4793 through 4796 removed outlier: 7.913A pdb=" N TYR C4793 " --> pdb=" O LYS C4805 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP C4803 " --> pdb=" O LYS C4795 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.279A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.226A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.672A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 160 through 164 Processing sheet with id= 70, first strand: chain 'D' and resid 231 through 235 removed outlier: 4.054A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 14.359A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 307 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 243 through 247 Processing sheet with id= 72, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 73, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 74, first strand: chain 'D' and resid 737 through 740 removed outlier: 5.558A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP D 728 " --> pdb=" O HIS D 731 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.812A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 776 through 780 removed outlier: 5.397A pdb=" N GLN D 776 " --> pdb=" O GLY D1470 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.357A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 948 through 952 Processing sheet with id= 79, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 7.372A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 7.170A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D1115 " --> pdb=" O PHE D1137 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 1257 through 1260 removed outlier: 4.698A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.658A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D1505 " --> pdb=" O ILE D1432 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 4.401A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'D' and resid 2741 through 2744 removed outlier: 3.513A pdb=" N GLY D2744 " --> pdb=" O GLN D2754 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 3.724A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.728A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'D' and resid 4521 through 4524 removed outlier: 3.612A pdb=" N SER D4523 " --> pdb=" O HIS D4558 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS D4558 " --> pdb=" O SER D4523 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'D' and resid 4793 through 4796 removed outlier: 7.913A pdb=" N TYR D4793 " --> pdb=" O LYS D4805 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP D4803 " --> pdb=" O LYS D4795 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.622A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'E' and resid 46 through 50 Processing sheet with id= 91, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.622A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 93, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.622A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'G' and resid 46 through 50 Processing sheet with id= 95, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.623A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'H' and resid 46 through 50 7264 hydrogen bonds defined for protein. 21676 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: 108.21 Time building geometry restraints manager: 44.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 39631 1.33 - 1.46: 30766 1.46 - 1.58: 69795 1.58 - 1.71: 36 1.71 - 1.83: 1520 Bond restraints: 141748 Sorted by residual: bond pdb=" N LEU B 918 " pdb=" CA LEU B 918 " ideal model delta sigma weight residual 1.457 1.496 -0.040 1.33e-02 5.65e+03 8.90e+00 bond pdb=" N LEU D 918 " pdb=" CA LEU D 918 " ideal model delta sigma weight residual 1.457 1.496 -0.040 1.33e-02 5.65e+03 8.88e+00 bond pdb=" N LEU A 918 " pdb=" CA LEU A 918 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.33e-02 5.65e+03 8.81e+00 bond pdb=" N LEU C 918 " pdb=" CA LEU C 918 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.33e-02 5.65e+03 8.75e+00 bond pdb=" N ILE B1012 " pdb=" CA ILE B1012 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.35e+00 ... (remaining 141743 not shown) Histogram of bond angle deviations from ideal: 95.46 - 105.14: 2906 105.14 - 114.81: 84755 114.81 - 124.48: 101311 124.48 - 134.16: 2536 134.16 - 143.83: 20 Bond angle restraints: 191528 Sorted by residual: angle pdb=" CA LEU A 943 " pdb=" CB LEU A 943 " pdb=" CG LEU A 943 " ideal model delta sigma weight residual 116.30 143.83 -27.53 3.50e+00 8.16e-02 6.19e+01 angle pdb=" CA LEU D 943 " pdb=" CB LEU D 943 " pdb=" CG LEU D 943 " ideal model delta sigma weight residual 116.30 143.81 -27.51 3.50e+00 8.16e-02 6.18e+01 angle pdb=" CA LEU C 943 " pdb=" CB LEU C 943 " pdb=" CG LEU C 943 " ideal model delta sigma weight residual 116.30 143.80 -27.50 3.50e+00 8.16e-02 6.18e+01 angle pdb=" CA LEU B 943 " pdb=" CB LEU B 943 " pdb=" CG LEU B 943 " ideal model delta sigma weight residual 116.30 143.78 -27.48 3.50e+00 8.16e-02 6.16e+01 angle pdb=" CA MET B2734 " pdb=" CB MET B2734 " pdb=" CG MET B2734 " ideal model delta sigma weight residual 114.10 129.02 -14.92 2.00e+00 2.50e-01 5.57e+01 ... (remaining 191523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.15: 83018 33.15 - 66.30: 2170 66.30 - 99.45: 260 99.45 - 132.60: 8 132.60 - 165.75: 24 Dihedral angle restraints: 85480 sinusoidal: 35120 harmonic: 50360 Sorted by residual: dihedral pdb=" CA ARG B 880 " pdb=" C ARG B 880 " pdb=" N ILE B 881 " pdb=" CA ILE B 881 " ideal model delta harmonic sigma weight residual 180.00 129.63 50.37 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ARG A 880 " pdb=" C ARG A 880 " pdb=" N ILE A 881 " pdb=" CA ILE A 881 " ideal model delta harmonic sigma weight residual 180.00 129.64 50.36 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ARG D 880 " pdb=" C ARG D 880 " pdb=" N ILE D 881 " pdb=" CA ILE D 881 " ideal model delta harmonic sigma weight residual 180.00 129.66 50.34 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 85477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 18076 0.059 - 0.119: 2648 0.119 - 0.178: 193 0.178 - 0.237: 59 0.237 - 0.296: 12 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CB ILE C3122 " pdb=" CA ILE C3122 " pdb=" CG1 ILE C3122 " pdb=" CG2 ILE C3122 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE D3122 " pdb=" CA ILE D3122 " pdb=" CG1 ILE D3122 " pdb=" CG2 ILE D3122 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+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 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 20985 not shown) Planarity restraints: 24600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B4640 " -0.121 5.00e-02 4.00e+02 1.87e-01 5.60e+01 pdb=" N PRO B4641 " 0.323 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " -0.114 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D4640 " 0.120 5.00e-02 4.00e+02 1.87e-01 5.59e+01 pdb=" N PRO D4641 " -0.323 5.00e-02 4.00e+02 pdb=" CA PRO D4641 " 0.114 5.00e-02 4.00e+02 pdb=" CD PRO D4641 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " -0.120 5.00e-02 4.00e+02 1.87e-01 5.59e+01 pdb=" N PRO A4641 " 0.323 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " -0.114 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " -0.089 5.00e-02 4.00e+02 ... (remaining 24597 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 953 2.59 - 3.17: 118471 3.17 - 3.74: 226165 3.74 - 4.32: 309291 4.32 - 4.90: 503952 Nonbonded interactions: 1158832 Sorted by model distance: nonbonded pdb=" OG1 THR C2832 " pdb=" O THR D1548 " model vdw 2.011 2.440 nonbonded pdb=" N GLU H 4 " pdb=" OE1 GLU H 4 " model vdw 2.131 2.520 nonbonded pdb=" N GLU G 4 " pdb=" OE1 GLU G 4 " model vdw 2.131 2.520 nonbonded pdb=" N GLU F 4 " pdb=" OE1 GLU F 4 " model vdw 2.131 2.520 nonbonded pdb=" N GLU E 4 " pdb=" OE1 GLU E 4 " model vdw 2.131 2.520 ... (remaining 1158827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 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: 0.100 Extract box with map and model: 30.230 Check model and map are aligned: 1.510 Set scattering table: 0.930 Process input model: 452.150 Find NCS groups from input model: 6.840 Set up NCS constraints: 0.980 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 501.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 141748 Z= 0.208 Angle : 0.745 27.529 191528 Z= 0.422 Chirality : 0.043 0.296 20988 Planarity : 0.005 0.187 24600 Dihedral : 15.505 165.749 53004 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 1.27 % Allowed : 0.61 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.10 % 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: 1.03 (0.06), residues: 17212 helix: 1.69 (0.06), residues: 8924 sheet: 0.15 (0.13), residues: 1672 loop : -0.53 (0.07), residues: 6616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B4481 HIS 0.013 0.001 HIS C3732 PHE 0.046 0.001 PHE B4291 TYR 0.037 0.001 TYR C3285 ARG 0.046 0.001 ARG C 880 *********************** 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 986 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 793 time to evaluate : 10.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1014 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: A 1031 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7729 (mmm160) REVERT: A 1047 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9186 (tppt) REVERT: A 2279 MET cc_start: 0.7778 (tmm) cc_final: 0.7503 (tmm) REVERT: A 2468 MET cc_start: 0.8433 (mmt) cc_final: 0.8062 (mmt) REVERT: A 2734 MET cc_start: 0.8644 (mmp) cc_final: 0.8389 (mmm) REVERT: A 2773 TRP cc_start: 0.8610 (t-100) cc_final: 0.8304 (t-100) REVERT: A 2826 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8720 (tp) REVERT: A 3072 MET cc_start: 0.9020 (mtt) cc_final: 0.8731 (mtt) REVERT: A 3246 MET cc_start: 0.8853 (mtp) cc_final: 0.8504 (ttm) REVERT: A 3605 MET cc_start: 0.5227 (ppp) cc_final: 0.3984 (pmm) REVERT: A 3819 MET cc_start: 0.7428 (pmm) cc_final: 0.7152 (pmm) REVERT: A 4002 MET cc_start: 0.8852 (tmm) cc_final: 0.8496 (tmm) REVERT: A 4046 ARG cc_start: 0.8971 (tpm170) cc_final: 0.8736 (tpm170) REVERT: A 4258 MET cc_start: 0.8457 (mtm) cc_final: 0.8214 (mtm) REVERT: A 4809 MET cc_start: 0.8094 (tpt) cc_final: 0.7691 (tpt) REVERT: E 108 GLU cc_start: 0.7874 (pp20) cc_final: 0.7545 (pp20) REVERT: F 53 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9076 (mppt) REVERT: F 108 GLU cc_start: 0.7861 (pp20) cc_final: 0.7530 (pp20) REVERT: G 108 GLU cc_start: 0.7863 (pp20) cc_final: 0.7497 (pp20) REVERT: H 18 LYS cc_start: 0.8618 (mppt) cc_final: 0.8414 (mppt) REVERT: H 54 GLN cc_start: 0.8768 (mp10) cc_final: 0.8552 (mp10) REVERT: H 108 GLU cc_start: 0.7884 (pp20) cc_final: 0.7488 (pp20) REVERT: B 1014 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: B 1031 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7391 (mmm-85) REVERT: B 1032 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8900 (mp) REVERT: B 1047 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9061 (tppt) REVERT: B 1050 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8953 (mm) REVERT: B 2279 MET cc_start: 0.7771 (tmm) cc_final: 0.7547 (tmm) REVERT: B 2734 MET cc_start: 0.8799 (mmp) cc_final: 0.8475 (mmm) REVERT: B 2773 TRP cc_start: 0.8621 (t-100) cc_final: 0.8362 (t-100) REVERT: B 2826 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8686 (tp) REVERT: B 3072 MET cc_start: 0.9005 (mtt) cc_final: 0.8719 (mtt) REVERT: B 3605 MET cc_start: 0.5307 (ppp) cc_final: 0.4067 (pmm) REVERT: B 3819 MET cc_start: 0.7439 (pmm) cc_final: 0.7164 (pmm) REVERT: B 4002 MET cc_start: 0.8809 (tmm) cc_final: 0.8465 (tmm) REVERT: B 4046 ARG cc_start: 0.8965 (tpm170) cc_final: 0.8719 (tpm170) REVERT: B 4258 MET cc_start: 0.8476 (mtm) cc_final: 0.8239 (mtm) REVERT: C 399 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6841 (tmm) REVERT: C 1031 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7886 (mmm160) REVERT: C 1045 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8877 (p) REVERT: C 1975 MET cc_start: 0.8326 (ptm) cc_final: 0.7838 (ptp) REVERT: C 2695 MET cc_start: 0.7143 (ppp) cc_final: 0.6692 (ppp) REVERT: C 2734 MET cc_start: 0.9104 (mmp) cc_final: 0.8761 (mmm) REVERT: C 2826 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8706 (tt) REVERT: C 3003 MET cc_start: 0.8758 (mtm) cc_final: 0.8540 (ptm) REVERT: C 3605 MET cc_start: 0.5357 (ppp) cc_final: 0.4182 (pmm) REVERT: C 3719 MET cc_start: 0.7730 (tmm) cc_final: 0.7477 (tmm) REVERT: C 3981 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: C 4046 ARG cc_start: 0.8929 (tpm170) cc_final: 0.8504 (tpm170) REVERT: C 4817 MET cc_start: 0.8660 (mmm) cc_final: 0.8452 (tpt) REVERT: C 4923 MET cc_start: 0.8608 (ttt) cc_final: 0.8278 (ttp) REVERT: D 393 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7555 (tpt) REVERT: D 940 LEU cc_start: 0.9499 (mp) cc_final: 0.9235 (pp) REVERT: D 1014 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: D 1031 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7690 (mmm160) REVERT: D 2279 MET cc_start: 0.7694 (tmm) cc_final: 0.7377 (tmm) REVERT: D 2681 MET cc_start: 0.8233 (tpp) cc_final: 0.7897 (tpt) REVERT: D 2763 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8228 (tp) REVERT: D 2826 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8401 (tp) REVERT: D 3605 MET cc_start: 0.5269 (ppp) cc_final: 0.3968 (pmm) REVERT: D 3719 MET cc_start: 0.7814 (tmm) cc_final: 0.7518 (tmm) REVERT: D 3819 MET cc_start: 0.7334 (pmm) cc_final: 0.7059 (pmm) REVERT: D 3981 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: D 4046 ARG cc_start: 0.8967 (tpm170) cc_final: 0.8632 (tpm170) outliers start: 193 outliers final: 40 residues processed: 891 average time/residue: 1.2131 time to fit residues: 1894.4628 Evaluate side-chains 793 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 732 time to evaluate : 11.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1047 LYS Chi-restraints excluded: chain A residue 2826 ILE Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4654 MET Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 943 LEU Chi-restraints excluded: chain B residue 1011 ARG Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1031 ARG Chi-restraints excluded: chain B residue 1032 LEU Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1047 LYS Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 2826 ILE Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 3981 MET Chi-restraints excluded: chain B residue 4654 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 926 GLU Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1031 ARG Chi-restraints excluded: chain C residue 1044 LYS Chi-restraints excluded: chain C residue 1045 SER Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 2826 ILE Chi-restraints excluded: chain C residue 3215 MET Chi-restraints excluded: chain C residue 3981 MET Chi-restraints excluded: chain C residue 4292 MET Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 926 GLU Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 1011 ARG Chi-restraints excluded: chain D residue 1014 GLN Chi-restraints excluded: chain D residue 1031 ARG Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1044 LYS Chi-restraints excluded: chain D residue 2763 LEU Chi-restraints excluded: chain D residue 2826 ILE Chi-restraints excluded: chain D residue 3981 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 8.9990 chunk 1309 optimal weight: 9.9990 chunk 726 optimal weight: 20.0000 chunk 447 optimal weight: 8.9990 chunk 883 optimal weight: 9.9990 chunk 699 optimal weight: 7.9990 chunk 1354 optimal weight: 3.9990 chunk 524 optimal weight: 0.0000 chunk 823 optimal weight: 0.6980 chunk 1008 optimal weight: 9.9990 chunk 1569 optimal weight: 10.0000 overall best weight: 4.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 ASN A1014 GLN A1026 ASN A1257 GLN A1451 HIS A1917 GLN ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN B1014 GLN B1026 ASN B1257 GLN B1451 HIS B1917 GLN ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1026 ASN C1257 GLN C1451 HIS C1917 GLN ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3304 GLN C3308 ASN ** C3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 896 ASN D1014 GLN D1026 ASN D1257 GLN D1451 HIS D1917 GLN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3304 GLN D3308 ASN ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 141748 Z= 0.300 Angle : 0.622 19.477 191528 Z= 0.316 Chirality : 0.042 0.300 20988 Planarity : 0.005 0.157 24600 Dihedral : 8.952 167.606 19288 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.06), residues: 17212 helix: 1.89 (0.06), residues: 8948 sheet: 0.12 (0.13), residues: 1628 loop : -0.56 (0.07), residues: 6636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D2773 HIS 0.012 0.001 HIS B3732 PHE 0.027 0.002 PHE D4846 TYR 0.027 0.002 TYR C4520 ARG 0.019 0.001 ARG D 880 *********************** 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 855 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 791 time to evaluate : 12.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8364 (mmp) cc_final: 0.8111 (mmm) REVERT: A 317 MET cc_start: 0.7826 (ptt) cc_final: 0.7572 (ptm) REVERT: A 892 LEU cc_start: 0.9605 (mt) cc_final: 0.9404 (mt) REVERT: A 1026 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7970 (t0) REVERT: A 1047 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9079 (tppt) REVERT: A 1948 MET cc_start: 0.8130 (mmp) cc_final: 0.7569 (mtp) REVERT: A 1975 MET cc_start: 0.8821 (ptm) cc_final: 0.8378 (ptp) REVERT: A 2279 MET cc_start: 0.7851 (tmm) cc_final: 0.7619 (tmm) REVERT: A 2798 MET cc_start: 0.8319 (mmm) cc_final: 0.8073 (mmm) REVERT: A 2826 ILE cc_start: 0.9078 (mp) cc_final: 0.8730 (tt) REVERT: A 2840 MET cc_start: 0.8350 (mmt) cc_final: 0.8002 (mmt) REVERT: A 2843 MET cc_start: 0.8879 (ptm) cc_final: 0.8654 (ptt) REVERT: A 2860 LEU cc_start: 0.8979 (mt) cc_final: 0.8579 (tp) REVERT: A 3072 MET cc_start: 0.8995 (mtt) cc_final: 0.8662 (mtt) REVERT: A 3285 TYR cc_start: 0.7344 (m-80) cc_final: 0.7056 (m-80) REVERT: A 3605 MET cc_start: 0.4982 (ppp) cc_final: 0.3696 (pmm) REVERT: A 3819 MET cc_start: 0.7424 (pmm) cc_final: 0.7142 (pmm) REVERT: A 4002 MET cc_start: 0.8798 (tmm) cc_final: 0.8543 (tmm) REVERT: A 4046 ARG cc_start: 0.8966 (tpm170) cc_final: 0.8634 (tpm170) REVERT: A 4052 MET cc_start: 0.8319 (mmm) cc_final: 0.8110 (mmm) REVERT: A 4258 MET cc_start: 0.8532 (mtm) cc_final: 0.8271 (mtm) REVERT: A 4279 MET cc_start: 0.8522 (tpt) cc_final: 0.8107 (tpt) REVERT: A 4814 MET cc_start: 0.7672 (tpp) cc_final: 0.7411 (mmt) REVERT: E 4 GLU cc_start: 0.7778 (mp0) cc_final: 0.7489 (mp0) REVERT: E 30 MET cc_start: 0.7647 (mtp) cc_final: 0.6970 (mmt) REVERT: E 108 GLU cc_start: 0.8055 (pp20) cc_final: 0.7522 (pp20) REVERT: F 4 GLU cc_start: 0.7773 (mp0) cc_final: 0.7509 (mp0) REVERT: F 30 MET cc_start: 0.7662 (mtp) cc_final: 0.7385 (mtp) REVERT: F 53 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9122 (mppt) REVERT: F 108 GLU cc_start: 0.8064 (pp20) cc_final: 0.7633 (pp20) REVERT: G 4 GLU cc_start: 0.7701 (mp0) cc_final: 0.7484 (mp0) REVERT: G 30 MET cc_start: 0.7703 (mtp) cc_final: 0.7462 (mtp) REVERT: G 108 GLU cc_start: 0.8051 (pp20) cc_final: 0.7630 (pp20) REVERT: H 30 MET cc_start: 0.7652 (mtp) cc_final: 0.7361 (mtp) REVERT: H 108 GLU cc_start: 0.8037 (pp20) cc_final: 0.7493 (pp20) REVERT: B 81 MET cc_start: 0.8306 (mmp) cc_final: 0.8024 (mmm) REVERT: B 317 MET cc_start: 0.7740 (ptt) cc_final: 0.7490 (ptm) REVERT: B 874 LEU cc_start: 0.9066 (tp) cc_final: 0.8840 (tt) REVERT: B 981 MET cc_start: 0.8440 (tmm) cc_final: 0.8200 (tmm) REVERT: B 1017 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8805 (t) REVERT: B 1026 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.7998 (t0) REVERT: B 1047 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9014 (tppt) REVERT: B 1720 MET cc_start: 0.8433 (ptm) cc_final: 0.8229 (ptp) REVERT: B 1948 MET cc_start: 0.8191 (mmp) cc_final: 0.7647 (mtp) REVERT: B 2150 MET cc_start: 0.8292 (mtp) cc_final: 0.8068 (mtt) REVERT: B 2279 MET cc_start: 0.7843 (tmm) cc_final: 0.7629 (tmm) REVERT: B 2773 TRP cc_start: 0.8656 (t-100) cc_final: 0.8349 (t-100) REVERT: B 2798 MET cc_start: 0.8265 (mmm) cc_final: 0.8059 (mmm) REVERT: B 2826 ILE cc_start: 0.9028 (mp) cc_final: 0.8697 (tt) REVERT: B 2840 MET cc_start: 0.8417 (mmt) cc_final: 0.8116 (mmt) REVERT: B 2860 LEU cc_start: 0.9046 (mt) cc_final: 0.8617 (tp) REVERT: B 3072 MET cc_start: 0.9000 (mtt) cc_final: 0.8650 (mtt) REVERT: B 3285 TYR cc_start: 0.7400 (m-80) cc_final: 0.7139 (m-80) REVERT: B 3605 MET cc_start: 0.5131 (ppp) cc_final: 0.3902 (pmm) REVERT: B 3819 MET cc_start: 0.7390 (pmm) cc_final: 0.7116 (pmm) REVERT: B 4002 MET cc_start: 0.8754 (tmm) cc_final: 0.8538 (tmm) REVERT: B 4046 ARG cc_start: 0.8978 (tpm170) cc_final: 0.8616 (tpm170) REVERT: B 4258 MET cc_start: 0.8509 (mtm) cc_final: 0.8264 (mtm) REVERT: B 4654 MET cc_start: 0.8541 (tpp) cc_final: 0.8324 (tpt) REVERT: B 4814 MET cc_start: 0.7725 (tpp) cc_final: 0.7465 (mmt) REVERT: C 81 MET cc_start: 0.8326 (mmp) cc_final: 0.8106 (mmm) REVERT: C 317 MET cc_start: 0.7857 (ptt) cc_final: 0.7632 (ptm) REVERT: C 399 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7092 (tmm) REVERT: C 892 LEU cc_start: 0.9604 (mt) cc_final: 0.9376 (mt) REVERT: C 1026 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7928 (t0) REVERT: C 1060 TYR cc_start: 0.7795 (m-80) cc_final: 0.6936 (m-80) REVERT: C 1062 TYR cc_start: 0.8298 (m-80) cc_final: 0.7993 (m-10) REVERT: C 1948 MET cc_start: 0.7937 (mmp) cc_final: 0.7658 (mmm) REVERT: C 1975 MET cc_start: 0.8563 (ptm) cc_final: 0.8012 (ptp) REVERT: C 2150 MET cc_start: 0.8197 (mtp) cc_final: 0.7989 (mtt) REVERT: C 2695 MET cc_start: 0.7227 (ppp) cc_final: 0.6816 (ppp) REVERT: C 2798 MET cc_start: 0.8260 (mmm) cc_final: 0.8038 (mmm) REVERT: C 2826 ILE cc_start: 0.8998 (mp) cc_final: 0.8730 (tt) REVERT: C 2840 MET cc_start: 0.8536 (mmt) cc_final: 0.8246 (mmt) REVERT: C 2860 LEU cc_start: 0.9087 (mt) cc_final: 0.8790 (tp) REVERT: C 3072 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: C 3605 MET cc_start: 0.5123 (ppp) cc_final: 0.3946 (pmm) REVERT: C 3719 MET cc_start: 0.7814 (tmm) cc_final: 0.7561 (tmm) REVERT: C 4046 ARG cc_start: 0.8915 (tpm170) cc_final: 0.8403 (tpm170) REVERT: C 4923 MET cc_start: 0.8635 (ttt) cc_final: 0.8304 (ttp) REVERT: D 81 MET cc_start: 0.8253 (mmp) cc_final: 0.7952 (mmm) REVERT: D 885 LEU cc_start: 0.9058 (tp) cc_final: 0.8775 (tp) REVERT: D 940 LEU cc_start: 0.9474 (mp) cc_final: 0.9208 (pp) REVERT: D 1026 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7932 (t0) REVERT: D 1300 MET cc_start: 0.8450 (mmm) cc_final: 0.8151 (mmm) REVERT: D 1948 MET cc_start: 0.8160 (mmp) cc_final: 0.7533 (mmm) REVERT: D 2150 MET cc_start: 0.8281 (mtp) cc_final: 0.8001 (mtt) REVERT: D 2279 MET cc_start: 0.7777 (tmm) cc_final: 0.7446 (tmm) REVERT: D 2468 MET cc_start: 0.8697 (mmt) cc_final: 0.8228 (mmt) REVERT: D 2773 TRP cc_start: 0.8642 (t-100) cc_final: 0.8277 (t-100) REVERT: D 2798 MET cc_start: 0.8280 (mmm) cc_final: 0.7972 (mmm) REVERT: D 2843 MET cc_start: 0.8764 (ptp) cc_final: 0.8479 (ptp) REVERT: D 3072 MET cc_start: 0.8723 (mmp) cc_final: 0.8336 (mmm) REVERT: D 3285 TYR cc_start: 0.7423 (m-80) cc_final: 0.7194 (m-80) REVERT: D 3605 MET cc_start: 0.5139 (ppp) cc_final: 0.3834 (pmm) REVERT: D 3719 MET cc_start: 0.7915 (tmm) cc_final: 0.7612 (tmm) REVERT: D 3819 MET cc_start: 0.7334 (pmm) cc_final: 0.7024 (pmm) REVERT: D 4046 ARG cc_start: 0.8969 (tpm170) cc_final: 0.8601 (tpm170) REVERT: D 4279 MET cc_start: 0.8729 (tpt) cc_final: 0.8417 (tpt) outliers start: 64 outliers final: 26 residues processed: 826 average time/residue: 1.1978 time to fit residues: 1744.8756 Evaluate side-chains 793 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 758 time to evaluate : 11.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain A residue 1026 ASN Chi-restraints excluded: chain A residue 1047 LYS Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1011 ARG Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1026 ASN Chi-restraints excluded: chain B residue 1047 LYS Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1026 ASN Chi-restraints excluded: chain C residue 2167 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 1011 ARG Chi-restraints excluded: chain D residue 1026 ASN Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3003 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 2.9990 chunk 487 optimal weight: 10.0000 chunk 1306 optimal weight: 20.0000 chunk 1068 optimal weight: 9.9990 chunk 432 optimal weight: 8.9990 chunk 1572 optimal weight: 6.9990 chunk 1698 optimal weight: 10.0000 chunk 1400 optimal weight: 20.0000 chunk 1558 optimal weight: 20.0000 chunk 535 optimal weight: 7.9990 chunk 1261 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 ASN A1589 GLN ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3304 GLN A3308 ASN ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1589 GLN ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3304 GLN B3308 ASN ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1589 GLN ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3200 ASN ** C3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 141748 Z= 0.415 Angle : 0.629 14.196 191528 Z= 0.322 Chirality : 0.043 0.339 20988 Planarity : 0.005 0.147 24600 Dihedral : 8.305 174.477 19147 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.20 % Rotamer: Outliers : 0.45 % Allowed : 5.25 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.06), residues: 17212 helix: 1.94 (0.06), residues: 8972 sheet: 0.09 (0.12), residues: 1684 loop : -0.62 (0.07), residues: 6556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 893 HIS 0.012 0.001 HIS A 692 PHE 0.026 0.002 PHE D4846 TYR 0.030 0.002 TYR D2220 ARG 0.012 0.001 ARG B2835 *********************** 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 845 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 776 time to evaluate : 10.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.7874 (ptt) cc_final: 0.7662 (ptm) REVERT: A 880 ARG cc_start: 0.8971 (tpp-160) cc_final: 0.8648 (tpm170) REVERT: A 1050 LEU cc_start: 0.9170 (mm) cc_final: 0.8847 (mp) REVERT: A 1168 MET cc_start: 0.8584 (mmm) cc_final: 0.8323 (mmm) REVERT: A 1948 MET cc_start: 0.8217 (mmp) cc_final: 0.7657 (mmm) REVERT: A 1975 MET cc_start: 0.8762 (ptm) cc_final: 0.8418 (ptp) REVERT: A 2234 MET cc_start: 0.8548 (mmm) cc_final: 0.8226 (mtp) REVERT: A 2279 MET cc_start: 0.7882 (tmm) cc_final: 0.7622 (tmm) REVERT: A 2798 MET cc_start: 0.8242 (mmm) cc_final: 0.7989 (mmm) REVERT: A 2826 ILE cc_start: 0.9161 (mp) cc_final: 0.8810 (tt) REVERT: A 3072 MET cc_start: 0.9025 (mtt) cc_final: 0.8647 (mtt) REVERT: A 3285 TYR cc_start: 0.7289 (m-80) cc_final: 0.6798 (m-80) REVERT: A 3605 MET cc_start: 0.5351 (ppp) cc_final: 0.4023 (pmm) REVERT: A 3819 MET cc_start: 0.7512 (pmm) cc_final: 0.7232 (pmm) REVERT: A 4046 ARG cc_start: 0.9007 (tpm170) cc_final: 0.8635 (tpm170) REVERT: A 4258 MET cc_start: 0.8549 (mtm) cc_final: 0.8264 (mtm) REVERT: A 4279 MET cc_start: 0.8543 (tpt) cc_final: 0.7894 (tpt) REVERT: A 4814 MET cc_start: 0.7813 (tpp) cc_final: 0.7553 (mmt) REVERT: A 4943 MET cc_start: 0.8742 (mtp) cc_final: 0.8396 (mtp) REVERT: E 4 GLU cc_start: 0.7732 (mp0) cc_final: 0.7482 (mp0) REVERT: E 108 GLU cc_start: 0.8071 (pp20) cc_final: 0.7483 (pp20) REVERT: F 4 GLU cc_start: 0.7694 (mp0) cc_final: 0.7452 (mp0) REVERT: F 30 MET cc_start: 0.7834 (mtp) cc_final: 0.7538 (mtp) REVERT: F 108 GLU cc_start: 0.8107 (pp20) cc_final: 0.7483 (pp20) REVERT: G 108 GLU cc_start: 0.8125 (pp20) cc_final: 0.7504 (pp20) REVERT: H 54 GLN cc_start: 0.8687 (mp10) cc_final: 0.8486 (mp10) REVERT: H 108 GLU cc_start: 0.8059 (pp20) cc_final: 0.7461 (pp20) REVERT: B 81 MET cc_start: 0.8396 (mmp) cc_final: 0.8191 (mmm) REVERT: B 317 MET cc_start: 0.7823 (ptt) cc_final: 0.7596 (ptm) REVERT: B 1948 MET cc_start: 0.8215 (mmp) cc_final: 0.7697 (mmm) REVERT: B 1975 MET cc_start: 0.8806 (ptp) cc_final: 0.8126 (ptp) REVERT: B 2150 MET cc_start: 0.8308 (mtp) cc_final: 0.8066 (mtt) REVERT: B 2798 MET cc_start: 0.8209 (mmm) cc_final: 0.7995 (mmm) REVERT: B 2826 ILE cc_start: 0.9090 (mp) cc_final: 0.8799 (tt) REVERT: B 2840 MET cc_start: 0.8542 (mmt) cc_final: 0.8132 (mmt) REVERT: B 2843 MET cc_start: 0.8894 (ptp) cc_final: 0.8659 (ptp) REVERT: B 3072 MET cc_start: 0.9013 (mtt) cc_final: 0.8635 (mtt) REVERT: B 3285 TYR cc_start: 0.7331 (m-80) cc_final: 0.6867 (m-80) REVERT: B 3605 MET cc_start: 0.5280 (ppp) cc_final: 0.4017 (pmm) REVERT: B 3819 MET cc_start: 0.7505 (pmm) cc_final: 0.7189 (pmm) REVERT: B 4046 ARG cc_start: 0.9013 (tpm170) cc_final: 0.8622 (tpm170) REVERT: B 4258 MET cc_start: 0.8556 (mtm) cc_final: 0.8280 (mtm) REVERT: B 4279 MET cc_start: 0.8515 (tpt) cc_final: 0.8192 (tpt) REVERT: B 4814 MET cc_start: 0.7810 (tpp) cc_final: 0.7526 (mmm) REVERT: C 1026 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: C 1050 LEU cc_start: 0.9316 (mm) cc_final: 0.9015 (mp) REVERT: C 1060 TYR cc_start: 0.7727 (m-80) cc_final: 0.6977 (m-80) REVERT: C 1062 TYR cc_start: 0.8344 (m-80) cc_final: 0.7996 (m-10) REVERT: C 1975 MET cc_start: 0.8610 (ptm) cc_final: 0.8055 (ptp) REVERT: C 2150 MET cc_start: 0.8214 (mtp) cc_final: 0.7977 (mtt) REVERT: C 2695 MET cc_start: 0.7486 (ppp) cc_final: 0.6991 (ppp) REVERT: C 2732 TRP cc_start: 0.9039 (t60) cc_final: 0.8556 (t60) REVERT: C 2757 MET cc_start: 0.7898 (mmm) cc_final: 0.7597 (mmm) REVERT: C 2798 MET cc_start: 0.8363 (mmm) cc_final: 0.8138 (mmm) REVERT: C 2826 ILE cc_start: 0.9130 (mp) cc_final: 0.8788 (tt) REVERT: C 3072 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8515 (mtt) REVERT: C 3285 TYR cc_start: 0.7260 (m-80) cc_final: 0.7018 (m-80) REVERT: C 3605 MET cc_start: 0.5218 (ppp) cc_final: 0.4041 (pmm) REVERT: C 3719 MET cc_start: 0.7863 (tmm) cc_final: 0.7424 (tmm) REVERT: C 4046 ARG cc_start: 0.8981 (tpm170) cc_final: 0.8551 (tpm170) REVERT: C 4052 MET cc_start: 0.8484 (mmm) cc_final: 0.8023 (mmm) REVERT: C 4239 LEU cc_start: 0.8521 (mp) cc_final: 0.8182 (tp) REVERT: C 4923 MET cc_start: 0.8637 (ttt) cc_final: 0.8308 (ttp) REVERT: D 81 MET cc_start: 0.8381 (mmp) cc_final: 0.8164 (mmm) REVERT: D 317 MET cc_start: 0.7981 (ptt) cc_final: 0.7593 (ptm) REVERT: D 940 LEU cc_start: 0.9434 (mp) cc_final: 0.9170 (pp) REVERT: D 1300 MET cc_start: 0.8435 (mmm) cc_final: 0.8214 (mmp) REVERT: D 1948 MET cc_start: 0.8220 (mmp) cc_final: 0.7675 (mmm) REVERT: D 2150 MET cc_start: 0.8385 (mtp) cc_final: 0.8054 (mtt) REVERT: D 2279 MET cc_start: 0.7808 (tmm) cc_final: 0.7497 (tmm) REVERT: D 2773 TRP cc_start: 0.8482 (t-100) cc_final: 0.7960 (t-100) REVERT: D 2843 MET cc_start: 0.8729 (ptp) cc_final: 0.8477 (ptp) REVERT: D 3285 TYR cc_start: 0.7308 (m-80) cc_final: 0.7057 (m-80) REVERT: D 3605 MET cc_start: 0.5286 (ppp) cc_final: 0.3906 (pmm) REVERT: D 3719 MET cc_start: 0.7907 (tmm) cc_final: 0.7622 (tmm) REVERT: D 3819 MET cc_start: 0.7487 (pmm) cc_final: 0.7193 (pmm) REVERT: D 4002 MET cc_start: 0.8683 (tmm) cc_final: 0.8456 (ttp) REVERT: D 4046 ARG cc_start: 0.8988 (tpm170) cc_final: 0.8602 (tpm170) REVERT: D 4279 MET cc_start: 0.8656 (tpt) cc_final: 0.8320 (tpt) outliers start: 69 outliers final: 40 residues processed: 803 average time/residue: 1.1744 time to fit residues: 1671.8469 Evaluate side-chains 795 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 753 time to evaluate : 11.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3320 LEU Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 4672 MET Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3320 LEU Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 4672 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1026 ASN Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2167 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3320 LEU Chi-restraints excluded: chain C residue 3322 LEU Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3320 LEU Chi-restraints excluded: chain D residue 3322 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 9.9990 chunk 1181 optimal weight: 7.9990 chunk 815 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 750 optimal weight: 20.0000 chunk 1055 optimal weight: 0.3980 chunk 1577 optimal weight: 7.9990 chunk 1670 optimal weight: 2.9990 chunk 824 optimal weight: 2.9990 chunk 1495 optimal weight: 8.9990 chunk 450 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4171 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2938 GLN ** C3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 HIS ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 141748 Z= 0.251 Angle : 0.565 15.471 191528 Z= 0.287 Chirality : 0.040 0.402 20988 Planarity : 0.005 0.138 24600 Dihedral : 8.015 177.043 19120 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 0.42 % Allowed : 6.26 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.06), residues: 17212 helix: 2.09 (0.06), residues: 8980 sheet: 0.19 (0.13), residues: 1612 loop : -0.57 (0.07), residues: 6620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 893 HIS 0.009 0.001 HIS B3732 PHE 0.018 0.001 PHE D4846 TYR 0.043 0.001 TYR D1060 ARG 0.013 0.000 ARG D1051 *********************** 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 835 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 771 time to evaluate : 11.807 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: A 81 MET cc_start: 0.8307 (mmm) cc_final: 0.8067 (mmm) REVERT: A 317 MET cc_start: 0.7847 (ptt) cc_final: 0.7647 (ptm) REVERT: A 1060 TYR cc_start: 0.7630 (m-80) cc_final: 0.7399 (m-80) REVERT: A 1168 MET cc_start: 0.8605 (mmm) cc_final: 0.8347 (mmm) REVERT: A 1948 MET cc_start: 0.8230 (mmp) cc_final: 0.7701 (mmm) REVERT: A 1975 MET cc_start: 0.8720 (ptm) cc_final: 0.8382 (ptp) REVERT: A 2234 MET cc_start: 0.8526 (mmm) cc_final: 0.8237 (mtp) REVERT: A 2279 MET cc_start: 0.7868 (tmm) cc_final: 0.7605 (tmm) REVERT: A 2798 MET cc_start: 0.8280 (mmm) cc_final: 0.8050 (mmm) REVERT: A 2826 ILE cc_start: 0.9150 (mp) cc_final: 0.8839 (tt) REVERT: A 2860 LEU cc_start: 0.8956 (mm) cc_final: 0.8658 (tp) REVERT: A 3072 MET cc_start: 0.9001 (mtt) cc_final: 0.8596 (mtt) REVERT: A 3285 TYR cc_start: 0.7320 (m-80) cc_final: 0.6972 (m-80) REVERT: A 3605 MET cc_start: 0.5223 (ppp) cc_final: 0.3888 (pmm) REVERT: A 3819 MET cc_start: 0.7499 (pmm) cc_final: 0.7193 (pmm) REVERT: A 4046 ARG cc_start: 0.8990 (tpm170) cc_final: 0.8589 (tpm170) REVERT: A 4052 MET cc_start: 0.8565 (mmm) cc_final: 0.8179 (mmm) REVERT: A 4258 MET cc_start: 0.8554 (mtm) cc_final: 0.8253 (mtm) REVERT: A 4279 MET cc_start: 0.8505 (tpt) cc_final: 0.8229 (tpt) REVERT: A 4654 MET cc_start: 0.8450 (tpp) cc_final: 0.8153 (tpp) REVERT: A 4672 MET cc_start: 0.8337 (mtp) cc_final: 0.7892 (ptp) REVERT: A 4814 MET cc_start: 0.7778 (tpp) cc_final: 0.7533 (mmt) REVERT: A 4923 MET cc_start: 0.8683 (ttt) cc_final: 0.8433 (ttp) REVERT: A 4943 MET cc_start: 0.8766 (mtp) cc_final: 0.8454 (mtp) REVERT: E 30 MET cc_start: 0.7744 (mtm) cc_final: 0.7468 (mtm) REVERT: E 108 GLU cc_start: 0.8070 (pp20) cc_final: 0.7424 (pp20) REVERT: F 30 MET cc_start: 0.7783 (mtp) cc_final: 0.7521 (mtp) REVERT: F 108 GLU cc_start: 0.8091 (pp20) cc_final: 0.7433 (pp20) REVERT: G 108 GLU cc_start: 0.8090 (pp20) cc_final: 0.7446 (pp20) REVERT: H 108 GLU cc_start: 0.8050 (pp20) cc_final: 0.7413 (pp20) REVERT: B 393 MET cc_start: 0.8248 (mmt) cc_final: 0.7889 (mmt) REVERT: B 981 MET cc_start: 0.8282 (tmm) cc_final: 0.7976 (tmm) REVERT: B 1060 TYR cc_start: 0.7944 (m-80) cc_final: 0.7481 (m-80) REVERT: B 1168 MET cc_start: 0.8585 (mmm) cc_final: 0.8259 (mmm) REVERT: B 1948 MET cc_start: 0.8222 (mmp) cc_final: 0.7703 (mmm) REVERT: B 1975 MET cc_start: 0.8754 (ptp) cc_final: 0.8082 (ptp) REVERT: B 2150 MET cc_start: 0.8275 (mtp) cc_final: 0.8026 (mtt) REVERT: B 2773 TRP cc_start: 0.8655 (t-100) cc_final: 0.8299 (t-100) REVERT: B 2798 MET cc_start: 0.8236 (mmm) cc_final: 0.8022 (mmm) REVERT: B 2826 ILE cc_start: 0.9057 (mp) cc_final: 0.8815 (tt) REVERT: B 2860 LEU cc_start: 0.8989 (mm) cc_final: 0.8704 (tp) REVERT: B 3072 MET cc_start: 0.8985 (mtt) cc_final: 0.8560 (mtt) REVERT: B 3285 TYR cc_start: 0.7308 (m-80) cc_final: 0.7016 (m-80) REVERT: B 3605 MET cc_start: 0.5207 (ppp) cc_final: 0.3973 (pmm) REVERT: B 4046 ARG cc_start: 0.8980 (tpm170) cc_final: 0.8541 (tpm170) REVERT: B 4258 MET cc_start: 0.8475 (mtm) cc_final: 0.8180 (mtm) REVERT: B 4279 MET cc_start: 0.8493 (tpt) cc_final: 0.8212 (tpt) REVERT: B 4814 MET cc_start: 0.7801 (tpp) cc_final: 0.7538 (mmm) REVERT: B 4923 MET cc_start: 0.8684 (ttt) cc_final: 0.8442 (ttp) REVERT: C 1051 ARG cc_start: 0.8774 (ptp-110) cc_final: 0.8371 (ptp-110) REVERT: C 1060 TYR cc_start: 0.7688 (m-80) cc_final: 0.6948 (m-80) REVERT: C 1062 TYR cc_start: 0.8302 (m-80) cc_final: 0.7967 (m-10) REVERT: C 1948 MET cc_start: 0.7731 (mmm) cc_final: 0.7440 (mmm) REVERT: C 1975 MET cc_start: 0.8593 (ptm) cc_final: 0.8024 (ptp) REVERT: C 2150 MET cc_start: 0.8194 (mtp) cc_final: 0.7850 (mtm) REVERT: C 2695 MET cc_start: 0.7439 (ppp) cc_final: 0.6924 (ppp) REVERT: C 2782 MET cc_start: 0.8629 (mtp) cc_final: 0.8429 (mtp) REVERT: C 2798 MET cc_start: 0.8342 (mmm) cc_final: 0.8124 (mmm) REVERT: C 2826 ILE cc_start: 0.9139 (mp) cc_final: 0.8808 (tt) REVERT: C 2860 LEU cc_start: 0.9068 (mm) cc_final: 0.8822 (tp) REVERT: C 3072 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8448 (mtt) REVERT: C 3285 TYR cc_start: 0.7141 (m-80) cc_final: 0.6924 (m-80) REVERT: C 3605 MET cc_start: 0.5079 (ppp) cc_final: 0.3898 (pmm) REVERT: C 3719 MET cc_start: 0.7849 (tmm) cc_final: 0.7397 (tmm) REVERT: C 4239 LEU cc_start: 0.8517 (mp) cc_final: 0.8184 (tp) REVERT: C 4923 MET cc_start: 0.8639 (ttt) cc_final: 0.8415 (ttp) REVERT: D 317 MET cc_start: 0.7965 (ptt) cc_final: 0.7610 (ptm) REVERT: D 940 LEU cc_start: 0.9416 (mp) cc_final: 0.9164 (pp) REVERT: D 1051 ARG cc_start: 0.9105 (mtm110) cc_final: 0.8869 (ptp-110) REVERT: D 1300 MET cc_start: 0.8396 (mmm) cc_final: 0.8188 (mmp) REVERT: D 1948 MET cc_start: 0.8225 (mmp) cc_final: 0.7747 (mmm) REVERT: D 1975 MET cc_start: 0.8842 (ptp) cc_final: 0.8234 (ptp) REVERT: D 2150 MET cc_start: 0.8306 (mtp) cc_final: 0.7979 (mtt) REVERT: D 2234 MET cc_start: 0.8533 (mmm) cc_final: 0.8218 (mtp) REVERT: D 2279 MET cc_start: 0.7811 (tmm) cc_final: 0.7502 (tmm) REVERT: D 2773 TRP cc_start: 0.8454 (t-100) cc_final: 0.8030 (t-100) REVERT: D 2798 MET cc_start: 0.8322 (mmm) cc_final: 0.8061 (mmm) REVERT: D 2826 ILE cc_start: 0.9074 (mp) cc_final: 0.8783 (tt) REVERT: D 2843 MET cc_start: 0.8727 (ptp) cc_final: 0.8476 (ptp) REVERT: D 3605 MET cc_start: 0.5214 (ppp) cc_final: 0.3847 (pmm) REVERT: D 3719 MET cc_start: 0.7872 (tmm) cc_final: 0.7524 (tmm) REVERT: D 3819 MET cc_start: 0.7414 (pmm) cc_final: 0.7112 (pmm) REVERT: D 3956 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7628 (mmp) REVERT: D 4046 ARG cc_start: 0.8965 (tpm170) cc_final: 0.8578 (tpm170) REVERT: D 4279 MET cc_start: 0.8540 (tpt) cc_final: 0.8089 (tpt) outliers start: 64 outliers final: 40 residues processed: 803 average time/residue: 1.2833 time to fit residues: 1845.0818 Evaluate side-chains 800 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 758 time to evaluate : 11.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3971 LEU Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 3971 LEU Chi-restraints excluded: chain B residue 4672 MET Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2167 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3971 LEU Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 1043 LYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3322 LEU Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 3971 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 7.9990 chunk 948 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 1243 optimal weight: 0.9990 chunk 689 optimal weight: 10.0000 chunk 1425 optimal weight: 4.9990 chunk 1154 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 852 optimal weight: 7.9990 chunk 1499 optimal weight: 10.0000 chunk 421 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 HIS ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 HIS ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4171 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 890 HIS ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2938 GLN ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 141748 Z= 0.304 Angle : 0.575 14.957 191528 Z= 0.292 Chirality : 0.041 0.349 20988 Planarity : 0.005 0.134 24600 Dihedral : 7.790 179.766 19120 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 0.46 % Allowed : 6.80 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.06), residues: 17212 helix: 2.11 (0.06), residues: 8980 sheet: 0.13 (0.12), residues: 1656 loop : -0.52 (0.07), residues: 6576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 893 HIS 0.009 0.001 HIS C3732 PHE 0.020 0.001 PHE C3854 TYR 0.033 0.001 TYR D1060 ARG 0.012 0.000 ARG B2835 *********************** 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 837 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 767 time to evaluate : 11.922 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: A 81 MET cc_start: 0.8368 (mmm) cc_final: 0.8148 (mmm) REVERT: A 1050 LEU cc_start: 0.9198 (mm) cc_final: 0.8905 (mp) REVERT: A 1060 TYR cc_start: 0.7687 (m-80) cc_final: 0.7427 (m-80) REVERT: A 1168 MET cc_start: 0.8617 (mmm) cc_final: 0.8383 (mmm) REVERT: A 1948 MET cc_start: 0.8237 (mmp) cc_final: 0.7769 (mmp) REVERT: A 1975 MET cc_start: 0.8706 (ptm) cc_final: 0.8366 (ptp) REVERT: A 2234 MET cc_start: 0.8526 (mmm) cc_final: 0.8232 (mtp) REVERT: A 2279 MET cc_start: 0.7910 (tmm) cc_final: 0.7651 (tmm) REVERT: A 2798 MET cc_start: 0.8285 (mmm) cc_final: 0.8058 (mmm) REVERT: A 2826 ILE cc_start: 0.9092 (mp) cc_final: 0.8826 (tt) REVERT: A 2843 MET cc_start: 0.8887 (ptt) cc_final: 0.8619 (ptp) REVERT: A 3072 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8590 (mtt) REVERT: A 3285 TYR cc_start: 0.7325 (m-80) cc_final: 0.7015 (m-80) REVERT: A 3605 MET cc_start: 0.5354 (ppp) cc_final: 0.4091 (pmm) REVERT: A 3956 MET cc_start: 0.7785 (mmt) cc_final: 0.7463 (mmt) REVERT: A 4052 MET cc_start: 0.8561 (mmm) cc_final: 0.8168 (mmm) REVERT: A 4258 MET cc_start: 0.8565 (mtm) cc_final: 0.8244 (mtm) REVERT: A 4279 MET cc_start: 0.8497 (tpt) cc_final: 0.8053 (tpt) REVERT: A 4707 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8036 (ttp) REVERT: A 4814 MET cc_start: 0.7788 (tpp) cc_final: 0.7525 (mmt) REVERT: A 4923 MET cc_start: 0.8667 (ttt) cc_final: 0.8430 (ttp) REVERT: A 4943 MET cc_start: 0.8773 (mtp) cc_final: 0.8439 (mtp) REVERT: E 30 MET cc_start: 0.7813 (mtm) cc_final: 0.7564 (mtm) REVERT: E 108 GLU cc_start: 0.8064 (pp20) cc_final: 0.7410 (pp20) REVERT: F 53 LYS cc_start: 0.8974 (mppt) cc_final: 0.8705 (mppt) REVERT: F 108 GLU cc_start: 0.8084 (pp20) cc_final: 0.7423 (pp20) REVERT: G 108 GLU cc_start: 0.8076 (pp20) cc_final: 0.7415 (pp20) REVERT: H 108 GLU cc_start: 0.8048 (pp20) cc_final: 0.7396 (pp20) REVERT: B 393 MET cc_start: 0.8244 (mmt) cc_final: 0.7881 (mmt) REVERT: B 1043 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8799 (ttmt) REVERT: B 1050 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8787 (mp) REVERT: B 1060 TYR cc_start: 0.7955 (m-80) cc_final: 0.7389 (m-80) REVERT: B 1168 MET cc_start: 0.8607 (mmm) cc_final: 0.8299 (mmm) REVERT: B 1948 MET cc_start: 0.8224 (mmp) cc_final: 0.7764 (mmm) REVERT: B 1975 MET cc_start: 0.8764 (ptp) cc_final: 0.8094 (ptp) REVERT: B 2150 MET cc_start: 0.8284 (mtp) cc_final: 0.8031 (mtt) REVERT: B 2695 MET cc_start: 0.7138 (ppp) cc_final: 0.6720 (ppp) REVERT: B 2773 TRP cc_start: 0.8674 (t-100) cc_final: 0.8317 (t-100) REVERT: B 2798 MET cc_start: 0.8267 (mmm) cc_final: 0.8055 (mmm) REVERT: B 2826 ILE cc_start: 0.9059 (mp) cc_final: 0.8813 (tt) REVERT: B 2843 MET cc_start: 0.8911 (ptp) cc_final: 0.8664 (ptp) REVERT: B 3072 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8562 (mtt) REVERT: B 3285 TYR cc_start: 0.7333 (m-80) cc_final: 0.7020 (m-80) REVERT: B 3605 MET cc_start: 0.5308 (ppp) cc_final: 0.4073 (pmm) REVERT: B 3819 MET cc_start: 0.7442 (pmm) cc_final: 0.7153 (pmm) REVERT: B 3956 MET cc_start: 0.7780 (mmt) cc_final: 0.7462 (mmt) REVERT: B 4052 MET cc_start: 0.8551 (mmm) cc_final: 0.8142 (mmm) REVERT: B 4258 MET cc_start: 0.8492 (mtm) cc_final: 0.8245 (mtm) REVERT: B 4279 MET cc_start: 0.8472 (tpt) cc_final: 0.8060 (tpt) REVERT: B 4654 MET cc_start: 0.8450 (tpp) cc_final: 0.8241 (tpt) REVERT: B 4672 MET cc_start: 0.8370 (mtp) cc_final: 0.7965 (ptp) REVERT: B 4814 MET cc_start: 0.7818 (tpp) cc_final: 0.7551 (mmm) REVERT: B 4923 MET cc_start: 0.8680 (ttt) cc_final: 0.8445 (ttp) REVERT: C 1050 LEU cc_start: 0.9293 (mm) cc_final: 0.8994 (mp) REVERT: C 1051 ARG cc_start: 0.8789 (ptp-110) cc_final: 0.8331 (ptp-110) REVERT: C 1060 TYR cc_start: 0.7662 (m-80) cc_final: 0.6960 (m-80) REVERT: C 1062 TYR cc_start: 0.8348 (m-80) cc_final: 0.8015 (m-10) REVERT: C 1948 MET cc_start: 0.7837 (mmm) cc_final: 0.7547 (mmm) REVERT: C 1975 MET cc_start: 0.8602 (ptm) cc_final: 0.8033 (ptp) REVERT: C 2150 MET cc_start: 0.8204 (mtp) cc_final: 0.7875 (mtm) REVERT: C 2695 MET cc_start: 0.7495 (ppp) cc_final: 0.6953 (ppp) REVERT: C 2826 ILE cc_start: 0.9092 (mp) cc_final: 0.8812 (tt) REVERT: C 3072 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8482 (mtt) REVERT: C 3285 TYR cc_start: 0.7176 (m-80) cc_final: 0.6901 (m-80) REVERT: C 3605 MET cc_start: 0.5138 (ppp) cc_final: 0.3882 (pmm) REVERT: C 3719 MET cc_start: 0.7849 (tmm) cc_final: 0.7384 (tmm) REVERT: C 4120 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: C 4239 LEU cc_start: 0.8522 (mp) cc_final: 0.8186 (tp) REVERT: C 4923 MET cc_start: 0.8652 (ttt) cc_final: 0.8423 (ttp) REVERT: D 940 LEU cc_start: 0.9419 (mp) cc_final: 0.9171 (pp) REVERT: D 964 MET cc_start: 0.4234 (mpp) cc_final: 0.3896 (mpp) REVERT: D 981 MET cc_start: 0.8135 (tmm) cc_final: 0.7819 (tmm) REVERT: D 1050 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8910 (mp) REVERT: D 1051 ARG cc_start: 0.9089 (mtm110) cc_final: 0.8858 (ptp-110) REVERT: D 1948 MET cc_start: 0.8232 (mmp) cc_final: 0.7768 (mmm) REVERT: D 1975 MET cc_start: 0.8857 (ptp) cc_final: 0.8210 (ptp) REVERT: D 2150 MET cc_start: 0.8310 (mtp) cc_final: 0.7976 (mtt) REVERT: D 2234 MET cc_start: 0.8532 (mmm) cc_final: 0.8245 (mtp) REVERT: D 2279 MET cc_start: 0.7842 (tmm) cc_final: 0.7543 (tmm) REVERT: D 2773 TRP cc_start: 0.8500 (t-100) cc_final: 0.8049 (t-100) REVERT: D 2798 MET cc_start: 0.8355 (mmm) cc_final: 0.8077 (mmm) REVERT: D 2826 ILE cc_start: 0.9094 (mp) cc_final: 0.8777 (tt) REVERT: D 2843 MET cc_start: 0.8717 (ptp) cc_final: 0.8510 (ptm) REVERT: D 3003 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8560 (mtm) REVERT: D 3605 MET cc_start: 0.5281 (ppp) cc_final: 0.3920 (pmm) REVERT: D 3719 MET cc_start: 0.7891 (tmm) cc_final: 0.7577 (tmm) REVERT: D 3819 MET cc_start: 0.7457 (pmm) cc_final: 0.7129 (pmm) REVERT: D 3956 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7628 (mmp) REVERT: D 4046 ARG cc_start: 0.9000 (tpm170) cc_final: 0.8557 (tpm170) REVERT: D 4052 MET cc_start: 0.8456 (mmm) cc_final: 0.8038 (mmm) REVERT: D 4279 MET cc_start: 0.8464 (tpt) cc_final: 0.8009 (tpt) outliers start: 70 outliers final: 41 residues processed: 797 average time/residue: 1.1907 time to fit residues: 1683.8512 Evaluate side-chains 802 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 751 time to evaluate : 10.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3971 LEU Chi-restraints excluded: chain A residue 4707 MET Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 3971 LEU Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1174 MET Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2167 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3322 LEU Chi-restraints excluded: chain C residue 3971 LEU Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 1043 LYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3003 MET Chi-restraints excluded: chain D residue 3322 LEU Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 3971 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 1.9990 chunk 1504 optimal weight: 8.9990 chunk 330 optimal weight: 7.9990 chunk 980 optimal weight: 30.0000 chunk 412 optimal weight: 8.9990 chunk 1671 optimal weight: 10.0000 chunk 1387 optimal weight: 0.9990 chunk 774 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 553 optimal weight: 20.0000 chunk 877 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 HIS ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 HIS ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 ASN ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2938 GLN ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 HIS C 890 HIS ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 HIS ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 141748 Z= 0.313 Angle : 0.575 14.785 191528 Z= 0.292 Chirality : 0.041 0.320 20988 Planarity : 0.005 0.132 24600 Dihedral : 7.589 178.862 19120 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.55 % Allowed : 7.23 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.06), residues: 17212 helix: 2.16 (0.06), residues: 8940 sheet: 0.14 (0.13), residues: 1624 loop : -0.46 (0.07), residues: 6648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 893 HIS 0.025 0.001 HIS B 890 PHE 0.021 0.001 PHE A3854 TYR 0.039 0.001 TYR A 931 ARG 0.011 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 847 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 763 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8383 (mmm) cc_final: 0.8162 (mmm) REVERT: A 946 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8117 (pt) REVERT: A 995 MET cc_start: 0.8359 (mtm) cc_final: 0.7799 (mtp) REVERT: A 999 LEU cc_start: 0.8983 (mm) cc_final: 0.8783 (mm) REVERT: A 1050 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8900 (mp) REVERT: A 1060 TYR cc_start: 0.7661 (m-80) cc_final: 0.7390 (m-80) REVERT: A 1168 MET cc_start: 0.8617 (mmm) cc_final: 0.8411 (mmm) REVERT: A 1948 MET cc_start: 0.8249 (mmp) cc_final: 0.7769 (mmp) REVERT: A 1975 MET cc_start: 0.8735 (ptm) cc_final: 0.8387 (ptp) REVERT: A 2234 MET cc_start: 0.8533 (mmm) cc_final: 0.8261 (mtp) REVERT: A 2279 MET cc_start: 0.7919 (tmm) cc_final: 0.7662 (tmm) REVERT: A 2798 MET cc_start: 0.8325 (mmm) cc_final: 0.8103 (mmm) REVERT: A 2826 ILE cc_start: 0.9112 (mp) cc_final: 0.8822 (tt) REVERT: A 2840 MET cc_start: 0.8390 (mmt) cc_final: 0.7944 (mmm) REVERT: A 2843 MET cc_start: 0.8889 (ptt) cc_final: 0.8583 (ptp) REVERT: A 3072 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8530 (mtt) REVERT: A 3285 TYR cc_start: 0.7295 (m-80) cc_final: 0.6983 (m-80) REVERT: A 3819 MET cc_start: 0.7450 (pmm) cc_final: 0.7152 (pmm) REVERT: A 4052 MET cc_start: 0.8563 (mmm) cc_final: 0.8191 (mmm) REVERT: A 4258 MET cc_start: 0.8511 (mtm) cc_final: 0.8265 (mtm) REVERT: A 4279 MET cc_start: 0.8489 (tpt) cc_final: 0.8041 (tpt) REVERT: A 4672 MET cc_start: 0.8406 (mtp) cc_final: 0.8015 (ptp) REVERT: A 4707 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: A 4814 MET cc_start: 0.7791 (tpp) cc_final: 0.7523 (mmt) REVERT: A 4923 MET cc_start: 0.8666 (ttt) cc_final: 0.8437 (ttp) REVERT: A 4943 MET cc_start: 0.8777 (mtp) cc_final: 0.8417 (mtp) REVERT: E 30 MET cc_start: 0.7828 (mtm) cc_final: 0.7605 (mtm) REVERT: E 108 GLU cc_start: 0.8053 (pp20) cc_final: 0.7384 (pp20) REVERT: F 108 GLU cc_start: 0.8107 (pp20) cc_final: 0.7452 (pp20) REVERT: G 108 GLU cc_start: 0.8084 (pp20) cc_final: 0.7422 (pp20) REVERT: H 108 GLU cc_start: 0.8059 (pp20) cc_final: 0.7398 (pp20) REVERT: B 317 MET cc_start: 0.7893 (ptt) cc_final: 0.7670 (ptm) REVERT: B 895 MET cc_start: 0.9197 (mmm) cc_final: 0.8873 (mpp) REVERT: B 946 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (pt) REVERT: B 981 MET cc_start: 0.8158 (tmm) cc_final: 0.7902 (tmm) REVERT: B 995 MET cc_start: 0.8323 (mtm) cc_final: 0.7879 (mtp) REVERT: B 1043 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8734 (ttmt) REVERT: B 1050 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8805 (mp) REVERT: B 1060 TYR cc_start: 0.7962 (m-80) cc_final: 0.7417 (m-80) REVERT: B 1168 MET cc_start: 0.8609 (mmm) cc_final: 0.8333 (mmm) REVERT: B 1948 MET cc_start: 0.8239 (mmp) cc_final: 0.7785 (mmm) REVERT: B 1975 MET cc_start: 0.8746 (ptp) cc_final: 0.8093 (ptp) REVERT: B 2134 MET cc_start: 0.8470 (tpt) cc_final: 0.8252 (tpp) REVERT: B 2150 MET cc_start: 0.8278 (mtp) cc_final: 0.8017 (mtt) REVERT: B 2192 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (ttp) REVERT: B 2757 MET cc_start: 0.7598 (mmm) cc_final: 0.6891 (mmm) REVERT: B 2773 TRP cc_start: 0.8662 (t-100) cc_final: 0.8274 (t-100) REVERT: B 2826 ILE cc_start: 0.9069 (mp) cc_final: 0.8807 (tt) REVERT: B 2840 MET cc_start: 0.8429 (mmt) cc_final: 0.8194 (mmm) REVERT: B 3072 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8526 (mtt) REVERT: B 3285 TYR cc_start: 0.7285 (m-80) cc_final: 0.6967 (m-80) REVERT: B 3819 MET cc_start: 0.7427 (pmm) cc_final: 0.7153 (pmm) REVERT: B 4052 MET cc_start: 0.8575 (mmm) cc_final: 0.8180 (mmm) REVERT: B 4258 MET cc_start: 0.8491 (mtm) cc_final: 0.8242 (mtm) REVERT: B 4279 MET cc_start: 0.8475 (tpt) cc_final: 0.8064 (tpt) REVERT: B 4654 MET cc_start: 0.8458 (tpp) cc_final: 0.8250 (tpt) REVERT: B 4814 MET cc_start: 0.7833 (tpp) cc_final: 0.7566 (mmm) REVERT: B 4923 MET cc_start: 0.8661 (ttt) cc_final: 0.8430 (ttp) REVERT: C 317 MET cc_start: 0.7849 (ptt) cc_final: 0.7581 (ptt) REVERT: C 935 MET cc_start: 0.8321 (ppp) cc_final: 0.8119 (ppp) REVERT: C 1050 LEU cc_start: 0.9273 (mm) cc_final: 0.8964 (mp) REVERT: C 1060 TYR cc_start: 0.7698 (m-80) cc_final: 0.7166 (m-80) REVERT: C 1062 TYR cc_start: 0.8314 (m-80) cc_final: 0.7986 (m-10) REVERT: C 1948 MET cc_start: 0.7860 (mmm) cc_final: 0.7588 (mmp) REVERT: C 1975 MET cc_start: 0.8615 (ptm) cc_final: 0.8035 (ptp) REVERT: C 2150 MET cc_start: 0.8194 (mtp) cc_final: 0.7871 (mtm) REVERT: C 2695 MET cc_start: 0.7536 (ppp) cc_final: 0.6986 (ppp) REVERT: C 2826 ILE cc_start: 0.9112 (mp) cc_final: 0.8867 (tt) REVERT: C 3072 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8488 (mtt) REVERT: C 3285 TYR cc_start: 0.7171 (m-80) cc_final: 0.6863 (m-80) REVERT: C 3605 MET cc_start: 0.5138 (ppp) cc_final: 0.3913 (pmm) REVERT: C 3719 MET cc_start: 0.7845 (tmm) cc_final: 0.7373 (tmm) REVERT: C 3819 MET cc_start: 0.7452 (pmm) cc_final: 0.7237 (pmm) REVERT: C 4046 ARG cc_start: 0.8972 (tpm170) cc_final: 0.8483 (tpm170) REVERT: C 4052 MET cc_start: 0.8499 (mmm) cc_final: 0.8078 (mmm) REVERT: C 4120 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: C 4239 LEU cc_start: 0.8492 (mp) cc_final: 0.8160 (tp) REVERT: C 4923 MET cc_start: 0.8652 (ttt) cc_final: 0.8427 (ttp) REVERT: D 940 LEU cc_start: 0.9385 (mp) cc_final: 0.9154 (pp) REVERT: D 946 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8078 (pt) REVERT: D 981 MET cc_start: 0.8196 (tmm) cc_final: 0.7882 (tmm) REVERT: D 995 MET cc_start: 0.8349 (mtm) cc_final: 0.7815 (mtp) REVERT: D 1051 ARG cc_start: 0.9079 (mtm110) cc_final: 0.8841 (ptp-110) REVERT: D 1948 MET cc_start: 0.8224 (mmp) cc_final: 0.7844 (mmm) REVERT: D 1975 MET cc_start: 0.8850 (ptp) cc_final: 0.8224 (ptp) REVERT: D 2150 MET cc_start: 0.8305 (mtp) cc_final: 0.7966 (mtt) REVERT: D 2234 MET cc_start: 0.8530 (mmm) cc_final: 0.8249 (mtp) REVERT: D 2279 MET cc_start: 0.7858 (tmm) cc_final: 0.7583 (tmm) REVERT: D 2773 TRP cc_start: 0.8514 (t-100) cc_final: 0.8043 (t-100) REVERT: D 2798 MET cc_start: 0.8350 (mmm) cc_final: 0.8104 (mmm) REVERT: D 2826 ILE cc_start: 0.9097 (mp) cc_final: 0.8800 (tt) REVERT: D 3719 MET cc_start: 0.7882 (tmm) cc_final: 0.7521 (tmm) REVERT: D 3819 MET cc_start: 0.7446 (pmm) cc_final: 0.7193 (pmm) REVERT: D 3956 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7608 (mmp) REVERT: D 4052 MET cc_start: 0.8453 (mmm) cc_final: 0.8047 (mmm) REVERT: D 4120 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: D 4279 MET cc_start: 0.8466 (tpt) cc_final: 0.7960 (tpt) outliers start: 84 outliers final: 46 residues processed: 804 average time/residue: 1.1811 time to fit residues: 1687.5642 Evaluate side-chains 817 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 757 time to evaluate : 11.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1050 LEU 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 2347 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3971 LEU Chi-restraints excluded: chain A residue 4707 MET Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 3971 LEU Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1896 MET Chi-restraints excluded: chain C residue 2167 MET Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3322 LEU Chi-restraints excluded: chain C residue 3971 LEU Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1043 LYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3322 LEU Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 3971 LEU Chi-restraints excluded: chain D residue 4120 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 952 optimal weight: 10.0000 chunk 1220 optimal weight: 2.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 40.0000 chunk 933 optimal weight: 1.9990 chunk 1665 optimal weight: 5.9990 chunk 1042 optimal weight: 7.9990 chunk 1015 optimal weight: 7.9990 chunk 768 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 ASN ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2938 GLN ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 ASN ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 141748 Z= 0.269 Angle : 0.570 14.738 191528 Z= 0.287 Chirality : 0.040 0.321 20988 Planarity : 0.004 0.130 24600 Dihedral : 7.530 179.870 19120 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 0.53 % Allowed : 7.74 % Favored : 91.73 % 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: 1.49 (0.06), residues: 17212 helix: 2.21 (0.06), residues: 8932 sheet: 0.06 (0.12), residues: 1680 loop : -0.44 (0.08), residues: 6600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 893 HIS 0.008 0.001 HIS B3732 PHE 0.019 0.001 PHE D3854 TYR 0.030 0.001 TYR D1060 ARG 0.012 0.000 ARG F 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 840 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 760 time to evaluate : 12.061 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: A 81 MET cc_start: 0.8401 (mmm) cc_final: 0.8173 (mmm) REVERT: A 995 MET cc_start: 0.8291 (mtm) cc_final: 0.7883 (mtp) REVERT: A 999 LEU cc_start: 0.8968 (mm) cc_final: 0.8747 (mm) REVERT: A 1050 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8886 (mp) REVERT: A 1060 TYR cc_start: 0.7624 (m-80) cc_final: 0.7391 (m-80) REVERT: A 1168 MET cc_start: 0.8623 (mmm) cc_final: 0.8411 (mmm) REVERT: A 1948 MET cc_start: 0.8253 (mmp) cc_final: 0.7775 (mmp) REVERT: A 1975 MET cc_start: 0.8725 (ptm) cc_final: 0.8373 (ptp) REVERT: A 2234 MET cc_start: 0.8527 (mmm) cc_final: 0.8253 (mtp) REVERT: A 2279 MET cc_start: 0.7918 (tmm) cc_final: 0.7670 (tmm) REVERT: A 2695 MET cc_start: 0.7054 (ppp) cc_final: 0.6657 (ppp) REVERT: A 2773 TRP cc_start: 0.8643 (t-100) cc_final: 0.8204 (t-100) REVERT: A 2798 MET cc_start: 0.8358 (mmm) cc_final: 0.8126 (mmm) REVERT: A 2826 ILE cc_start: 0.9124 (mp) cc_final: 0.8824 (tt) REVERT: A 2840 MET cc_start: 0.8369 (mmt) cc_final: 0.7863 (mmm) REVERT: A 2843 MET cc_start: 0.8896 (ptt) cc_final: 0.8517 (ptp) REVERT: A 2860 LEU cc_start: 0.9028 (mm) cc_final: 0.8697 (tp) REVERT: A 3072 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8503 (mtt) REVERT: A 3285 TYR cc_start: 0.7257 (m-80) cc_final: 0.7008 (m-80) REVERT: A 3819 MET cc_start: 0.7430 (pmm) cc_final: 0.7117 (pmm) REVERT: A 4052 MET cc_start: 0.8574 (mmm) cc_final: 0.8205 (mmm) REVERT: A 4258 MET cc_start: 0.8504 (mtm) cc_final: 0.8126 (mtm) REVERT: A 4279 MET cc_start: 0.8485 (tpt) cc_final: 0.8039 (tpt) REVERT: A 4672 MET cc_start: 0.8404 (mtp) cc_final: 0.8180 (ptp) REVERT: A 4707 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8045 (ttp) REVERT: A 4814 MET cc_start: 0.7787 (tpp) cc_final: 0.7527 (mmt) REVERT: A 4923 MET cc_start: 0.8660 (ttt) cc_final: 0.8447 (ttp) REVERT: A 4943 MET cc_start: 0.8779 (mtp) cc_final: 0.8418 (mtp) REVERT: E 30 MET cc_start: 0.7828 (mtm) cc_final: 0.7613 (mtm) REVERT: E 108 GLU cc_start: 0.8074 (pp20) cc_final: 0.7404 (pp20) REVERT: F 108 GLU cc_start: 0.8076 (pp20) cc_final: 0.7407 (pp20) REVERT: G 108 GLU cc_start: 0.8063 (pp20) cc_final: 0.7392 (pp20) REVERT: H 108 GLU cc_start: 0.8047 (pp20) cc_final: 0.7380 (pp20) REVERT: B 117 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8093 (m-70) REVERT: B 995 MET cc_start: 0.8406 (mtm) cc_final: 0.7936 (mtp) REVERT: B 1017 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8721 (t) REVERT: B 1043 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8717 (ttmt) REVERT: B 1050 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8807 (mp) REVERT: B 1060 TYR cc_start: 0.7938 (m-80) cc_final: 0.7403 (m-80) REVERT: B 1168 MET cc_start: 0.8611 (mmm) cc_final: 0.8341 (mmm) REVERT: B 1721 MET cc_start: 0.7315 (mmt) cc_final: 0.7064 (mmm) REVERT: B 1948 MET cc_start: 0.8261 (mmp) cc_final: 0.7796 (mmm) REVERT: B 2150 MET cc_start: 0.8266 (mtp) cc_final: 0.8002 (mtt) REVERT: B 2695 MET cc_start: 0.7150 (ppp) cc_final: 0.6767 (ppp) REVERT: B 2773 TRP cc_start: 0.8657 (t-100) cc_final: 0.8261 (t-100) REVERT: B 2826 ILE cc_start: 0.9061 (mp) cc_final: 0.8808 (tt) REVERT: B 2840 MET cc_start: 0.8408 (mmt) cc_final: 0.8155 (mmm) REVERT: B 2843 MET cc_start: 0.8942 (ptp) cc_final: 0.8710 (ptp) REVERT: B 3072 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8508 (mtt) REVERT: B 3285 TYR cc_start: 0.7249 (m-80) cc_final: 0.7016 (m-80) REVERT: B 3819 MET cc_start: 0.7412 (pmm) cc_final: 0.7125 (pmm) REVERT: B 4052 MET cc_start: 0.8560 (mmm) cc_final: 0.8160 (mmm) REVERT: B 4258 MET cc_start: 0.8489 (mtm) cc_final: 0.8236 (mtm) REVERT: B 4279 MET cc_start: 0.8450 (tpt) cc_final: 0.8034 (tpt) REVERT: B 4814 MET cc_start: 0.7834 (tpp) cc_final: 0.7568 (mmm) REVERT: B 4923 MET cc_start: 0.8665 (ttt) cc_final: 0.8445 (ttp) REVERT: C 317 MET cc_start: 0.7808 (ptt) cc_final: 0.7562 (ptt) REVERT: C 393 MET cc_start: 0.8449 (mmp) cc_final: 0.8212 (mmm) REVERT: C 1060 TYR cc_start: 0.7656 (m-80) cc_final: 0.7130 (m-80) REVERT: C 1062 TYR cc_start: 0.8286 (m-80) cc_final: 0.7926 (m-10) REVERT: C 1948 MET cc_start: 0.7893 (mmm) cc_final: 0.7612 (mmp) REVERT: C 1975 MET cc_start: 0.8604 (ptm) cc_final: 0.8020 (ptp) REVERT: C 2142 MET cc_start: 0.8666 (tpt) cc_final: 0.8284 (tpt) REVERT: C 2150 MET cc_start: 0.8170 (mtp) cc_final: 0.7961 (mtt) REVERT: C 2695 MET cc_start: 0.7558 (ppp) cc_final: 0.7006 (ppp) REVERT: C 2773 TRP cc_start: 0.8669 (t-100) cc_final: 0.8428 (t-100) REVERT: C 2798 MET cc_start: 0.8350 (mmm) cc_final: 0.8000 (mmm) REVERT: C 2840 MET cc_start: 0.8985 (mmm) cc_final: 0.8757 (mmt) REVERT: C 3072 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8477 (mtt) REVERT: C 3285 TYR cc_start: 0.7163 (m-80) cc_final: 0.6834 (m-80) REVERT: C 3605 MET cc_start: 0.5099 (ppp) cc_final: 0.3894 (pmm) REVERT: C 3719 MET cc_start: 0.7848 (tmm) cc_final: 0.7365 (tmm) REVERT: C 3819 MET cc_start: 0.7473 (pmm) cc_final: 0.7261 (pmm) REVERT: C 4052 MET cc_start: 0.8498 (mmm) cc_final: 0.8073 (mmm) REVERT: C 4120 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7641 (mm-30) REVERT: C 4239 LEU cc_start: 0.8505 (mp) cc_final: 0.8175 (tp) REVERT: C 4923 MET cc_start: 0.8686 (ttt) cc_final: 0.8464 (ttp) REVERT: D 940 LEU cc_start: 0.9370 (mp) cc_final: 0.9130 (pp) REVERT: D 981 MET cc_start: 0.8177 (tmm) cc_final: 0.7917 (tmm) REVERT: D 995 MET cc_start: 0.8324 (mtm) cc_final: 0.7914 (mtp) REVERT: D 1051 ARG cc_start: 0.9066 (mtm110) cc_final: 0.8833 (ptp-110) REVERT: D 1300 MET cc_start: 0.8200 (mmm) cc_final: 0.7969 (mmp) REVERT: D 1948 MET cc_start: 0.8237 (mmp) cc_final: 0.7882 (mmm) REVERT: D 1975 MET cc_start: 0.8830 (ptp) cc_final: 0.8222 (ptp) REVERT: D 2150 MET cc_start: 0.8292 (mtp) cc_final: 0.7970 (mtt) REVERT: D 2234 MET cc_start: 0.8522 (mmm) cc_final: 0.8242 (mtp) REVERT: D 2279 MET cc_start: 0.7866 (tmm) cc_final: 0.7629 (tmm) REVERT: D 2773 TRP cc_start: 0.8516 (t-100) cc_final: 0.8026 (t-100) REVERT: D 2798 MET cc_start: 0.8367 (mmm) cc_final: 0.8131 (mmm) REVERT: D 2826 ILE cc_start: 0.9087 (mp) cc_final: 0.8794 (tt) REVERT: D 2843 MET cc_start: 0.8868 (ptm) cc_final: 0.8510 (ptp) REVERT: D 3719 MET cc_start: 0.7870 (tmm) cc_final: 0.7459 (tmm) REVERT: D 3819 MET cc_start: 0.7418 (pmm) cc_final: 0.7179 (pmm) REVERT: D 3956 MET cc_start: 0.7904 (mmt) cc_final: 0.7623 (mmp) REVERT: D 4052 MET cc_start: 0.8452 (mmm) cc_final: 0.8071 (mmm) REVERT: D 4120 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: D 4279 MET cc_start: 0.8439 (tpt) cc_final: 0.7916 (tpt) outliers start: 80 outliers final: 49 residues processed: 806 average time/residue: 1.1967 time to fit residues: 1711.7481 Evaluate side-chains 815 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 755 time to evaluate : 12.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3971 LEU Chi-restraints excluded: chain A residue 4118 PHE Chi-restraints excluded: chain A residue 4707 MET Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 3971 LEU Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2167 MET Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3971 LEU Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 1043 LYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2893 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3322 LEU Chi-restraints excluded: chain D residue 3971 LEU Chi-restraints excluded: chain D residue 4120 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 7.9990 chunk 665 optimal weight: 10.0000 chunk 994 optimal weight: 0.8980 chunk 501 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 1058 optimal weight: 0.8980 chunk 1134 optimal weight: 20.0000 chunk 823 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 1309 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 HIS ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3831 GLN ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 141748 Z= 0.216 Angle : 0.562 17.212 191528 Z= 0.281 Chirality : 0.040 0.382 20988 Planarity : 0.004 0.129 24600 Dihedral : 7.407 179.475 19120 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 7.95 % Favored : 91.54 % 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: 1.56 (0.07), residues: 17212 helix: 2.25 (0.06), residues: 8928 sheet: 0.13 (0.13), residues: 1624 loop : -0.39 (0.08), residues: 6660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 893 HIS 0.008 0.001 HIS C3732 PHE 0.016 0.001 PHE D4846 TYR 0.030 0.001 TYR D1060 ARG 0.014 0.000 ARG B2835 *********************** 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 838 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 761 time to evaluate : 11.976 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: A 81 MET cc_start: 0.8415 (mmm) cc_final: 0.8199 (mmm) REVERT: A 317 MET cc_start: 0.7827 (ptt) cc_final: 0.7586 (ptm) REVERT: A 995 MET cc_start: 0.8353 (mtm) cc_final: 0.7808 (mtp) REVERT: A 999 LEU cc_start: 0.8951 (mm) cc_final: 0.8719 (mm) REVERT: A 1050 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8876 (mp) REVERT: A 1060 TYR cc_start: 0.7572 (m-80) cc_final: 0.7365 (m-80) REVERT: A 1168 MET cc_start: 0.8625 (mmm) cc_final: 0.8406 (mmm) REVERT: A 1948 MET cc_start: 0.8237 (mmp) cc_final: 0.7868 (mmm) REVERT: A 1975 MET cc_start: 0.8697 (ptm) cc_final: 0.8348 (ptp) REVERT: A 2234 MET cc_start: 0.8523 (mmm) cc_final: 0.8240 (mtp) REVERT: A 2279 MET cc_start: 0.7913 (tmm) cc_final: 0.7669 (tmm) REVERT: A 2695 MET cc_start: 0.7097 (ppp) cc_final: 0.6674 (ppp) REVERT: A 2773 TRP cc_start: 0.8645 (t-100) cc_final: 0.8218 (t-100) REVERT: A 2798 MET cc_start: 0.8370 (mmm) cc_final: 0.8149 (mmm) REVERT: A 2826 ILE cc_start: 0.9095 (mp) cc_final: 0.8801 (tt) REVERT: A 2840 MET cc_start: 0.8350 (mmt) cc_final: 0.7845 (mmm) REVERT: A 2843 MET cc_start: 0.8887 (ptt) cc_final: 0.8499 (ptp) REVERT: A 3072 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8486 (mtt) REVERT: A 3285 TYR cc_start: 0.7247 (m-80) cc_final: 0.7011 (m-80) REVERT: A 3819 MET cc_start: 0.7418 (pmm) cc_final: 0.7103 (pmm) REVERT: A 3971 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 4046 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.7998 (tpm170) REVERT: A 4052 MET cc_start: 0.8579 (mmm) cc_final: 0.8200 (mmm) REVERT: A 4258 MET cc_start: 0.8498 (mtm) cc_final: 0.8232 (mtm) REVERT: A 4279 MET cc_start: 0.8437 (tpt) cc_final: 0.7717 (tpt) REVERT: A 4654 MET cc_start: 0.8318 (tpp) cc_final: 0.8116 (tpt) REVERT: A 4814 MET cc_start: 0.7785 (tpp) cc_final: 0.7543 (mmt) REVERT: A 4923 MET cc_start: 0.8654 (ttt) cc_final: 0.8451 (ttp) REVERT: A 4943 MET cc_start: 0.8784 (mtp) cc_final: 0.8400 (mtp) REVERT: E 30 MET cc_start: 0.7817 (mtm) cc_final: 0.7611 (mtm) REVERT: E 108 GLU cc_start: 0.8055 (pp20) cc_final: 0.7385 (pp20) REVERT: F 108 GLU cc_start: 0.8078 (pp20) cc_final: 0.7407 (pp20) REVERT: G 30 MET cc_start: 0.7705 (mtm) cc_final: 0.7293 (mtm) REVERT: G 108 GLU cc_start: 0.8079 (pp20) cc_final: 0.7416 (pp20) REVERT: H 108 GLU cc_start: 0.8043 (pp20) cc_final: 0.7371 (pp20) REVERT: B 117 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.8087 (m-70) REVERT: B 393 MET cc_start: 0.8313 (mmt) cc_final: 0.7957 (mmt) REVERT: B 995 MET cc_start: 0.8408 (mtm) cc_final: 0.7901 (mtp) REVERT: B 1017 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8706 (t) REVERT: B 1050 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 1060 TYR cc_start: 0.7955 (m-80) cc_final: 0.7408 (m-80) REVERT: B 1168 MET cc_start: 0.8617 (mmm) cc_final: 0.8344 (mmm) REVERT: B 1721 MET cc_start: 0.7284 (mmt) cc_final: 0.7022 (mmm) REVERT: B 1948 MET cc_start: 0.8269 (mmp) cc_final: 0.7806 (mmm) REVERT: B 1975 MET cc_start: 0.8826 (ptp) cc_final: 0.8172 (ptp) REVERT: B 2150 MET cc_start: 0.8256 (mtp) cc_final: 0.7956 (mtt) REVERT: B 2234 MET cc_start: 0.8524 (mmm) cc_final: 0.8218 (mtp) REVERT: B 2695 MET cc_start: 0.7156 (ppp) cc_final: 0.6759 (ppp) REVERT: B 2773 TRP cc_start: 0.8672 (t-100) cc_final: 0.8301 (t-100) REVERT: B 2826 ILE cc_start: 0.9037 (mp) cc_final: 0.8776 (tt) REVERT: B 2840 MET cc_start: 0.8365 (mmt) cc_final: 0.8076 (mmm) REVERT: B 2843 MET cc_start: 0.8893 (ptp) cc_final: 0.8617 (ptp) REVERT: B 3072 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8490 (mtt) REVERT: B 3285 TYR cc_start: 0.7232 (m-80) cc_final: 0.7007 (m-80) REVERT: B 3819 MET cc_start: 0.7391 (pmm) cc_final: 0.7116 (pmm) REVERT: B 3971 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8255 (mt) REVERT: B 4046 ARG cc_start: 0.8575 (tpp-160) cc_final: 0.7964 (tpm170) REVERT: B 4052 MET cc_start: 0.8570 (mmm) cc_final: 0.8163 (mmm) REVERT: B 4258 MET cc_start: 0.8496 (mtm) cc_final: 0.8229 (mtm) REVERT: B 4279 MET cc_start: 0.8423 (tpt) cc_final: 0.7777 (tpt) REVERT: B 4814 MET cc_start: 0.7830 (tpp) cc_final: 0.7576 (mmm) REVERT: B 4923 MET cc_start: 0.8658 (ttt) cc_final: 0.8450 (ttp) REVERT: C 317 MET cc_start: 0.7783 (ptt) cc_final: 0.7540 (ptt) REVERT: C 393 MET cc_start: 0.8444 (mmp) cc_final: 0.8224 (mmm) REVERT: C 1050 LEU cc_start: 0.9222 (mm) cc_final: 0.8960 (mp) REVERT: C 1060 TYR cc_start: 0.7682 (m-80) cc_final: 0.7308 (m-80) REVERT: C 1062 TYR cc_start: 0.8263 (m-80) cc_final: 0.7752 (m-80) REVERT: C 1975 MET cc_start: 0.8596 (ptm) cc_final: 0.7980 (ptp) REVERT: C 2234 MET cc_start: 0.8515 (mmm) cc_final: 0.8236 (mtp) REVERT: C 2695 MET cc_start: 0.7592 (ppp) cc_final: 0.7081 (ppp) REVERT: C 2798 MET cc_start: 0.8357 (mmm) cc_final: 0.7985 (mmm) REVERT: C 2843 MET cc_start: 0.8946 (ptp) cc_final: 0.8651 (ptp) REVERT: C 2860 LEU cc_start: 0.9032 (mm) cc_final: 0.8725 (tp) REVERT: C 3072 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8459 (mtt) REVERT: C 3285 TYR cc_start: 0.7131 (m-80) cc_final: 0.6834 (m-80) REVERT: C 3605 MET cc_start: 0.5120 (ppp) cc_final: 0.3882 (pmm) REVERT: C 3719 MET cc_start: 0.7836 (tmm) cc_final: 0.7523 (tmm) REVERT: C 4120 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: C 4239 LEU cc_start: 0.8503 (mp) cc_final: 0.8174 (tp) REVERT: C 4923 MET cc_start: 0.8682 (ttt) cc_final: 0.8471 (ttp) REVERT: D 317 MET cc_start: 0.7825 (ptt) cc_final: 0.7567 (ptm) REVERT: D 981 MET cc_start: 0.8201 (tmm) cc_final: 0.7962 (tmm) REVERT: D 995 MET cc_start: 0.8305 (mtm) cc_final: 0.7754 (mtp) REVERT: D 1051 ARG cc_start: 0.9069 (mtm110) cc_final: 0.8807 (ptp-110) REVERT: D 1948 MET cc_start: 0.8240 (mmp) cc_final: 0.7891 (mmm) REVERT: D 1975 MET cc_start: 0.8805 (ptp) cc_final: 0.8178 (ptp) REVERT: D 2150 MET cc_start: 0.8271 (mtp) cc_final: 0.7950 (mtt) REVERT: D 2234 MET cc_start: 0.8515 (mmm) cc_final: 0.8252 (mtp) REVERT: D 2279 MET cc_start: 0.7864 (tmm) cc_final: 0.7632 (tmm) REVERT: D 2773 TRP cc_start: 0.8511 (t-100) cc_final: 0.8056 (t-100) REVERT: D 2798 MET cc_start: 0.8349 (mmm) cc_final: 0.8116 (mmm) REVERT: D 2826 ILE cc_start: 0.9114 (mp) cc_final: 0.8780 (tt) REVERT: D 3719 MET cc_start: 0.7840 (tmm) cc_final: 0.7429 (tmm) REVERT: D 3819 MET cc_start: 0.7407 (pmm) cc_final: 0.7160 (pmm) REVERT: D 3956 MET cc_start: 0.7910 (mmt) cc_final: 0.7635 (mmp) REVERT: D 4052 MET cc_start: 0.8479 (mmm) cc_final: 0.8095 (mmm) REVERT: D 4120 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: D 4279 MET cc_start: 0.8387 (tpt) cc_final: 0.7864 (tpt) outliers start: 77 outliers final: 50 residues processed: 807 average time/residue: 1.2042 time to fit residues: 1724.6161 Evaluate side-chains 816 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 755 time to evaluate : 11.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3971 LEU Chi-restraints excluded: chain A residue 4118 PHE Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 3971 LEU Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3322 LEU Chi-restraints excluded: chain C residue 3971 LEU Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 1043 LYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2757 MET Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2893 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3322 LEU Chi-restraints excluded: chain D residue 3971 LEU Chi-restraints excluded: chain D residue 4120 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 9.9990 chunk 1595 optimal weight: 3.9990 chunk 1455 optimal weight: 6.9990 chunk 1552 optimal weight: 10.0000 chunk 934 optimal weight: 9.9990 chunk 676 optimal weight: 5.9990 chunk 1218 optimal weight: 10.0000 chunk 476 optimal weight: 8.9990 chunk 1402 optimal weight: 7.9990 chunk 1467 optimal weight: 5.9990 chunk 1546 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2316 ASN ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS A3200 ASN ** A3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2316 ASN ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3200 ASN ** B3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2316 ASN ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3811 GLN ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1589 GLN D2316 ASN ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2802 ASN D3200 ASN ** D3831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 141748 Z= 0.399 Angle : 0.611 15.450 191528 Z= 0.308 Chirality : 0.042 0.419 20988 Planarity : 0.005 0.129 24600 Dihedral : 7.345 176.153 19120 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 0.51 % Allowed : 8.02 % Favored : 91.46 % 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: 1.47 (0.07), residues: 17212 helix: 2.17 (0.06), residues: 8940 sheet: 0.09 (0.13), residues: 1640 loop : -0.43 (0.08), residues: 6632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 893 HIS 0.010 0.001 HIS C 692 PHE 0.030 0.002 PHE A3854 TYR 0.053 0.002 TYR C 931 ARG 0.014 0.001 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 840 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 762 time to evaluate : 11.860 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: A 117 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8129 (m-70) REVERT: A 317 MET cc_start: 0.7829 (ptt) cc_final: 0.7592 (ptt) REVERT: A 880 ARG cc_start: 0.8806 (tpp-160) cc_final: 0.8180 (tpm170) REVERT: A 999 LEU cc_start: 0.8994 (mm) cc_final: 0.8767 (mm) REVERT: A 1050 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8891 (mp) REVERT: A 1060 TYR cc_start: 0.7640 (m-80) cc_final: 0.7385 (m-80) REVERT: A 1729 MET cc_start: 0.8567 (mmp) cc_final: 0.8266 (mmm) REVERT: A 1948 MET cc_start: 0.8237 (mmp) cc_final: 0.7877 (mmm) REVERT: A 1975 MET cc_start: 0.8747 (ptm) cc_final: 0.8429 (ptp) REVERT: A 2234 MET cc_start: 0.8534 (mmm) cc_final: 0.8239 (mtp) REVERT: A 2279 MET cc_start: 0.7972 (tmm) cc_final: 0.7751 (tmm) REVERT: A 2695 MET cc_start: 0.7193 (ppp) cc_final: 0.6815 (ppp) REVERT: A 2773 TRP cc_start: 0.8664 (t-100) cc_final: 0.8277 (t-100) REVERT: A 2798 MET cc_start: 0.8402 (mmm) cc_final: 0.8182 (mmm) REVERT: A 2826 ILE cc_start: 0.9136 (mp) cc_final: 0.8830 (tt) REVERT: A 2840 MET cc_start: 0.8402 (mmt) cc_final: 0.8144 (mmm) REVERT: A 3072 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8529 (mtt) REVERT: A 3285 TYR cc_start: 0.7257 (m-80) cc_final: 0.7007 (m-80) REVERT: A 3819 MET cc_start: 0.7455 (pmm) cc_final: 0.7138 (pmm) REVERT: A 4046 ARG cc_start: 0.8540 (tpp-160) cc_final: 0.7856 (tpm170) REVERT: A 4052 MET cc_start: 0.8620 (mmm) cc_final: 0.8257 (mmm) REVERT: A 4258 MET cc_start: 0.8503 (mtm) cc_final: 0.8136 (mtm) REVERT: A 4279 MET cc_start: 0.8432 (tpt) cc_final: 0.7694 (tpt) REVERT: A 4814 MET cc_start: 0.7800 (tpp) cc_final: 0.7514 (mmt) REVERT: A 4923 MET cc_start: 0.8661 (ttt) cc_final: 0.8438 (ttp) REVERT: A 4943 MET cc_start: 0.8817 (mtp) cc_final: 0.8449 (mtp) REVERT: E 108 GLU cc_start: 0.8058 (pp20) cc_final: 0.7361 (pp20) REVERT: F 108 GLU cc_start: 0.8096 (pp20) cc_final: 0.7429 (pp20) REVERT: G 30 MET cc_start: 0.7759 (mtm) cc_final: 0.7303 (mtm) REVERT: G 108 GLU cc_start: 0.8072 (pp20) cc_final: 0.7392 (pp20) REVERT: H 108 GLU cc_start: 0.8049 (pp20) cc_final: 0.7353 (pp20) REVERT: B 117 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.8122 (m-70) REVERT: B 895 MET cc_start: 0.9179 (mmm) cc_final: 0.8888 (mpp) REVERT: B 995 MET cc_start: 0.8432 (mtm) cc_final: 0.7913 (mtp) REVERT: B 1050 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8848 (mp) REVERT: B 1060 TYR cc_start: 0.8026 (m-80) cc_final: 0.7474 (m-80) REVERT: B 1168 MET cc_start: 0.8604 (mmm) cc_final: 0.8355 (mmm) REVERT: B 1721 MET cc_start: 0.7264 (mmt) cc_final: 0.6975 (mmm) REVERT: B 1948 MET cc_start: 0.8266 (mmp) cc_final: 0.7890 (mmm) REVERT: B 1975 MET cc_start: 0.8833 (ptp) cc_final: 0.8188 (ptp) REVERT: B 2150 MET cc_start: 0.8281 (mtp) cc_final: 0.8023 (mtt) REVERT: B 2695 MET cc_start: 0.7229 (ppp) cc_final: 0.6811 (ppp) REVERT: B 2798 MET cc_start: 0.8158 (mmm) cc_final: 0.7810 (mmm) REVERT: B 2826 ILE cc_start: 0.9098 (mp) cc_final: 0.8807 (tt) REVERT: B 2840 MET cc_start: 0.8421 (mmt) cc_final: 0.8116 (mmm) REVERT: B 2843 MET cc_start: 0.8921 (ptp) cc_final: 0.8639 (ptp) REVERT: B 3072 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8536 (mtt) REVERT: B 3285 TYR cc_start: 0.7248 (m-80) cc_final: 0.6992 (m-80) REVERT: B 4002 MET cc_start: 0.8700 (tmm) cc_final: 0.8476 (ttp) REVERT: B 4046 ARG cc_start: 0.8544 (tpp-160) cc_final: 0.7857 (tpm170) REVERT: B 4052 MET cc_start: 0.8596 (mmm) cc_final: 0.8228 (mmm) REVERT: B 4258 MET cc_start: 0.8493 (mtm) cc_final: 0.8119 (mtm) REVERT: B 4279 MET cc_start: 0.8409 (tpt) cc_final: 0.7786 (tpt) REVERT: B 4814 MET cc_start: 0.7854 (tpp) cc_final: 0.7493 (mmm) REVERT: B 4923 MET cc_start: 0.8663 (ttt) cc_final: 0.8440 (ttp) REVERT: C 317 MET cc_start: 0.7796 (ptt) cc_final: 0.7542 (ptt) REVERT: C 393 MET cc_start: 0.8477 (mmp) cc_final: 0.8252 (mmm) REVERT: C 995 MET cc_start: 0.8640 (ptp) cc_final: 0.8311 (mtm) REVERT: C 1050 LEU cc_start: 0.9228 (mm) cc_final: 0.8974 (mp) REVERT: C 1060 TYR cc_start: 0.7745 (m-80) cc_final: 0.7363 (m-80) REVERT: C 1062 TYR cc_start: 0.8279 (m-80) cc_final: 0.7775 (m-80) REVERT: C 1948 MET cc_start: 0.7823 (mmm) cc_final: 0.7345 (mmp) REVERT: C 1975 MET cc_start: 0.8588 (ptm) cc_final: 0.8006 (ptp) REVERT: C 2695 MET cc_start: 0.7693 (ppp) cc_final: 0.7174 (ppp) REVERT: C 2732 TRP cc_start: 0.8963 (t60) cc_final: 0.8622 (t60) REVERT: C 2798 MET cc_start: 0.8350 (mmm) cc_final: 0.7982 (mmm) REVERT: C 3072 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8528 (mtt) REVERT: C 3285 TYR cc_start: 0.7256 (m-80) cc_final: 0.6898 (m-80) REVERT: C 3605 MET cc_start: 0.5172 (ppp) cc_final: 0.3966 (pmm) REVERT: C 3719 MET cc_start: 0.7859 (tmm) cc_final: 0.7417 (tmm) REVERT: C 3819 MET cc_start: 0.7392 (pmm) cc_final: 0.7183 (pmm) REVERT: C 4052 MET cc_start: 0.8506 (mmm) cc_final: 0.8099 (mmm) REVERT: C 4120 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: C 4239 LEU cc_start: 0.8533 (mp) cc_final: 0.8205 (tp) REVERT: C 4923 MET cc_start: 0.8674 (ttt) cc_final: 0.8442 (ttp) REVERT: D 317 MET cc_start: 0.7829 (ptt) cc_final: 0.7581 (ptt) REVERT: D 946 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8033 (pt) REVERT: D 981 MET cc_start: 0.8295 (tmm) cc_final: 0.8064 (tmm) REVERT: D 995 MET cc_start: 0.8300 (mtm) cc_final: 0.7894 (mtp) REVERT: D 1051 ARG cc_start: 0.9092 (mtm110) cc_final: 0.8808 (ptp-110) REVERT: D 1060 TYR cc_start: 0.7806 (m-80) cc_final: 0.7550 (m-80) REVERT: D 1721 MET cc_start: 0.7287 (mmt) cc_final: 0.7034 (mmm) REVERT: D 1729 MET cc_start: 0.8573 (mmp) cc_final: 0.8267 (mmm) REVERT: D 1948 MET cc_start: 0.8275 (mmp) cc_final: 0.7912 (mmm) REVERT: D 1975 MET cc_start: 0.8831 (ptp) cc_final: 0.8208 (ptp) REVERT: D 2150 MET cc_start: 0.8304 (mtp) cc_final: 0.7973 (mtt) REVERT: D 2234 MET cc_start: 0.8518 (mmm) cc_final: 0.8233 (mtp) REVERT: D 2279 MET cc_start: 0.7939 (tmm) cc_final: 0.7687 (tmm) REVERT: D 2773 TRP cc_start: 0.8544 (t-100) cc_final: 0.8011 (t-100) REVERT: D 2798 MET cc_start: 0.8328 (mmm) cc_final: 0.8107 (mmm) REVERT: D 2826 ILE cc_start: 0.9136 (mp) cc_final: 0.8810 (tt) REVERT: D 2843 MET cc_start: 0.8943 (ptm) cc_final: 0.8647 (ptp) REVERT: D 3719 MET cc_start: 0.7860 (tmm) cc_final: 0.7456 (tmm) REVERT: D 3819 MET cc_start: 0.7451 (pmm) cc_final: 0.7218 (pmm) REVERT: D 3956 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7587 (mmp) REVERT: D 4052 MET cc_start: 0.8507 (mmm) cc_final: 0.8136 (mmm) REVERT: D 4120 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7700 (mm-30) REVERT: D 4279 MET cc_start: 0.8385 (tpt) cc_final: 0.7840 (tpt) outliers start: 78 outliers final: 58 residues processed: 809 average time/residue: 1.2633 time to fit residues: 1815.9229 Evaluate side-chains 828 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 759 time to evaluate : 11.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3971 LEU Chi-restraints excluded: chain A residue 4118 PHE Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3322 LEU Chi-restraints excluded: chain B residue 3971 LEU Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1174 MET Chi-restraints excluded: chain C residue 1241 VAL Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3322 LEU Chi-restraints excluded: chain C residue 3971 LEU Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1043 LYS Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2757 MET Chi-restraints excluded: chain D residue 2800 LEU Chi-restraints excluded: chain D residue 2893 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3322 LEU Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 3971 LEU Chi-restraints excluded: chain D residue 4120 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 0.5980 chunk 1641 optimal weight: 3.9990 chunk 1001 optimal weight: 0.4980 chunk 778 optimal weight: 3.9990 chunk 1140 optimal weight: 0.7980 chunk 1721 optimal weight: 1.9990 chunk 1584 optimal weight: 10.0000 chunk 1370 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 1058 optimal weight: 4.9990 chunk 840 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3831 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3831 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3831 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 141748 Z= 0.162 Angle : 0.562 15.812 191528 Z= 0.281 Chirality : 0.039 0.443 20988 Planarity : 0.004 0.127 24600 Dihedral : 7.161 173.171 19120 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 0.40 % Allowed : 8.14 % Favored : 91.46 % 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: 1.59 (0.07), residues: 17212 helix: 2.27 (0.06), residues: 8948 sheet: 0.14 (0.13), residues: 1624 loop : -0.38 (0.08), residues: 6640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 893 HIS 0.008 0.001 HIS D3732 PHE 0.015 0.001 PHE D4016 TYR 0.046 0.001 TYR B 931 ARG 0.021 0.000 ARG C1941 ********************** 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 814 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 753 time to evaluate : 11.779 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: A 117 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.8085 (m-70) REVERT: A 317 MET cc_start: 0.7788 (ptt) cc_final: 0.7539 (ptt) REVERT: A 880 ARG cc_start: 0.8748 (tpp-160) cc_final: 0.8148 (tpm170) REVERT: A 999 LEU cc_start: 0.8938 (mm) cc_final: 0.8697 (mm) REVERT: A 1050 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8867 (mp) REVERT: A 1060 TYR cc_start: 0.7583 (m-80) cc_final: 0.7325 (m-80) REVERT: A 1729 MET cc_start: 0.8519 (mmp) cc_final: 0.8262 (mmm) REVERT: A 1948 MET cc_start: 0.8243 (mmp) cc_final: 0.7877 (mmm) REVERT: A 1975 MET cc_start: 0.8674 (ptm) cc_final: 0.8120 (ptp) REVERT: A 2234 MET cc_start: 0.8510 (mmm) cc_final: 0.8235 (mtp) REVERT: A 2279 MET cc_start: 0.7932 (tmm) cc_final: 0.7681 (tmm) REVERT: A 2695 MET cc_start: 0.7147 (ppp) cc_final: 0.6714 (ppp) REVERT: A 2773 TRP cc_start: 0.8622 (t-100) cc_final: 0.8204 (t-100) REVERT: A 2798 MET cc_start: 0.8396 (mmm) cc_final: 0.8184 (mmm) REVERT: A 2840 MET cc_start: 0.8395 (mmt) cc_final: 0.8036 (mmm) REVERT: A 2843 MET cc_start: 0.8957 (ptp) cc_final: 0.8695 (ptp) REVERT: A 3072 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8473 (mtt) REVERT: A 3285 TYR cc_start: 0.7199 (m-80) cc_final: 0.6970 (m-80) REVERT: A 3819 MET cc_start: 0.7399 (pmm) cc_final: 0.7065 (pmm) REVERT: A 4046 ARG cc_start: 0.8537 (tpp-160) cc_final: 0.7839 (tpm170) REVERT: A 4052 MET cc_start: 0.8589 (mmm) cc_final: 0.8206 (mmm) REVERT: A 4258 MET cc_start: 0.8492 (mtm) cc_final: 0.8220 (mtm) REVERT: A 4279 MET cc_start: 0.8398 (tpt) cc_final: 0.7692 (tpt) REVERT: A 4814 MET cc_start: 0.7781 (tpp) cc_final: 0.7573 (tpt) REVERT: A 4943 MET cc_start: 0.8773 (mtp) cc_final: 0.8382 (mtp) REVERT: E 108 GLU cc_start: 0.8063 (pp20) cc_final: 0.7392 (pp20) REVERT: F 108 GLU cc_start: 0.8066 (pp20) cc_final: 0.7399 (pp20) REVERT: G 108 GLU cc_start: 0.8063 (pp20) cc_final: 0.7395 (pp20) REVERT: H 18 LYS cc_start: 0.8652 (mppt) cc_final: 0.8435 (mppt) REVERT: H 108 GLU cc_start: 0.8059 (pp20) cc_final: 0.7374 (pp20) REVERT: B 117 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.8102 (m-70) REVERT: B 317 MET cc_start: 0.7818 (ptt) cc_final: 0.7571 (ptt) REVERT: B 393 MET cc_start: 0.8296 (mmt) cc_final: 0.7937 (mmt) REVERT: B 995 MET cc_start: 0.8366 (mtm) cc_final: 0.7861 (mtp) REVERT: B 1050 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8779 (mp) REVERT: B 1060 TYR cc_start: 0.7964 (m-80) cc_final: 0.7414 (m-80) REVERT: B 1168 MET cc_start: 0.8590 (mmm) cc_final: 0.8319 (mmm) REVERT: B 1721 MET cc_start: 0.7274 (mmt) cc_final: 0.7006 (mmm) REVERT: B 1948 MET cc_start: 0.8270 (mmp) cc_final: 0.7815 (mmm) REVERT: B 1975 MET cc_start: 0.8798 (ptp) cc_final: 0.8126 (ptp) REVERT: B 2150 MET cc_start: 0.8251 (mtp) cc_final: 0.7948 (mtt) REVERT: B 2234 MET cc_start: 0.8514 (mmm) cc_final: 0.8228 (mtp) REVERT: B 2695 MET cc_start: 0.7164 (ppp) cc_final: 0.6774 (ppp) REVERT: B 2773 TRP cc_start: 0.8659 (t-100) cc_final: 0.8302 (t-100) REVERT: B 2798 MET cc_start: 0.8155 (mmm) cc_final: 0.7792 (mmm) REVERT: B 2840 MET cc_start: 0.8317 (mmt) cc_final: 0.8016 (mmm) REVERT: B 2843 MET cc_start: 0.8867 (ptp) cc_final: 0.8593 (ptp) REVERT: B 2860 LEU cc_start: 0.9030 (mm) cc_final: 0.8619 (mm) REVERT: B 3072 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8486 (mtt) REVERT: B 3285 TYR cc_start: 0.7187 (m-80) cc_final: 0.6980 (m-80) REVERT: B 3819 MET cc_start: 0.7301 (pmm) cc_final: 0.6992 (pmm) REVERT: B 3971 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8229 (mt) REVERT: B 4046 ARG cc_start: 0.8512 (tpp-160) cc_final: 0.7832 (tpm170) REVERT: B 4052 MET cc_start: 0.8586 (mmm) cc_final: 0.8206 (mmm) REVERT: B 4258 MET cc_start: 0.8508 (mtm) cc_final: 0.8241 (mtm) REVERT: B 4279 MET cc_start: 0.8370 (tpt) cc_final: 0.7747 (tpt) REVERT: B 4814 MET cc_start: 0.7820 (tpp) cc_final: 0.7573 (mmm) REVERT: C 317 MET cc_start: 0.7767 (ptt) cc_final: 0.7509 (ptt) REVERT: C 995 MET cc_start: 0.8602 (ptp) cc_final: 0.8250 (mtm) REVERT: C 1050 LEU cc_start: 0.9205 (mm) cc_final: 0.8941 (mp) REVERT: C 1060 TYR cc_start: 0.7697 (m-80) cc_final: 0.7283 (m-80) REVERT: C 1948 MET cc_start: 0.7844 (mmm) cc_final: 0.7371 (mmm) REVERT: C 1975 MET cc_start: 0.8534 (ptm) cc_final: 0.7948 (ptp) REVERT: C 2234 MET cc_start: 0.8510 (mmm) cc_final: 0.8232 (mtp) REVERT: C 2695 MET cc_start: 0.7621 (ppp) cc_final: 0.7116 (ppp) REVERT: C 2732 TRP cc_start: 0.8899 (t60) cc_final: 0.8567 (t60) REVERT: C 2773 TRP cc_start: 0.8654 (t-100) cc_final: 0.8387 (t-100) REVERT: C 2798 MET cc_start: 0.8337 (mmm) cc_final: 0.7963 (mmm) REVERT: C 2843 MET cc_start: 0.8991 (ptp) cc_final: 0.8603 (pmm) REVERT: C 3072 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8441 (mtt) REVERT: C 3273 MET cc_start: 0.9070 (ptt) cc_final: 0.8823 (mtt) REVERT: C 3285 TYR cc_start: 0.7155 (m-80) cc_final: 0.6870 (m-80) REVERT: C 3605 MET cc_start: 0.4980 (ppp) cc_final: 0.3732 (pmm) REVERT: C 3719 MET cc_start: 0.7824 (tmm) cc_final: 0.7509 (tmm) REVERT: C 4120 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: C 4923 MET cc_start: 0.8656 (ttt) cc_final: 0.8453 (ttp) REVERT: D 317 MET cc_start: 0.7780 (ptt) cc_final: 0.7524 (ptt) REVERT: D 946 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7993 (pt) REVERT: D 981 MET cc_start: 0.8255 (tmm) cc_final: 0.8018 (tmm) REVERT: D 995 MET cc_start: 0.8314 (mtm) cc_final: 0.7723 (mtp) REVERT: D 1051 ARG cc_start: 0.9068 (mtm110) cc_final: 0.8792 (ptp-110) REVERT: D 1721 MET cc_start: 0.7246 (mmt) cc_final: 0.7000 (mmm) REVERT: D 1729 MET cc_start: 0.8523 (mmp) cc_final: 0.8304 (mmm) REVERT: D 1948 MET cc_start: 0.8285 (mmp) cc_final: 0.7919 (mmm) REVERT: D 1975 MET cc_start: 0.8761 (ptp) cc_final: 0.8130 (ptp) REVERT: D 2150 MET cc_start: 0.8268 (mtp) cc_final: 0.7950 (mtt) REVERT: D 2234 MET cc_start: 0.8492 (mmm) cc_final: 0.8228 (mtp) REVERT: D 2279 MET cc_start: 0.7899 (tmm) cc_final: 0.7614 (tmm) REVERT: D 2695 MET cc_start: 0.6868 (ppp) cc_final: 0.6539 (ppp) REVERT: D 2732 TRP cc_start: 0.9073 (t60) cc_final: 0.8689 (t60) REVERT: D 2773 TRP cc_start: 0.8502 (t-100) cc_final: 0.8030 (t-100) REVERT: D 2826 ILE cc_start: 0.9101 (mp) cc_final: 0.8797 (tt) REVERT: D 2843 MET cc_start: 0.8899 (ptm) cc_final: 0.8583 (ptp) REVERT: D 3719 MET cc_start: 0.7823 (tmm) cc_final: 0.7543 (tmm) REVERT: D 3819 MET cc_start: 0.7393 (pmm) cc_final: 0.7153 (pmm) REVERT: D 3971 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8218 (mt) REVERT: D 4052 MET cc_start: 0.8488 (mmm) cc_final: 0.8105 (mmm) REVERT: D 4120 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: D 4279 MET cc_start: 0.8315 (tpt) cc_final: 0.7790 (tpt) outliers start: 61 outliers final: 45 residues processed: 789 average time/residue: 1.1869 time to fit residues: 1662.7432 Evaluate side-chains 806 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 749 time to evaluate : 11.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2990 LEU Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 4118 PHE Chi-restraints excluded: chain A residue 4748 MET Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2766 LYS Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2990 LEU Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3971 LEU Chi-restraints excluded: chain B residue 4118 PHE Chi-restraints excluded: chain B residue 4748 MET Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain C residue 1241 VAL Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2990 LEU Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 929 ARG Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2757 MET Chi-restraints excluded: chain D residue 2893 LEU Chi-restraints excluded: chain D residue 2990 LEU Chi-restraints excluded: chain D residue 3322 LEU Chi-restraints excluded: chain D residue 3971 LEU Chi-restraints excluded: chain D residue 4120 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 9.9990 chunk 1460 optimal weight: 0.4980 chunk 419 optimal weight: 10.0000 chunk 1264 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 1373 optimal weight: 0.2980 chunk 574 optimal weight: 20.0000 chunk 1409 optimal weight: 50.0000 chunk 173 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.038939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.029939 restraints weight = 1488306.775| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.88 r_work: 0.2906 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 141748 Z= 0.238 Angle : 0.569 15.469 191528 Z= 0.285 Chirality : 0.040 0.451 20988 Planarity : 0.004 0.127 24600 Dihedral : 7.088 170.844 19120 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 0.43 % Allowed : 8.13 % Favored : 91.43 % 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: 1.59 (0.07), residues: 17212 helix: 2.26 (0.06), residues: 8956 sheet: 0.15 (0.13), residues: 1624 loop : -0.36 (0.08), residues: 6632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 893 HIS 0.013 0.001 HIS D 890 PHE 0.018 0.001 PHE D3854 TYR 0.050 0.001 TYR C 931 ARG 0.016 0.000 ARG C1941 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33942.74 seconds wall clock time: 595 minutes 37.60 seconds (35737.60 seconds total)