Starting phenix.real_space_refine on Wed Mar 27 05:42:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua3_26413/03_2024/7ua3_26413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua3_26413/03_2024/7ua3_26413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua3_26413/03_2024/7ua3_26413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua3_26413/03_2024/7ua3_26413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua3_26413/03_2024/7ua3_26413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua3_26413/03_2024/7ua3_26413_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.034 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 1004 5.16 5 C 95516 2.51 5 N 25576 2.21 5 O 28128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3150": "NH1" <-> "NH2" Residue "A PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3381": "NH1" <-> "NH2" Residue "A PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4046": "NH1" <-> "NH2" Residue "A PHE 4118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "I TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3150": "NH1" <-> "NH2" Residue "B PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3381": "NH1" <-> "NH2" Residue "B PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4046": "NH1" <-> "NH2" Residue "B PHE 4118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3150": "NH1" <-> "NH2" Residue "C PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3381": "NH1" <-> "NH2" Residue "C PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4046": "NH1" <-> "NH2" Residue "C PHE 4118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3150": "NH1" <-> "NH2" Residue "D PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3381": "NH1" <-> "NH2" Residue "D PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4046": "NH1" <-> "NH2" Residue "D PHE 4118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150252 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 35570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 36317 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "I" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 35570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 36317 Chain: "C" Number of atoms: 35570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 36317 Chain: "D" Number of atoms: 35570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 4443, 35562 Classifications: {'peptide': 4443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 163, 'TRANS': 4278} Chain breaks: 14 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: 36317 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34891 SG CYS A4888 168.899 194.300 121.599 1.00 81.23 S ATOM 34916 SG CYS A4891 169.283 191.747 118.755 1.00 78.77 S ATOM 78181 SG CYS B4888 194.260 198.863 121.596 1.00 81.58 S ATOM 78206 SG CYS B4891 191.708 198.481 118.751 1.00 79.17 S ATOM A0ALZ SG CYS C4888 198.848 173.451 121.619 1.00 81.59 S ATOM A0AMO SG CYS C4891 198.463 176.002 118.774 1.00 79.42 S ATOM A1221 SG CYS D4888 173.444 168.882 121.612 1.00 81.05 S ATOM A122Q SG CYS D4891 175.996 169.267 118.768 1.00 79.34 S Time building chain proxies: 102.69, per 1000 atoms: 0.68 Number of scatterers: 150252 At special positions: 0 Unit cell: (368.576, 368.576, 210.496, 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 1004 16.00 P 24 15.00 O 28128 8.00 N 25576 7.00 C 95516 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=2.04 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.04 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.04 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.04 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: 45.94 Conformation dependent library (CDL) restraints added in 37.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 8 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 35240 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: 764 helices and 80 sheets defined 60.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 44.30 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.766A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 266 through 271 removed outlier: 5.329A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 5.549A pdb=" N THR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 removed outlier: 4.096A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 4.670A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 removed outlier: 3.838A pdb=" N VAL A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 3.710A pdb=" N SER A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 4.361A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.547A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 5.320A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.674A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.551A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.506A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.999A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.242A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 4.432A pdb=" N ASP A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 3.988A pdb=" N GLN A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 972' Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.704A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1231 removed outlier: 3.688A pdb=" N GLY A1231 " --> pdb=" O PHE A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.791A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 4.015A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.910A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1647 removed outlier: 4.408A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1666 removed outlier: 3.589A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.719A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.835A 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 Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.770A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 3.957A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A1805 " --> pdb=" O GLU A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.223A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.834A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 4.981A 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: 3.943A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1966 removed outlier: 4.197A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 3.611A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.501A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.588A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 4.002A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2152 Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2159 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 5.082A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 4.041A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.655A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.187A 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 removed outlier: 3.551A pdb=" N VAL A2247 " --> pdb=" O ALA A2243 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.710A pdb=" N VAL A2265 " --> pdb=" O ASP A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 removed outlier: 3.640A pdb=" N GLY A2284 " --> pdb=" O LEU A2280 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.641A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.566A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2332 through 2337 removed outlier: 3.799A pdb=" N ARG A2336 " --> pdb=" O GLY A2332 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY A2337 " --> pdb=" O PRO A2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2332 through 2337' Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2439 removed outlier: 5.645A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.797A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A2467 " --> pdb=" O ASP A2463 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.124A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2504 through 2510 removed outlier: 4.523A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) Processing helix chain 'A' and resid 2511 through 2532 removed outlier: 5.481A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 5.254A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2581 removed outlier: 5.298A pdb=" N ARG A2581 " --> pdb=" O CYS A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2582 through 2596 removed outlier: 4.760A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.248A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 4.898A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP A2696 " --> pdb=" O GLN A2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2691 through 2696' Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.724A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.354A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2769 through 2786 Proline residue: A2774 - end of helix removed outlier: 3.805A pdb=" N GLY A2786 " --> pdb=" O MET A2782 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.328A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.575A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2915 through 2950 removed outlier: 7.456A pdb=" N PHE A2921 " --> pdb=" O ILE A2917 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA A2922 " --> pdb=" O GLU A2918 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR A2923 " --> pdb=" O LYS A2919 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A2949 " --> pdb=" O GLY A2945 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 3.600A pdb=" N VAL A2967 " --> pdb=" O PHE A2963 " (cutoff:3.500A) removed outlier: 4.988A 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 Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.447A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3049 Processing helix chain 'A' and resid 3050 through 3078 removed outlier: 3.561A pdb=" N LEU A3061 " --> pdb=" O LEU A3057 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN A3077 " --> pdb=" O GLU A3073 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 3.718A pdb=" N GLN A3092 " --> pdb=" O LYS A3088 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3124 through 3143 Processing helix chain 'A' and resid 3145 through 3150 removed outlier: 4.363A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) Processing helix chain 'A' and resid 3151 through 3166 Processing helix chain 'A' and resid 3172 through 3177 removed outlier: 4.640A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3177' Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.426A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3201 through 3206 removed outlier: 4.838A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix No H-bonds generated for 'chain 'A' and resid 3201 through 3206' Processing helix chain 'A' and resid 3210 through 3224 removed outlier: 4.436A pdb=" N ALA A3222 " --> pdb=" O ILE A3218 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A3223 " --> pdb=" O VAL A3219 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3232 Proline residue: A3232 - end of helix Processing helix chain 'A' and resid 3233 through 3254 removed outlier: 5.646A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 5.101A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N HIS A3252 " --> pdb=" O ARG A3248 " (cutoff:3.500A) Proline residue: A3254 - end of helix Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3294 through 3308 removed outlier: 3.671A pdb=" N GLN A3304 " --> pdb=" O ALA A3300 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 4.913A pdb=" N ASN A3308 " --> pdb=" O GLN A3304 " (cutoff:3.500A) Processing helix chain 'A' and resid 3311 through 3344 removed outlier: 4.915A pdb=" N LEU A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS A3316 " --> pdb=" O PRO A3312 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 3.833A pdb=" N ALA A3342 " --> pdb=" O ASP A3338 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A3343 " --> pdb=" O HIS A3339 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA A3344 " --> pdb=" O LEU A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3348 through 3381 removed outlier: 4.642A pdb=" N LEU A3354 " --> pdb=" O GLU A3350 " (cutoff:3.500A) Proline residue: A3371 - end of helix Processing helix chain 'A' and resid 3382 through 3388 Proline residue: A3388 - end of helix Processing helix chain 'A' and resid 3389 through 3410 removed outlier: 3.563A pdb=" N GLU A3401 " --> pdb=" O ARG A3397 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS A3410 " --> pdb=" O TRP A3406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3411 through 3424 Processing helix chain 'A' and resid 3427 through 3437 removed outlier: 4.538A pdb=" N LEU A3431 " --> pdb=" O ASN A3427 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A3437 " --> pdb=" O THR A3433 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3482 Proline residue: A3475 - end of helix removed outlier: 4.597A pdb=" N ALA A3482 " --> pdb=" O LEU A3478 " (cutoff:3.500A) Processing helix chain 'A' and resid 3484 through 3499 removed outlier: 5.525A pdb=" N LEU A3488 " --> pdb=" O GLY A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3501 through 3514 removed outlier: 4.853A pdb=" N HIS A3514 " --> pdb=" O ARG A3510 " (cutoff:3.500A) Processing helix chain 'A' and resid 3523 through 3533 Processing helix chain 'A' and resid 3543 through 3564 Processing helix chain 'A' and resid 3594 through 3605 Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.737A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3628 Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.712A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.732A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.880A 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: 4.565A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.557A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.335A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.564A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 4.354A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.535A pdb=" N HIS A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.135A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.903A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 4.309A pdb=" N ASP A4093 " --> pdb=" O GLU A4089 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY A4095 " --> pdb=" O ALA A4091 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4184 through 4208 removed outlier: 4.752A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4260 removed outlier: 4.007A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4262 through 4272 removed outlier: 4.590A pdb=" N LYS A4266 " --> pdb=" O LYS A4262 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A4271 " --> pdb=" O GLN A4267 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.688A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 3.567A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4521 removed outlier: 4.235A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS A4521 " --> pdb=" O LEU A4517 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4613 removed outlier: 4.524A pdb=" N TYR A4590 " --> pdb=" O CYS A4586 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU A4593 " --> pdb=" O GLY A4589 " (cutoff:3.500A) removed outlier: 4.301A 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: 3.864A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.885A 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: 5.105A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) Processing helix chain 'A' and resid 4695 through 4702 removed outlier: 5.896A 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: 3.863A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4750 removed outlier: 4.621A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4751 through 4762 removed outlier: 3.672A pdb=" N THR A4755 " --> pdb=" O LYS A4751 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.337A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 4.442A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.213A 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: 4.137A 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: 5.461A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.928A 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 3117 through 3122 removed outlier: 4.229A pdb=" N ILE A3122 " --> pdb=" O PHE A3117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3117 through 3122' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.765A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 266 through 271 removed outlier: 5.329A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 5.549A pdb=" N THR B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 removed outlier: 4.096A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 4.669A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.838A pdb=" N VAL B 517 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 3.711A pdb=" N SER B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 4.361A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 563 removed outlier: 3.547A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 5.321A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.673A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.552A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.504A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 875 through 901 removed outlier: 5.000A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.242A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 removed outlier: 4.432A pdb=" N ASP B 959 " --> pdb=" O GLU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 3.988A pdb=" N GLN B 971 " --> pdb=" O PRO B 967 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 967 through 972' Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.703A pdb=" N SER B1049 " --> pdb=" O SER B1045 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1231 removed outlier: 3.687A pdb=" N GLY B1231 " --> pdb=" O PHE B1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.792A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 4.015A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.910A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1647 removed outlier: 4.408A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) Processing helix chain 'B' and resid 1648 through 1666 removed outlier: 3.588A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.719A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.835A 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 Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.770A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 3.958A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS B1805 " --> pdb=" O GLU B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1835 through 1847 removed outlier: 4.224A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.835A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 4.980A 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: 3.943A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1966 removed outlier: 4.197A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 3.612A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.501A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.588A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 4.003A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2152 Processing helix chain 'B' and resid 2153 through 2158 Processing helix chain 'B' and resid 2159 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 5.082A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 4.042A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.655A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.188A 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 removed outlier: 3.552A pdb=" N VAL B2247 " --> pdb=" O ALA B2243 " (cutoff:3.500A) Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.710A pdb=" N VAL B2265 " --> pdb=" O ASP B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 removed outlier: 3.641A pdb=" N GLY B2284 " --> pdb=" O LEU B2280 " (cutoff:3.500A) Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.641A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.566A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2332 through 2337 removed outlier: 3.799A pdb=" N ARG B2336 " --> pdb=" O GLY B2332 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY B2337 " --> pdb=" O PRO B2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2332 through 2337' Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2439 removed outlier: 5.645A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.796A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B2467 " --> pdb=" O ASP B2463 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.124A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2504 through 2510 removed outlier: 4.523A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) Processing helix chain 'B' and resid 2511 through 2532 removed outlier: 5.481A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 5.254A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2581 removed outlier: 5.297A pdb=" N ARG B2581 " --> pdb=" O CYS B2577 " (cutoff:3.500A) Processing helix chain 'B' and resid 2582 through 2596 removed outlier: 4.760A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.249A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 4.898A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP B2696 " --> pdb=" O GLN B2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2691 through 2696' Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.724A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.354A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2769 through 2786 Proline residue: B2774 - end of helix removed outlier: 3.805A pdb=" N GLY B2786 " --> pdb=" O MET B2782 " (cutoff:3.500A) Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.328A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.576A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2915 through 2950 removed outlier: 7.456A pdb=" N PHE B2921 " --> pdb=" O ILE B2917 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA B2922 " --> pdb=" O GLU B2918 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR B2923 " --> pdb=" O LYS B2919 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY B2949 " --> pdb=" O GLY B2945 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 3.600A pdb=" N VAL B2967 " --> pdb=" O PHE B2963 " (cutoff:3.500A) removed outlier: 4.988A 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 Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.447A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3049 Processing helix chain 'B' and resid 3050 through 3078 removed outlier: 3.560A pdb=" N LEU B3061 " --> pdb=" O LEU B3057 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN B3077 " --> pdb=" O GLU B3073 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B3078 " --> pdb=" O ASN B3074 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 3.717A pdb=" N GLN B3092 " --> pdb=" O LYS B3088 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3124 through 3143 Processing helix chain 'B' and resid 3145 through 3150 removed outlier: 4.364A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) Processing helix chain 'B' and resid 3151 through 3166 Processing helix chain 'B' and resid 3172 through 3177 removed outlier: 4.639A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3177' Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.426A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3201 through 3206 removed outlier: 4.838A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix No H-bonds generated for 'chain 'B' and resid 3201 through 3206' Processing helix chain 'B' and resid 3210 through 3224 removed outlier: 4.435A pdb=" N ALA B3222 " --> pdb=" O ILE B3218 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B3223 " --> pdb=" O VAL B3219 " (cutoff:3.500A) Processing helix chain 'B' and resid 3227 through 3232 Proline residue: B3232 - end of helix Processing helix chain 'B' and resid 3233 through 3254 removed outlier: 5.646A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 5.101A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N HIS B3252 " --> pdb=" O ARG B3248 " (cutoff:3.500A) Proline residue: B3254 - end of helix Processing helix chain 'B' and resid 3269 through 3288 Processing helix chain 'B' and resid 3294 through 3308 removed outlier: 3.670A pdb=" N GLN B3304 " --> pdb=" O ALA B3300 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 4.913A pdb=" N ASN B3308 " --> pdb=" O GLN B3304 " (cutoff:3.500A) Processing helix chain 'B' and resid 3311 through 3344 removed outlier: 4.914A pdb=" N LEU B3315 " --> pdb=" O LYS B3311 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS B3316 " --> pdb=" O PRO B3312 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 3.832A pdb=" N ALA B3342 " --> pdb=" O ASP B3338 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B3343 " --> pdb=" O HIS B3339 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA B3344 " --> pdb=" O LEU B3340 " (cutoff:3.500A) Processing helix chain 'B' and resid 3348 through 3381 removed outlier: 4.641A pdb=" N LEU B3354 " --> pdb=" O GLU B3350 " (cutoff:3.500A) Proline residue: B3371 - end of helix Processing helix chain 'B' and resid 3382 through 3388 Proline residue: B3388 - end of helix Processing helix chain 'B' and resid 3389 through 3410 removed outlier: 3.562A pdb=" N GLU B3401 " --> pdb=" O ARG B3397 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS B3410 " --> pdb=" O TRP B3406 " (cutoff:3.500A) Processing helix chain 'B' and resid 3411 through 3424 Processing helix chain 'B' and resid 3427 through 3437 removed outlier: 4.537A pdb=" N LEU B3431 " --> pdb=" O ASN B3427 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER B3437 " --> pdb=" O THR B3433 " (cutoff:3.500A) Processing helix chain 'B' and resid 3464 through 3482 Proline residue: B3475 - end of helix removed outlier: 4.596A pdb=" N ALA B3482 " --> pdb=" O LEU B3478 " (cutoff:3.500A) Processing helix chain 'B' and resid 3484 through 3499 removed outlier: 5.524A pdb=" N LEU B3488 " --> pdb=" O GLY B3484 " (cutoff:3.500A) Processing helix chain 'B' and resid 3501 through 3514 removed outlier: 4.854A pdb=" N HIS B3514 " --> pdb=" O ARG B3510 " (cutoff:3.500A) Processing helix chain 'B' and resid 3523 through 3533 Processing helix chain 'B' and resid 3543 through 3564 Processing helix chain 'B' and resid 3594 through 3605 Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.738A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3628 Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.713A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.732A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.880A 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: 4.566A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.557A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.336A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.564A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 4.354A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.535A pdb=" N HIS B4055 " --> pdb=" O ALA B4051 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.135A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.904A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 4.309A pdb=" N ASP B4093 " --> pdb=" O GLU B4089 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY B4095 " --> pdb=" O ALA B4091 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4184 through 4208 removed outlier: 4.752A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4260 removed outlier: 4.007A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4262 through 4272 removed outlier: 4.590A pdb=" N LYS B4266 " --> pdb=" O LYS B4262 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B4271 " --> pdb=" O GLN B4267 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.688A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 3.567A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4521 removed outlier: 4.236A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS B4521 " --> pdb=" O LEU B4517 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4613 removed outlier: 4.524A pdb=" N TYR B4590 " --> pdb=" O CYS B4586 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU B4593 " --> pdb=" O GLY B4589 " (cutoff:3.500A) removed outlier: 4.301A 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: 3.864A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.886A 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: 5.105A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) Processing helix chain 'B' and resid 4695 through 4702 removed outlier: 5.896A 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: 3.862A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4750 removed outlier: 4.621A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) Processing helix chain 'B' and resid 4751 through 4762 removed outlier: 3.673A pdb=" N THR B4755 " --> pdb=" O LYS B4751 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.336A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 4.442A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.213A 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: 4.138A 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: 5.461A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.928A 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 3117 through 3122 removed outlier: 4.231A pdb=" N ILE B3122 " --> pdb=" O PHE B3117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3117 through 3122' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.765A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 266 through 271 removed outlier: 5.328A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 5.548A pdb=" N THR C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 removed outlier: 4.096A pdb=" N LYS C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.670A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 removed outlier: 3.837A pdb=" N VAL C 517 " --> pdb=" O HIS C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 3.710A pdb=" N SER C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 555 removed outlier: 4.361A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 removed outlier: 3.547A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 556 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 5.320A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.674A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.551A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.505A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.999A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.243A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 961 removed outlier: 4.432A pdb=" N ASP C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 3.988A pdb=" N GLN C 971 " --> pdb=" O PRO C 967 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 967 through 972' Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.704A pdb=" N SER C1049 " --> pdb=" O SER C1045 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1226 through 1231 removed outlier: 3.688A pdb=" N GLY C1231 " --> pdb=" O PHE C1227 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.792A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 4.016A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.910A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1647 removed outlier: 4.409A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) Processing helix chain 'C' and resid 1648 through 1666 removed outlier: 3.589A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.720A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.835A 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 Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.770A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 3.957A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS C1805 " --> pdb=" O GLU C1801 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1835 through 1847 removed outlier: 4.223A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.834A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 4.981A 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: 3.942A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1966 removed outlier: 4.197A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 3.612A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.502A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.588A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 4.003A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2152 Processing helix chain 'C' and resid 2153 through 2158 Processing helix chain 'C' and resid 2159 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 5.081A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 4.042A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.655A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.187A 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 removed outlier: 3.551A pdb=" N VAL C2247 " --> pdb=" O ALA C2243 " (cutoff:3.500A) Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.711A pdb=" N VAL C2265 " --> pdb=" O ASP C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 removed outlier: 3.640A pdb=" N GLY C2284 " --> pdb=" O LEU C2280 " (cutoff:3.500A) Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.641A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.566A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2332 through 2337 removed outlier: 3.799A pdb=" N ARG C2336 " --> pdb=" O GLY C2332 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY C2337 " --> pdb=" O PRO C2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2332 through 2337' Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2439 removed outlier: 5.644A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.796A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C2467 " --> pdb=" O ASP C2463 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.125A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 2504 through 2510 removed outlier: 4.523A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) Processing helix chain 'C' and resid 2511 through 2532 removed outlier: 5.481A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 5.253A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2581 removed outlier: 5.298A pdb=" N ARG C2581 " --> pdb=" O CYS C2577 " (cutoff:3.500A) Processing helix chain 'C' and resid 2582 through 2596 removed outlier: 4.759A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.248A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 4.898A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP C2696 " --> pdb=" O GLN C2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2691 through 2696' Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.724A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.353A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2769 through 2786 Proline residue: C2774 - end of helix removed outlier: 3.805A pdb=" N GLY C2786 " --> pdb=" O MET C2782 " (cutoff:3.500A) Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.328A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.576A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2915 through 2950 removed outlier: 7.456A pdb=" N PHE C2921 " --> pdb=" O ILE C2917 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA C2922 " --> pdb=" O GLU C2918 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR C2923 " --> pdb=" O LYS C2919 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY C2949 " --> pdb=" O GLY C2945 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 3.600A pdb=" N VAL C2967 " --> pdb=" O PHE C2963 " (cutoff:3.500A) removed outlier: 4.988A 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 Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.447A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3049 Processing helix chain 'C' and resid 3050 through 3078 removed outlier: 3.561A pdb=" N LEU C3061 " --> pdb=" O LEU C3057 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN C3077 " --> pdb=" O GLU C3073 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY C3078 " --> pdb=" O ASN C3074 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 3.719A pdb=" N GLN C3092 " --> pdb=" O LYS C3088 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3124 through 3143 Processing helix chain 'C' and resid 3145 through 3150 removed outlier: 4.364A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) Processing helix chain 'C' and resid 3151 through 3166 Processing helix chain 'C' and resid 3172 through 3177 removed outlier: 4.640A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3177' Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.426A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3201 through 3206 removed outlier: 4.839A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix No H-bonds generated for 'chain 'C' and resid 3201 through 3206' Processing helix chain 'C' and resid 3210 through 3224 removed outlier: 4.435A pdb=" N ALA C3222 " --> pdb=" O ILE C3218 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C3223 " --> pdb=" O VAL C3219 " (cutoff:3.500A) Processing helix chain 'C' and resid 3227 through 3232 Proline residue: C3232 - end of helix Processing helix chain 'C' and resid 3233 through 3254 removed outlier: 5.645A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 5.100A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS C3252 " --> pdb=" O ARG C3248 " (cutoff:3.500A) Proline residue: C3254 - end of helix Processing helix chain 'C' and resid 3269 through 3288 Processing helix chain 'C' and resid 3294 through 3308 removed outlier: 3.670A pdb=" N GLN C3304 " --> pdb=" O ALA C3300 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 4.913A pdb=" N ASN C3308 " --> pdb=" O GLN C3304 " (cutoff:3.500A) Processing helix chain 'C' and resid 3311 through 3344 removed outlier: 4.915A pdb=" N LEU C3315 " --> pdb=" O LYS C3311 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS C3316 " --> pdb=" O PRO C3312 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 3.833A pdb=" N ALA C3342 " --> pdb=" O ASP C3338 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C3343 " --> pdb=" O HIS C3339 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA C3344 " --> pdb=" O LEU C3340 " (cutoff:3.500A) Processing helix chain 'C' and resid 3348 through 3381 removed outlier: 4.641A pdb=" N LEU C3354 " --> pdb=" O GLU C3350 " (cutoff:3.500A) Proline residue: C3371 - end of helix Processing helix chain 'C' and resid 3382 through 3388 Proline residue: C3388 - end of helix Processing helix chain 'C' and resid 3389 through 3410 removed outlier: 3.562A pdb=" N GLU C3401 " --> pdb=" O ARG C3397 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS C3410 " --> pdb=" O TRP C3406 " (cutoff:3.500A) Processing helix chain 'C' and resid 3411 through 3424 Processing helix chain 'C' and resid 3427 through 3437 removed outlier: 4.538A pdb=" N LEU C3431 " --> pdb=" O ASN C3427 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER C3437 " --> pdb=" O THR C3433 " (cutoff:3.500A) Processing helix chain 'C' and resid 3464 through 3482 Proline residue: C3475 - end of helix removed outlier: 4.595A pdb=" N ALA C3482 " --> pdb=" O LEU C3478 " (cutoff:3.500A) Processing helix chain 'C' and resid 3484 through 3499 removed outlier: 5.524A pdb=" N LEU C3488 " --> pdb=" O GLY C3484 " (cutoff:3.500A) Processing helix chain 'C' and resid 3501 through 3514 removed outlier: 4.852A pdb=" N HIS C3514 " --> pdb=" O ARG C3510 " (cutoff:3.500A) Processing helix chain 'C' and resid 3523 through 3533 Processing helix chain 'C' and resid 3543 through 3564 Processing helix chain 'C' and resid 3594 through 3605 Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.738A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3628 Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.713A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.732A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.880A 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: 4.566A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.557A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.336A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.564A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 4.354A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.535A pdb=" N HIS C4055 " --> pdb=" O ALA C4051 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.134A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.903A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 4.308A pdb=" N ASP C4093 " --> pdb=" O GLU C4089 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY C4095 " --> pdb=" O ALA C4091 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4184 through 4208 removed outlier: 4.752A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4260 removed outlier: 4.006A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4262 through 4272 removed outlier: 4.590A pdb=" N LYS C4266 " --> pdb=" O LYS C4262 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL C4271 " --> pdb=" O GLN C4267 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.688A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 3.567A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4521 removed outlier: 4.235A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS C4521 " --> pdb=" O LEU C4517 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4613 removed outlier: 4.525A pdb=" N TYR C4590 " --> pdb=" O CYS C4586 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU C4593 " --> pdb=" O GLY C4589 " (cutoff:3.500A) removed outlier: 4.301A 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: 3.865A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.886A 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: 5.105A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) Processing helix chain 'C' and resid 4695 through 4702 removed outlier: 5.896A 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: 3.863A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4750 removed outlier: 4.621A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) Processing helix chain 'C' and resid 4751 through 4762 removed outlier: 3.673A pdb=" N THR C4755 " --> pdb=" O LYS C4751 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.337A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 4.442A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.213A 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: 4.138A 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: 5.461A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.929A 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 3117 through 3122 removed outlier: 4.229A pdb=" N ILE C3122 " --> pdb=" O PHE C3117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3117 through 3122' Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.766A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 266 through 271 removed outlier: 5.329A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 5.548A pdb=" N THR D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 removed outlier: 4.096A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 4.669A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 removed outlier: 3.838A pdb=" N VAL D 517 " --> pdb=" O HIS D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 3.710A pdb=" N SER D 525 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 555 removed outlier: 4.361A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 563 removed outlier: 3.548A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 556 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 5.320A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.674A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.551A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.505A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.999A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.242A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 961 removed outlier: 4.432A pdb=" N ASP D 959 " --> pdb=" O GLU D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 3.987A pdb=" N GLN D 971 " --> pdb=" O PRO D 967 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 967 through 972' Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.704A pdb=" N SER D1049 " --> pdb=" O SER D1045 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1231 removed outlier: 3.688A pdb=" N GLY D1231 " --> pdb=" O PHE D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 4.015A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.910A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1647 removed outlier: 4.409A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) Processing helix chain 'D' and resid 1648 through 1666 removed outlier: 3.589A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.718A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.835A 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 Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.770A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 3.958A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS D1805 " --> pdb=" O GLU D1801 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.223A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.834A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 4.980A 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: 3.942A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1966 removed outlier: 4.197A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 3.612A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.502A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.589A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 4.004A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2152 Processing helix chain 'D' and resid 2153 through 2158 Processing helix chain 'D' and resid 2159 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 5.082A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 4.042A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.655A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.187A 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 removed outlier: 3.551A pdb=" N VAL D2247 " --> pdb=" O ALA D2243 " (cutoff:3.500A) Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.711A pdb=" N VAL D2265 " --> pdb=" O ASP D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 removed outlier: 3.641A pdb=" N GLY D2284 " --> pdb=" O LEU D2280 " (cutoff:3.500A) Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.642A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.565A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2332 through 2337 removed outlier: 3.800A pdb=" N ARG D2336 " --> pdb=" O GLY D2332 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY D2337 " --> pdb=" O PRO D2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2332 through 2337' Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2439 removed outlier: 5.644A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.796A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D2467 " --> pdb=" O ASP D2463 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.125A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2504 through 2510 removed outlier: 4.523A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) Processing helix chain 'D' and resid 2511 through 2532 removed outlier: 5.481A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 5.253A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2581 removed outlier: 5.297A pdb=" N ARG D2581 " --> pdb=" O CYS D2577 " (cutoff:3.500A) Processing helix chain 'D' and resid 2582 through 2596 removed outlier: 4.760A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.249A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 4.898A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP D2696 " --> pdb=" O GLN D2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2691 through 2696' Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.724A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.354A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2769 through 2786 Proline residue: D2774 - end of helix removed outlier: 3.805A pdb=" N GLY D2786 " --> pdb=" O MET D2782 " (cutoff:3.500A) Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.327A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.576A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2915 through 2950 removed outlier: 7.455A pdb=" N PHE D2921 " --> pdb=" O ILE D2917 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA D2922 " --> pdb=" O GLU D2918 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR D2923 " --> pdb=" O LYS D2919 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY D2949 " --> pdb=" O GLY D2945 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 3.600A pdb=" N VAL D2967 " --> pdb=" O PHE D2963 " (cutoff:3.500A) removed outlier: 4.988A 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 Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.447A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3049 Processing helix chain 'D' and resid 3050 through 3078 removed outlier: 3.562A pdb=" N LEU D3061 " --> pdb=" O LEU D3057 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN D3077 " --> pdb=" O GLU D3073 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY D3078 " --> pdb=" O ASN D3074 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 3.719A pdb=" N GLN D3092 " --> pdb=" O LYS D3088 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3124 through 3143 Processing helix chain 'D' and resid 3145 through 3150 removed outlier: 4.363A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) Processing helix chain 'D' and resid 3151 through 3166 Processing helix chain 'D' and resid 3172 through 3177 removed outlier: 4.638A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3177' Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.425A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3201 through 3206 removed outlier: 4.838A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix No H-bonds generated for 'chain 'D' and resid 3201 through 3206' Processing helix chain 'D' and resid 3210 through 3224 removed outlier: 4.436A pdb=" N ALA D3222 " --> pdb=" O ILE D3218 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D3223 " --> pdb=" O VAL D3219 " (cutoff:3.500A) Processing helix chain 'D' and resid 3227 through 3232 Proline residue: D3232 - end of helix Processing helix chain 'D' and resid 3233 through 3254 removed outlier: 5.646A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 5.100A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N HIS D3252 " --> pdb=" O ARG D3248 " (cutoff:3.500A) Proline residue: D3254 - end of helix Processing helix chain 'D' and resid 3269 through 3288 Processing helix chain 'D' and resid 3294 through 3308 removed outlier: 3.670A pdb=" N GLN D3304 " --> pdb=" O ALA D3300 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 4.913A pdb=" N ASN D3308 " --> pdb=" O GLN D3304 " (cutoff:3.500A) Processing helix chain 'D' and resid 3311 through 3344 removed outlier: 4.914A pdb=" N LEU D3315 " --> pdb=" O LYS D3311 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS D3316 " --> pdb=" O PRO D3312 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 3.833A pdb=" N ALA D3342 " --> pdb=" O ASP D3338 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D3343 " --> pdb=" O HIS D3339 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA D3344 " --> pdb=" O LEU D3340 " (cutoff:3.500A) Processing helix chain 'D' and resid 3348 through 3381 removed outlier: 4.642A pdb=" N LEU D3354 " --> pdb=" O GLU D3350 " (cutoff:3.500A) Proline residue: D3371 - end of helix Processing helix chain 'D' and resid 3382 through 3388 Proline residue: D3388 - end of helix Processing helix chain 'D' and resid 3389 through 3410 removed outlier: 3.563A pdb=" N GLU D3401 " --> pdb=" O ARG D3397 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS D3410 " --> pdb=" O TRP D3406 " (cutoff:3.500A) Processing helix chain 'D' and resid 3411 through 3424 Processing helix chain 'D' and resid 3427 through 3437 removed outlier: 4.537A pdb=" N LEU D3431 " --> pdb=" O ASN D3427 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER D3437 " --> pdb=" O THR D3433 " (cutoff:3.500A) Processing helix chain 'D' and resid 3464 through 3482 Proline residue: D3475 - end of helix removed outlier: 4.595A pdb=" N ALA D3482 " --> pdb=" O LEU D3478 " (cutoff:3.500A) Processing helix chain 'D' and resid 3484 through 3499 removed outlier: 5.524A pdb=" N LEU D3488 " --> pdb=" O GLY D3484 " (cutoff:3.500A) Processing helix chain 'D' and resid 3501 through 3514 removed outlier: 4.853A pdb=" N HIS D3514 " --> pdb=" O ARG D3510 " (cutoff:3.500A) Processing helix chain 'D' and resid 3523 through 3533 Processing helix chain 'D' and resid 3543 through 3564 Processing helix chain 'D' and resid 3594 through 3605 Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.738A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3628 Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.713A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.731A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.880A 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: 4.566A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.556A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.336A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.565A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 4.353A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.535A pdb=" N HIS D4055 " --> pdb=" O ALA D4051 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.134A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.903A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 4.308A pdb=" N ASP D4093 " --> pdb=" O GLU D4089 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY D4095 " --> pdb=" O ALA D4091 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4184 through 4208 removed outlier: 4.752A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4260 removed outlier: 4.007A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4262 through 4272 removed outlier: 4.591A pdb=" N LYS D4266 " --> pdb=" O LYS D4262 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL D4271 " --> pdb=" O GLN D4267 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.688A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 3.567A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4521 removed outlier: 4.236A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS D4521 " --> pdb=" O LEU D4517 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4613 removed outlier: 4.524A pdb=" N TYR D4590 " --> pdb=" O CYS D4586 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D4593 " --> pdb=" O GLY D4589 " (cutoff:3.500A) removed outlier: 4.302A 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: 3.864A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.886A 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: 5.105A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) Processing helix chain 'D' and resid 4695 through 4702 removed outlier: 5.896A 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: 3.862A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4750 removed outlier: 4.621A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) Processing helix chain 'D' and resid 4751 through 4762 removed outlier: 3.673A pdb=" N THR D4755 " --> pdb=" O LYS D4751 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.337A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 4.442A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.213A 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: 4.138A 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: 5.461A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.928A 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 3117 through 3122 removed outlier: 4.230A pdb=" N ILE D3122 " --> pdb=" O PHE D3117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3117 through 3122' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.734A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.178A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.734A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.179A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.735A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.179A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.734A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.179A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'I' and resid 6 through 21 removed outlier: 4.041A pdb=" N PHE I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 41 removed outlier: 4.667A pdb=" N GLY I 34 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N MET I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 56 removed outlier: 5.014A pdb=" N GLU I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL I 56 " --> pdb=" O MET I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 78 removed outlier: 3.508A pdb=" N ARG I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 4.624A pdb=" N ILE I 86 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 111 Processing helix chain 'I' and resid 119 through 128 Processing helix chain 'I' and resid 138 through 148 removed outlier: 3.900A pdb=" N MET I 145 " --> pdb=" O GLU I 141 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET I 146 " --> pdb=" O PHE I 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 21 removed outlier: 4.041A pdb=" N PHE J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 41 removed outlier: 4.666A pdb=" N GLY J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR J 35 " --> pdb=" O LYS J 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N MET J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 56 removed outlier: 5.015A pdb=" N GLU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL J 56 " --> pdb=" O MET J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 78 removed outlier: 3.508A pdb=" N ARG J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 4.625A pdb=" N ILE J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 111 Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'J' and resid 138 through 148 removed outlier: 3.899A pdb=" N MET J 145 " --> pdb=" O GLU J 141 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET J 146 " --> pdb=" O PHE J 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 21 removed outlier: 4.041A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 41 removed outlier: 4.667A pdb=" N GLY K 34 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR K 35 " --> pdb=" O LYS K 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N MET K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 5.015A pdb=" N GLU K 55 " --> pdb=" O ASP K 51 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL K 56 " --> pdb=" O MET K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 78 removed outlier: 3.508A pdb=" N ARG K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS K 78 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 93 removed outlier: 4.624A pdb=" N ILE K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 111 Processing helix chain 'K' and resid 119 through 128 Processing helix chain 'K' and resid 138 through 148 removed outlier: 3.900A pdb=" N MET K 145 " --> pdb=" O GLU K 141 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 21 removed outlier: 4.040A pdb=" N PHE L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 removed outlier: 4.667A pdb=" N GLY L 34 " --> pdb=" O THR L 30 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET L 37 " --> pdb=" O LEU L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 removed outlier: 5.014A pdb=" N GLU L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 78 removed outlier: 3.509A pdb=" N ARG L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 4.625A pdb=" N ILE L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 111 Processing helix chain 'L' and resid 119 through 128 Processing helix chain 'L' and resid 138 through 148 removed outlier: 3.900A pdb=" N MET L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET L 146 " --> pdb=" O PHE L 142 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.406A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.449A 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: 6.536A 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 193 through 196 Processing sheet with id= 5, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.824A pdb=" N GLY A 264 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 387 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 313 through 318 removed outlier: 3.630A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 13.966A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 8, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.664A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.786A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 11, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= 12, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 7.161A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1171 through 1177 removed outlier: 3.763A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.611A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A1433 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 5.069A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 3.684A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2788 through 2791 Processing sheet with id= 18, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.704A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.406A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.449A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.537A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 160 through 164 Processing sheet with id= 22, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= 23, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.826A pdb=" N GLY B 264 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 387 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.629A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 13.966A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 26, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.662A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.786A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 29, first strand: chain 'B' and resid 1016 through 1019 Processing sheet with id= 30, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 7.161A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1171 through 1177 removed outlier: 3.764A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.610A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B1433 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 5.069A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 3.684A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 2788 through 2791 Processing sheet with id= 36, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.703A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.406A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.449A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.536A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 160 through 164 Processing sheet with id= 40, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= 41, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.825A pdb=" N GLY C 264 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE C 387 " --> pdb=" O GLY C 264 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 313 through 318 removed outlier: 3.629A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 13.966A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 44, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.664A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.785A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 47, first strand: chain 'C' and resid 1016 through 1019 Processing sheet with id= 48, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 7.162A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 1171 through 1177 removed outlier: 3.763A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.611A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C1433 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 5.068A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 3.684A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 2788 through 2791 Processing sheet with id= 54, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.704A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.406A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.449A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.537A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 160 through 164 Processing sheet with id= 58, first strand: chain 'D' and resid 193 through 196 Processing sheet with id= 59, first strand: chain 'D' and resid 243 through 246 removed outlier: 6.824A pdb=" N GLY D 264 " --> pdb=" O ILE D 387 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE D 387 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 313 through 318 removed outlier: 3.630A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 13.966A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 62, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.663A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.785A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 65, first strand: chain 'D' and resid 1016 through 1019 Processing sheet with id= 66, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 7.161A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 1171 through 1177 removed outlier: 3.763A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.611A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D1433 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 5.069A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 3.683A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 2788 through 2791 Processing sheet with id= 72, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.704A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.698A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'E' and resid 46 through 50 Processing sheet with id= 75, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.698A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 77, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.699A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'G' and resid 46 through 50 Processing sheet with id= 79, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.699A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 46 through 50 8188 hydrogen bonds defined for protein. 24412 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: 121.46 Time building geometry restraints manager: 50.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 47903 1.34 - 1.46: 25323 1.46 - 1.58: 78530 1.58 - 1.70: 44 1.70 - 1.82: 1644 Bond restraints: 153444 Sorted by residual: bond pdb=" CB GLN C1293 " pdb=" CG GLN C1293 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 4.95e+00 bond pdb=" CB GLN B1293 " pdb=" CG GLN B1293 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" CB GLN D1293 " pdb=" CG GLN D1293 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" CB GLN A1293 " pdb=" CG GLN A1293 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.87e+00 bond pdb=" CB ARG D 880 " pdb=" CG ARG D 880 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.10e+00 ... (remaining 153439 not shown) Histogram of bond angle deviations from ideal: 91.46 - 101.15: 519 101.15 - 110.85: 52553 110.85 - 120.54: 97879 120.54 - 130.24: 55468 130.24 - 139.93: 837 Bond angle restraints: 207256 Sorted by residual: angle pdb=" CA GLN D1293 " pdb=" CB GLN D1293 " pdb=" CG GLN D1293 " ideal model delta sigma weight residual 114.10 130.02 -15.92 2.00e+00 2.50e-01 6.34e+01 angle pdb=" CA GLN A1293 " pdb=" CB GLN A1293 " pdb=" CG GLN A1293 " ideal model delta sigma weight residual 114.10 129.98 -15.88 2.00e+00 2.50e-01 6.31e+01 angle pdb=" CA GLN B1293 " pdb=" CB GLN B1293 " pdb=" CG GLN B1293 " ideal model delta sigma weight residual 114.10 129.96 -15.86 2.00e+00 2.50e-01 6.29e+01 angle pdb=" CA GLN C1293 " pdb=" CB GLN C1293 " pdb=" CG GLN C1293 " ideal model delta sigma weight residual 114.10 129.94 -15.84 2.00e+00 2.50e-01 6.28e+01 angle pdb=" CG ARG D4046 " pdb=" CD ARG D4046 " pdb=" NE ARG D4046 " ideal model delta sigma weight residual 112.00 126.04 -14.04 2.20e+00 2.07e-01 4.08e+01 ... (remaining 207251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 83933 17.84 - 35.69: 7015 35.69 - 53.53: 1293 53.53 - 71.38: 311 71.38 - 89.22: 160 Dihedral angle restraints: 92712 sinusoidal: 38116 harmonic: 54596 Sorted by residual: dihedral pdb=" CA GLU B3520 " pdb=" C GLU B3520 " pdb=" N ASP B3521 " pdb=" CA ASP B3521 " ideal model delta harmonic sigma weight residual -180.00 -146.25 -33.75 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA GLU C3520 " pdb=" C GLU C3520 " pdb=" N ASP C3521 " pdb=" CA ASP C3521 " ideal model delta harmonic sigma weight residual -180.00 -146.27 -33.73 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CA GLU A3520 " pdb=" C GLU A3520 " pdb=" N ASP A3521 " pdb=" CA ASP A3521 " ideal model delta harmonic sigma weight residual -180.00 -146.29 -33.71 0 5.00e+00 4.00e-02 4.55e+01 ... (remaining 92709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 21049 0.080 - 0.160: 1644 0.160 - 0.240: 47 0.240 - 0.320: 8 0.320 - 0.400: 8 Chirality restraints: 22756 Sorted by residual: chirality pdb=" CA MET L 110 " pdb=" N MET L 110 " pdb=" C MET L 110 " pdb=" CB MET L 110 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA MET J 110 " pdb=" N MET J 110 " pdb=" C MET J 110 " pdb=" CB MET J 110 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA MET K 110 " pdb=" N MET K 110 " pdb=" C MET K 110 " pdb=" CB MET K 110 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 22753 not shown) Planarity restraints: 26676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 107 " 0.441 9.50e-02 1.11e+02 1.98e-01 2.40e+01 pdb=" NE ARG K 107 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG K 107 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG K 107 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 107 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 107 " 0.440 9.50e-02 1.11e+02 1.97e-01 2.39e+01 pdb=" NE ARG L 107 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG L 107 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG L 107 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG L 107 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 107 " 0.440 9.50e-02 1.11e+02 1.97e-01 2.39e+01 pdb=" NE ARG I 107 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG I 107 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG I 107 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 107 " 0.017 2.00e-02 2.50e+03 ... (remaining 26673 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 1071 2.55 - 3.14: 120469 3.14 - 3.73: 247062 3.73 - 4.31: 334802 4.31 - 4.90: 552211 Nonbonded interactions: 1255615 Sorted by model distance: nonbonded pdb=" NH1 ARG A2905 " pdb=" O PHE A2907 " model vdw 1.967 2.520 nonbonded pdb=" NH1 ARG D2905 " pdb=" O PHE D2907 " model vdw 1.967 2.520 nonbonded pdb=" NH1 ARG B2905 " pdb=" O PHE B2907 " model vdw 1.967 2.520 nonbonded pdb=" NH1 ARG C2905 " pdb=" O PHE C2907 " model vdw 1.968 2.520 nonbonded pdb=" NH2 ARG C 882 " pdb=" O LEU C 933 " model vdw 2.132 2.520 ... (remaining 1255610 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 5003)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 31.900 Check model and map are aligned: 1.630 Set scattering table: 1.030 Process input model: 499.160 Find NCS groups from input model: 9.230 Set up NCS constraints: 1.250 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: 0.040 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 565.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 0.067 153444 Z= 0.199 Angle : 0.686 16.067 207256 Z= 0.361 Chirality : 0.042 0.400 22756 Planarity : 0.005 0.198 26676 Dihedral : 14.131 89.223 57460 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.92 % Favored : 95.93 % Rotamer: Outliers : 0.52 % Allowed : 0.52 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.12 (0.06), residues: 18624 helix: 1.74 (0.05), residues: 9924 sheet: -0.17 (0.12), residues: 1908 loop : -0.42 (0.08), residues: 6792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D1156 HIS 0.011 0.001 HIS B3017 PHE 0.060 0.002 PHE J 142 TYR 0.029 0.001 TYR J 139 ARG 0.017 0.000 ARG C2905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1089 time to evaluate : 12.591 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 1501 ASN cc_start: 0.6536 (m110) cc_final: 0.6240 (m110) REVERT: A 3074 ASN cc_start: 0.8076 (m110) cc_final: 0.7805 (m110) REVERT: A 3104 MET cc_start: 0.7888 (mtm) cc_final: 0.7593 (mtp) REVERT: A 3162 PHE cc_start: 0.8855 (t80) cc_final: 0.8536 (t80) REVERT: A 3200 ASN cc_start: 0.8328 (m-40) cc_final: 0.7936 (m-40) REVERT: A 3231 MET cc_start: 0.6558 (mmp) cc_final: 0.6341 (mpm) REVERT: A 3264 CYS cc_start: 0.7414 (m) cc_final: 0.6705 (m) REVERT: A 3323 MET cc_start: 0.7766 (mmp) cc_final: 0.7259 (mmt) REVERT: A 3359 PHE cc_start: 0.8813 (m-80) cc_final: 0.8347 (m-80) REVERT: A 3398 MET cc_start: 0.8410 (ttm) cc_final: 0.7975 (mmm) REVERT: A 3981 MET cc_start: 0.8427 (tmm) cc_final: 0.8218 (tmm) REVERT: A 4804 MET cc_start: 0.8750 (mmm) cc_final: 0.8523 (mmm) REVERT: H 55 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8288 (mt-10) REVERT: I 40 LEU cc_start: 0.7958 (tt) cc_final: 0.7459 (tt) REVERT: K 42 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: B 1501 ASN cc_start: 0.6407 (m110) cc_final: 0.6129 (m110) REVERT: B 3074 ASN cc_start: 0.8081 (m110) cc_final: 0.7828 (m110) REVERT: B 3200 ASN cc_start: 0.8371 (m-40) cc_final: 0.7993 (m-40) REVERT: B 3231 MET cc_start: 0.6671 (mmp) cc_final: 0.6424 (mpm) REVERT: B 3276 LEU cc_start: 0.8963 (tt) cc_final: 0.8692 (tp) REVERT: B 3359 PHE cc_start: 0.8837 (m-80) cc_final: 0.8348 (m-80) REVERT: B 3398 MET cc_start: 0.8358 (ttm) cc_final: 0.7961 (mmm) REVERT: B 3981 MET cc_start: 0.8464 (tmm) cc_final: 0.8261 (tmt) REVERT: C 1300 MET cc_start: 0.8124 (mmp) cc_final: 0.7711 (mmt) REVERT: C 1501 ASN cc_start: 0.6495 (m110) cc_final: 0.6178 (m110) REVERT: C 3074 ASN cc_start: 0.8077 (m110) cc_final: 0.7803 (m110) REVERT: C 3200 ASN cc_start: 0.8310 (m-40) cc_final: 0.7915 (m-40) REVERT: C 3231 MET cc_start: 0.6585 (mmp) cc_final: 0.6365 (mpm) REVERT: C 3264 CYS cc_start: 0.7480 (m) cc_final: 0.6810 (m) REVERT: C 3323 MET cc_start: 0.7742 (mmp) cc_final: 0.7223 (mmt) REVERT: C 3359 PHE cc_start: 0.8816 (m-80) cc_final: 0.8355 (m-80) REVERT: C 3398 MET cc_start: 0.8374 (ttm) cc_final: 0.7903 (mmm) REVERT: C 3981 MET cc_start: 0.8449 (tmm) cc_final: 0.8233 (tmm) REVERT: C 4804 MET cc_start: 0.8745 (mmm) cc_final: 0.8542 (mmm) REVERT: D 1501 ASN cc_start: 0.6518 (m110) cc_final: 0.6230 (m110) REVERT: D 2605 MET cc_start: 0.8131 (tmm) cc_final: 0.7905 (tmm) REVERT: D 3074 ASN cc_start: 0.8075 (m110) cc_final: 0.7803 (m110) REVERT: D 3104 MET cc_start: 0.7918 (mtm) cc_final: 0.7608 (mtp) REVERT: D 3200 ASN cc_start: 0.8311 (m-40) cc_final: 0.7938 (m-40) REVERT: D 3231 MET cc_start: 0.6524 (mmp) cc_final: 0.6309 (mpm) REVERT: D 3264 CYS cc_start: 0.7472 (m) cc_final: 0.6753 (m) REVERT: D 3314 LEU cc_start: 0.8181 (tp) cc_final: 0.7976 (tt) REVERT: D 3323 MET cc_start: 0.7719 (mmp) cc_final: 0.7195 (mmt) REVERT: D 3359 PHE cc_start: 0.8798 (m-80) cc_final: 0.8338 (m-80) REVERT: D 3398 MET cc_start: 0.8362 (ttm) cc_final: 0.7898 (mmm) REVERT: D 3981 MET cc_start: 0.8452 (tmm) cc_final: 0.8196 (tmm) REVERT: D 4804 MET cc_start: 0.8765 (mmm) cc_final: 0.8559 (mmm) outliers start: 80 outliers final: 12 residues processed: 1122 average time/residue: 2.1789 time to fit residues: 3551.4657 Evaluate side-chains 958 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 945 time to evaluate : 12.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 2594 PHE Chi-restraints excluded: chain A residue 2788 ARG Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 2788 ARG Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 2788 ARG Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 2788 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1580 optimal weight: 7.9990 chunk 1418 optimal weight: 6.9990 chunk 787 optimal weight: 9.9990 chunk 484 optimal weight: 30.0000 chunk 957 optimal weight: 20.0000 chunk 758 optimal weight: 4.9990 chunk 1467 optimal weight: 10.0000 chunk 567 optimal weight: 9.9990 chunk 892 optimal weight: 50.0000 chunk 1092 optimal weight: 7.9990 chunk 1699 optimal weight: 2.9990 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 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3512 ASN A3955 GLN A3975 GLN I 108 HIS J 108 HIS K 9 GLN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3512 ASN B3955 GLN B3975 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3512 ASN C3955 GLN C3975 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3512 ASN D3955 GLN D3975 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 153444 Z= 0.452 Angle : 0.677 12.907 207256 Z= 0.345 Chirality : 0.045 0.201 22756 Planarity : 0.005 0.064 26676 Dihedral : 6.282 87.213 20624 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.17 % Favored : 95.68 % Rotamer: Outliers : 0.74 % Allowed : 5.19 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.03 (0.06), residues: 18624 helix: 1.69 (0.05), residues: 9928 sheet: -0.31 (0.12), residues: 1912 loop : -0.47 (0.08), residues: 6784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C1156 HIS 0.011 0.001 HIS D3732 PHE 0.034 0.002 PHE B2594 TYR 0.024 0.002 TYR D2760 ARG 0.010 0.001 ARG A3190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1003 time to evaluate : 12.724 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: A 78 LEU cc_start: 0.8487 (tp) cc_final: 0.8282 (tp) REVERT: A 844 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6761 (mtm-85) REVERT: A 1501 ASN cc_start: 0.6584 (m110) cc_final: 0.6317 (m110) REVERT: A 2584 MET cc_start: 0.7385 (ppp) cc_final: 0.6838 (ppp) REVERT: A 2939 TYR cc_start: 0.8444 (m-80) cc_final: 0.8241 (m-80) REVERT: A 3074 ASN cc_start: 0.8155 (m110) cc_final: 0.7870 (m110) REVERT: A 3130 CYS cc_start: 0.8367 (m) cc_final: 0.7551 (m) REVERT: A 3162 PHE cc_start: 0.8949 (t80) cc_final: 0.8654 (t80) REVERT: A 3200 ASN cc_start: 0.8407 (m-40) cc_final: 0.8040 (m-40) REVERT: A 3273 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: A 3348 MET cc_start: 0.3238 (pmm) cc_final: 0.2357 (pmm) REVERT: A 3359 PHE cc_start: 0.8876 (m-80) cc_final: 0.8368 (m-80) REVERT: A 3398 MET cc_start: 0.8436 (mtt) cc_final: 0.8179 (mtp) REVERT: A 4256 MET cc_start: 0.7843 (mtp) cc_final: 0.7562 (mtt) REVERT: A 4567 TYR cc_start: 0.6850 (p90) cc_final: 0.6139 (p90) REVERT: A 4804 MET cc_start: 0.8759 (mmm) cc_final: 0.8557 (mmm) REVERT: K 70 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7619 (tp) REVERT: B 844 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6782 (mtm-85) REVERT: B 981 MET cc_start: 0.7722 (ppp) cc_final: 0.7332 (mpp) REVERT: B 1501 ASN cc_start: 0.6594 (m110) cc_final: 0.6320 (m110) REVERT: B 3074 ASN cc_start: 0.8169 (m110) cc_final: 0.7874 (m110) REVERT: B 3130 CYS cc_start: 0.8396 (m) cc_final: 0.7647 (m) REVERT: B 3200 ASN cc_start: 0.8459 (m-40) cc_final: 0.8117 (m-40) REVERT: B 3315 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8963 (pp) REVERT: B 3348 MET cc_start: 0.3184 (pmm) cc_final: 0.2304 (pmm) REVERT: B 3359 PHE cc_start: 0.8872 (m-80) cc_final: 0.8363 (m-80) REVERT: B 3398 MET cc_start: 0.8436 (mtt) cc_final: 0.8171 (mtp) REVERT: B 4256 MET cc_start: 0.7800 (mtp) cc_final: 0.7512 (mtt) REVERT: B 4660 PHE cc_start: 0.8242 (t80) cc_final: 0.8033 (t80) REVERT: C 78 LEU cc_start: 0.8506 (tp) cc_final: 0.8302 (tp) REVERT: C 844 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6738 (mtm-85) REVERT: C 1300 MET cc_start: 0.8153 (mmp) cc_final: 0.7726 (mmt) REVERT: C 1501 ASN cc_start: 0.6512 (m110) cc_final: 0.6251 (m110) REVERT: C 2187 ILE cc_start: 0.8360 (mm) cc_final: 0.8051 (pp) REVERT: C 2584 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7145 (ptm) REVERT: C 3074 ASN cc_start: 0.8191 (m110) cc_final: 0.7893 (m110) REVERT: C 3162 PHE cc_start: 0.8957 (t80) cc_final: 0.8635 (t80) REVERT: C 3200 ASN cc_start: 0.8384 (m-40) cc_final: 0.8025 (m-40) REVERT: C 3273 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8417 (mtp) REVERT: C 3348 MET cc_start: 0.3179 (pmm) cc_final: 0.2305 (pmm) REVERT: C 3359 PHE cc_start: 0.8865 (m-80) cc_final: 0.8363 (m-80) REVERT: C 3398 MET cc_start: 0.8391 (mtt) cc_final: 0.8134 (mtp) REVERT: C 4256 MET cc_start: 0.7851 (mtp) cc_final: 0.7575 (mtt) REVERT: C 4567 TYR cc_start: 0.6805 (p90) cc_final: 0.6029 (p90) REVERT: D 78 LEU cc_start: 0.8494 (tp) cc_final: 0.8291 (tp) REVERT: D 844 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6764 (mtm-85) REVERT: D 1501 ASN cc_start: 0.6602 (m110) cc_final: 0.6340 (m110) REVERT: D 2187 ILE cc_start: 0.8367 (mm) cc_final: 0.8060 (pp) REVERT: D 2584 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7157 (ptm) REVERT: D 2939 TYR cc_start: 0.8475 (m-80) cc_final: 0.8266 (m-80) REVERT: D 3074 ASN cc_start: 0.8187 (m110) cc_final: 0.7885 (m110) REVERT: D 3130 CYS cc_start: 0.8393 (m) cc_final: 0.7584 (m) REVERT: D 3162 PHE cc_start: 0.8938 (t80) cc_final: 0.8648 (t80) REVERT: D 3200 ASN cc_start: 0.8399 (m-40) cc_final: 0.8032 (m-40) REVERT: D 3264 CYS cc_start: 0.7656 (m) cc_final: 0.6992 (m) REVERT: D 3273 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8399 (mtp) REVERT: D 3348 MET cc_start: 0.3251 (pmm) cc_final: 0.2349 (pmm) REVERT: D 3359 PHE cc_start: 0.8853 (m-80) cc_final: 0.8358 (m-80) REVERT: D 3398 MET cc_start: 0.8406 (mtt) cc_final: 0.8159 (mtp) REVERT: D 4256 MET cc_start: 0.7831 (mtp) cc_final: 0.7552 (mtt) REVERT: D 4567 TYR cc_start: 0.6792 (p90) cc_final: 0.6069 (p90) outliers start: 113 outliers final: 22 residues processed: 1018 average time/residue: 2.1728 time to fit residues: 3248.5624 Evaluate side-chains 992 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 959 time to evaluate : 12.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 1249 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain C residue 844 ARG Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 3273 MET Chi-restraints excluded: chain C residue 3439 MET Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain D residue 844 ARG Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2584 MET Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3439 MET Chi-restraints excluded: chain D residue 3739 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 944 optimal weight: 5.9990 chunk 527 optimal weight: 20.0000 chunk 1414 optimal weight: 2.9990 chunk 1157 optimal weight: 0.8980 chunk 468 optimal weight: 2.9990 chunk 1703 optimal weight: 20.0000 chunk 1839 optimal weight: 6.9990 chunk 1516 optimal weight: 9.9990 chunk 1688 optimal weight: 20.0000 chunk 580 optimal weight: 10.0000 chunk 1366 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 GLN ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 GLN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1615 GLN ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1615 GLN ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1615 GLN ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 153444 Z= 0.237 Angle : 0.596 14.786 207256 Z= 0.301 Chirality : 0.041 0.235 22756 Planarity : 0.004 0.060 26676 Dihedral : 5.957 87.513 20576 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Rotamer: Outliers : 0.83 % Allowed : 6.82 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.18 (0.06), residues: 18624 helix: 1.84 (0.05), residues: 9936 sheet: -0.32 (0.12), residues: 1900 loop : -0.43 (0.08), residues: 6788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B2773 HIS 0.009 0.001 HIS C3732 PHE 0.035 0.001 PHE B 985 TYR 0.024 0.001 TYR B2939 ARG 0.008 0.000 ARG C2835 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 997 time to evaluate : 12.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8451 (tp) cc_final: 0.8196 (tp) REVERT: A 893 TRP cc_start: 0.9002 (t-100) cc_final: 0.8411 (t-100) REVERT: A 1062 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: A 1501 ASN cc_start: 0.6441 (m110) cc_final: 0.6173 (m110) REVERT: A 2187 ILE cc_start: 0.8379 (mm) cc_final: 0.8060 (pp) REVERT: A 3074 ASN cc_start: 0.8194 (m110) cc_final: 0.7187 (m110) REVERT: A 3162 PHE cc_start: 0.8889 (t80) cc_final: 0.8571 (t80) REVERT: A 3200 ASN cc_start: 0.8428 (m-40) cc_final: 0.8054 (m-40) REVERT: A 3215 MET cc_start: 0.8403 (mmt) cc_final: 0.8201 (mmm) REVERT: A 3264 CYS cc_start: 0.7620 (m) cc_final: 0.6937 (m) REVERT: A 3315 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8799 (pp) REVERT: A 3348 MET cc_start: 0.3208 (pmm) cc_final: 0.2312 (pmm) REVERT: A 3359 PHE cc_start: 0.8831 (m-80) cc_final: 0.8305 (m-80) REVERT: A 3398 MET cc_start: 0.8354 (mtm) cc_final: 0.8094 (mtp) REVERT: A 3981 MET cc_start: 0.8536 (tmm) cc_final: 0.8188 (tmm) REVERT: A 4256 MET cc_start: 0.7802 (mtp) cc_final: 0.7497 (mtt) REVERT: A 4567 TYR cc_start: 0.6731 (p90) cc_final: 0.6061 (p90) REVERT: A 4804 MET cc_start: 0.8790 (mmm) cc_final: 0.8581 (mmm) REVERT: E 6 GLU cc_start: 0.8010 (mp0) cc_final: 0.7446 (mp0) REVERT: F 6 GLU cc_start: 0.8049 (mp0) cc_final: 0.7563 (mp0) REVERT: G 3 VAL cc_start: 0.7702 (OUTLIER) cc_final: 0.7436 (t) REVERT: H 6 GLU cc_start: 0.7962 (mp0) cc_final: 0.7279 (mp0) REVERT: I 1 MET cc_start: 0.7174 (ptp) cc_final: 0.6742 (tpt) REVERT: K 50 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: K 70 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7594 (tp) REVERT: B 981 MET cc_start: 0.7407 (ppp) cc_final: 0.6788 (mpp) REVERT: B 1501 ASN cc_start: 0.6590 (m110) cc_final: 0.6300 (m110) REVERT: B 2187 ILE cc_start: 0.8383 (mm) cc_final: 0.8063 (pp) REVERT: B 2688 MET cc_start: 0.5646 (pp-130) cc_final: 0.5146 (ppp) REVERT: B 2844 MET cc_start: 0.8345 (ppp) cc_final: 0.7525 (tmm) REVERT: B 2848 TYR cc_start: 0.7507 (m-10) cc_final: 0.7143 (m-10) REVERT: B 3074 ASN cc_start: 0.8198 (m110) cc_final: 0.7160 (m110) REVERT: B 3200 ASN cc_start: 0.8404 (m-40) cc_final: 0.8059 (m-40) REVERT: B 3264 CYS cc_start: 0.7689 (m) cc_final: 0.7036 (m) REVERT: B 3314 LEU cc_start: 0.7998 (tm) cc_final: 0.7791 (tp) REVERT: B 3315 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8893 (pp) REVERT: B 3348 MET cc_start: 0.3211 (pmm) cc_final: 0.2305 (pmm) REVERT: B 3359 PHE cc_start: 0.8837 (m-80) cc_final: 0.8359 (m-80) REVERT: B 3398 MET cc_start: 0.8352 (mtt) cc_final: 0.8101 (mtp) REVERT: B 3981 MET cc_start: 0.8548 (tmm) cc_final: 0.8239 (tmm) REVERT: B 4256 MET cc_start: 0.7785 (mtp) cc_final: 0.7476 (mtt) REVERT: C 78 LEU cc_start: 0.8468 (tp) cc_final: 0.8213 (tp) REVERT: C 893 TRP cc_start: 0.8954 (t-100) cc_final: 0.8372 (t-100) REVERT: C 1062 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: C 1300 MET cc_start: 0.8136 (mmp) cc_final: 0.7699 (mmt) REVERT: C 1501 ASN cc_start: 0.6515 (m110) cc_final: 0.6243 (m110) REVERT: C 2187 ILE cc_start: 0.8380 (mm) cc_final: 0.8065 (pp) REVERT: C 2689 MET cc_start: 0.6973 (tmm) cc_final: 0.6722 (tmt) REVERT: C 2734 MET cc_start: 0.8376 (mmm) cc_final: 0.8147 (mmm) REVERT: C 3074 ASN cc_start: 0.8204 (m110) cc_final: 0.7171 (m110) REVERT: C 3162 PHE cc_start: 0.8898 (t80) cc_final: 0.8550 (t80) REVERT: C 3200 ASN cc_start: 0.8392 (m-40) cc_final: 0.8027 (m-40) REVERT: C 3215 MET cc_start: 0.8438 (mmt) cc_final: 0.8235 (mmm) REVERT: C 3264 CYS cc_start: 0.7651 (m) cc_final: 0.6988 (m) REVERT: C 3315 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8836 (pp) REVERT: C 3348 MET cc_start: 0.3196 (pmm) cc_final: 0.2310 (pmm) REVERT: C 3359 PHE cc_start: 0.8828 (m-80) cc_final: 0.8320 (m-80) REVERT: C 3398 MET cc_start: 0.8332 (mtm) cc_final: 0.8083 (mtp) REVERT: C 3981 MET cc_start: 0.8552 (tmm) cc_final: 0.8250 (tmm) REVERT: C 4256 MET cc_start: 0.7802 (mtp) cc_final: 0.7537 (mtt) REVERT: C 4567 TYR cc_start: 0.6711 (p90) cc_final: 0.6020 (p90) REVERT: D 78 LEU cc_start: 0.8429 (tp) cc_final: 0.8192 (tp) REVERT: D 893 TRP cc_start: 0.9004 (t-100) cc_final: 0.8428 (t-100) REVERT: D 1062 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: D 1501 ASN cc_start: 0.6547 (m110) cc_final: 0.6284 (m110) REVERT: D 2187 ILE cc_start: 0.8381 (mm) cc_final: 0.8067 (pp) REVERT: D 2734 MET cc_start: 0.8357 (mmm) cc_final: 0.8143 (mmm) REVERT: D 3074 ASN cc_start: 0.8198 (m110) cc_final: 0.7199 (m110) REVERT: D 3162 PHE cc_start: 0.8886 (t80) cc_final: 0.8570 (t80) REVERT: D 3200 ASN cc_start: 0.8405 (m-40) cc_final: 0.8041 (m-40) REVERT: D 3215 MET cc_start: 0.8421 (mmt) cc_final: 0.8217 (mmm) REVERT: D 3264 CYS cc_start: 0.7663 (m) cc_final: 0.6981 (m) REVERT: D 3315 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8871 (pp) REVERT: D 3348 MET cc_start: 0.3237 (pmm) cc_final: 0.2317 (pmm) REVERT: D 3359 PHE cc_start: 0.8821 (m-80) cc_final: 0.8318 (m-80) REVERT: D 3398 MET cc_start: 0.8333 (mtm) cc_final: 0.8078 (mtp) REVERT: D 3981 MET cc_start: 0.8550 (tmm) cc_final: 0.8201 (tmm) REVERT: D 4256 MET cc_start: 0.7788 (mtp) cc_final: 0.7488 (mtt) REVERT: D 4567 TYR cc_start: 0.6702 (p90) cc_final: 0.5963 (p90) outliers start: 128 outliers final: 39 residues processed: 1039 average time/residue: 2.1888 time to fit residues: 3334.3827 Evaluate side-chains 1021 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 972 time to evaluate : 12.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1062 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3024 ASN Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3439 MET Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain B residue 1249 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2448 ASP Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain C residue 1062 TYR Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3024 ASN Chi-restraints excluded: chain C residue 3315 LEU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3024 ASN Chi-restraints excluded: chain D residue 3315 LEU Chi-restraints excluded: chain D residue 3525 ARG Chi-restraints excluded: chain D residue 3739 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1682 optimal weight: 7.9990 chunk 1280 optimal weight: 10.0000 chunk 883 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 812 optimal weight: 9.9990 chunk 1143 optimal weight: 7.9990 chunk 1709 optimal weight: 9.9990 chunk 1809 optimal weight: 10.0000 chunk 892 optimal weight: 0.4980 chunk 1619 optimal weight: 3.9990 chunk 487 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 ASN ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4178 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3095 ASN ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3095 ASN ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4178 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 153444 Z= 0.367 Angle : 0.623 13.087 207256 Z= 0.315 Chirality : 0.042 0.250 22756 Planarity : 0.004 0.060 26676 Dihedral : 5.878 83.046 20576 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 0.87 % Allowed : 7.72 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.15 (0.06), residues: 18624 helix: 1.83 (0.05), residues: 9948 sheet: -0.35 (0.12), residues: 1900 loop : -0.46 (0.08), residues: 6776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C2773 HIS 0.010 0.001 HIS A3732 PHE 0.046 0.002 PHE K 13 TYR 0.025 0.002 TYR D2956 ARG 0.010 0.000 ARG C2835 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 996 time to evaluate : 12.684 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 78 LEU cc_start: 0.8422 (tp) cc_final: 0.8218 (tp) REVERT: A 844 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6734 (mtm-85) REVERT: A 981 MET cc_start: 0.6424 (mpt) cc_final: 0.5919 (mpp) REVERT: A 1062 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: A 1300 MET cc_start: 0.8119 (mmp) cc_final: 0.7660 (mmt) REVERT: A 1501 ASN cc_start: 0.6507 (m110) cc_final: 0.6232 (m110) REVERT: A 2187 ILE cc_start: 0.8374 (mm) cc_final: 0.8062 (pp) REVERT: A 2688 MET cc_start: 0.5806 (pp-130) cc_final: 0.5287 (ppp) REVERT: A 2734 MET cc_start: 0.8415 (mmm) cc_final: 0.8153 (mmm) REVERT: A 2844 MET cc_start: 0.8345 (ppp) cc_final: 0.7640 (tmm) REVERT: A 2848 TYR cc_start: 0.7486 (m-10) cc_final: 0.7182 (m-10) REVERT: A 3072 MET cc_start: 0.8520 (tpp) cc_final: 0.8278 (tpt) REVERT: A 3074 ASN cc_start: 0.7565 (m110) cc_final: 0.7357 (m110) REVERT: A 3130 CYS cc_start: 0.8380 (m) cc_final: 0.7583 (m) REVERT: A 3162 PHE cc_start: 0.8910 (t80) cc_final: 0.8616 (t80) REVERT: A 3200 ASN cc_start: 0.8443 (m-40) cc_final: 0.8082 (m-40) REVERT: A 3215 MET cc_start: 0.8433 (mmt) cc_final: 0.8179 (mmm) REVERT: A 3264 CYS cc_start: 0.7673 (m) cc_final: 0.7061 (m) REVERT: A 3283 ILE cc_start: 0.8869 (tt) cc_final: 0.8585 (pt) REVERT: A 3315 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8892 (pp) REVERT: A 3348 MET cc_start: 0.3238 (pmm) cc_final: 0.2312 (pmm) REVERT: A 3359 PHE cc_start: 0.8810 (m-80) cc_final: 0.8325 (m-80) REVERT: A 3398 MET cc_start: 0.8363 (mtm) cc_final: 0.8114 (mtp) REVERT: A 4256 MET cc_start: 0.7805 (mtp) cc_final: 0.7496 (mtt) REVERT: A 4567 TYR cc_start: 0.6741 (p90) cc_final: 0.6043 (p90) REVERT: A 4804 MET cc_start: 0.8785 (mmm) cc_final: 0.8568 (mmm) REVERT: F 6 GLU cc_start: 0.7887 (mp0) cc_final: 0.7367 (mp0) REVERT: F 30 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7188 (mtm) REVERT: G 3 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7513 (t) REVERT: I 1 MET cc_start: 0.7193 (ptp) cc_final: 0.6738 (tpt) REVERT: I 72 MET cc_start: 0.8050 (ptp) cc_final: 0.7675 (ptm) REVERT: I 110 MET cc_start: 0.3915 (tpt) cc_final: 0.3343 (tpt) REVERT: K 50 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: L 110 MET cc_start: 0.5866 (tpt) cc_final: 0.5247 (tpp) REVERT: B 349 MET cc_start: 0.8718 (tpt) cc_final: 0.8511 (tpp) REVERT: B 844 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6756 (mtm-85) REVERT: B 893 TRP cc_start: 0.9035 (t-100) cc_final: 0.8421 (t-100) REVERT: B 981 MET cc_start: 0.7746 (ppp) cc_final: 0.6875 (mpp) REVERT: B 1501 ASN cc_start: 0.6561 (m110) cc_final: 0.6283 (m110) REVERT: B 1721 MET cc_start: 0.7822 (tpp) cc_final: 0.7516 (mmp) REVERT: B 1896 MET cc_start: 0.7895 (ttt) cc_final: 0.7682 (ttp) REVERT: B 2187 ILE cc_start: 0.8385 (mm) cc_final: 0.8071 (pp) REVERT: B 2688 MET cc_start: 0.5841 (pp-130) cc_final: 0.5355 (ppp) REVERT: B 2734 MET cc_start: 0.8393 (mmm) cc_final: 0.8128 (mmm) REVERT: B 2844 MET cc_start: 0.8345 (ppp) cc_final: 0.7474 (tmm) REVERT: B 2848 TYR cc_start: 0.7569 (m-10) cc_final: 0.7280 (m-10) REVERT: B 2890 GLN cc_start: 0.8845 (mm110) cc_final: 0.8622 (mp10) REVERT: B 3074 ASN cc_start: 0.7616 (m110) cc_final: 0.7412 (m110) REVERT: B 3130 CYS cc_start: 0.8345 (m) cc_final: 0.7561 (m) REVERT: B 3162 PHE cc_start: 0.8929 (t80) cc_final: 0.8634 (t80) REVERT: B 3200 ASN cc_start: 0.8425 (m-40) cc_final: 0.8096 (m-40) REVERT: B 3231 MET cc_start: 0.6582 (tmt) cc_final: 0.6372 (tmt) REVERT: B 3246 MET cc_start: 0.8994 (mtm) cc_final: 0.8764 (mtm) REVERT: B 3264 CYS cc_start: 0.7661 (m) cc_final: 0.6980 (m) REVERT: B 3273 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8396 (mtp) REVERT: B 3315 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8868 (pp) REVERT: B 3323 MET cc_start: 0.7225 (mpp) cc_final: 0.6840 (mpp) REVERT: B 3348 MET cc_start: 0.3233 (pmm) cc_final: 0.2301 (pmm) REVERT: B 3359 PHE cc_start: 0.8831 (m-80) cc_final: 0.8332 (m-80) REVERT: B 3398 MET cc_start: 0.8366 (mtm) cc_final: 0.7996 (mtp) REVERT: B 4256 MET cc_start: 0.7801 (mtp) cc_final: 0.7482 (mtt) REVERT: C 78 LEU cc_start: 0.8436 (tp) cc_final: 0.8234 (tp) REVERT: C 678 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7312 (ttp) REVERT: C 844 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6786 (mtm-85) REVERT: C 981 MET cc_start: 0.6093 (mpp) cc_final: 0.5757 (mpp) REVERT: C 1062 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: C 1300 MET cc_start: 0.8152 (mmp) cc_final: 0.7719 (mmt) REVERT: C 1501 ASN cc_start: 0.6589 (m110) cc_final: 0.6276 (m110) REVERT: C 2187 ILE cc_start: 0.8359 (mm) cc_final: 0.8035 (pp) REVERT: C 2688 MET cc_start: 0.5771 (pp-130) cc_final: 0.5451 (ppp) REVERT: C 2734 MET cc_start: 0.8409 (mmm) cc_final: 0.8155 (mmm) REVERT: C 2844 MET cc_start: 0.8373 (ppp) cc_final: 0.7616 (tmm) REVERT: C 2848 TYR cc_start: 0.7506 (m-10) cc_final: 0.7216 (m-10) REVERT: C 3074 ASN cc_start: 0.7558 (m110) cc_final: 0.7358 (m110) REVERT: C 3130 CYS cc_start: 0.8380 (m) cc_final: 0.7613 (m) REVERT: C 3162 PHE cc_start: 0.8911 (t80) cc_final: 0.8611 (t80) REVERT: C 3200 ASN cc_start: 0.8443 (m-40) cc_final: 0.8085 (m-40) REVERT: C 3264 CYS cc_start: 0.7653 (m) cc_final: 0.7025 (m) REVERT: C 3283 ILE cc_start: 0.8777 (tt) cc_final: 0.8522 (pt) REVERT: C 3315 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8896 (pp) REVERT: C 3348 MET cc_start: 0.3194 (pmm) cc_final: 0.2300 (pmm) REVERT: C 3359 PHE cc_start: 0.8820 (m-80) cc_final: 0.8363 (m-80) REVERT: C 3398 MET cc_start: 0.8340 (mtm) cc_final: 0.8078 (mtp) REVERT: C 4256 MET cc_start: 0.7817 (mtp) cc_final: 0.7541 (mtt) REVERT: C 4567 TYR cc_start: 0.6755 (p90) cc_final: 0.5990 (p90) REVERT: D 844 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6769 (mtm-85) REVERT: D 981 MET cc_start: 0.6088 (mpp) cc_final: 0.5775 (mpp) REVERT: D 1062 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: D 1300 MET cc_start: 0.8177 (mmp) cc_final: 0.7744 (mmt) REVERT: D 1501 ASN cc_start: 0.6566 (m110) cc_final: 0.6260 (m110) REVERT: D 2187 ILE cc_start: 0.8366 (mm) cc_final: 0.8041 (pp) REVERT: D 2688 MET cc_start: 0.5784 (pp-130) cc_final: 0.5361 (ppp) REVERT: D 2844 MET cc_start: 0.8369 (ppp) cc_final: 0.7643 (tmm) REVERT: D 2848 TYR cc_start: 0.7498 (m-10) cc_final: 0.7204 (m-10) REVERT: D 3072 MET cc_start: 0.8507 (tpp) cc_final: 0.8284 (tpt) REVERT: D 3074 ASN cc_start: 0.7595 (m110) cc_final: 0.7382 (m110) REVERT: D 3162 PHE cc_start: 0.8913 (t80) cc_final: 0.8595 (t80) REVERT: D 3200 ASN cc_start: 0.8442 (m-40) cc_final: 0.8080 (m-40) REVERT: D 3250 TRP cc_start: 0.8555 (t-100) cc_final: 0.8353 (t-100) REVERT: D 3264 CYS cc_start: 0.7682 (m) cc_final: 0.7033 (m) REVERT: D 3348 MET cc_start: 0.3136 (pmm) cc_final: 0.2205 (pmm) REVERT: D 3359 PHE cc_start: 0.8810 (m-80) cc_final: 0.8347 (m-80) REVERT: D 3398 MET cc_start: 0.8349 (mtm) cc_final: 0.8107 (mtp) REVERT: D 4256 MET cc_start: 0.7806 (mtp) cc_final: 0.7531 (mtt) REVERT: D 4567 TYR cc_start: 0.6731 (p90) cc_final: 0.6006 (p90) outliers start: 135 outliers final: 56 residues processed: 1036 average time/residue: 2.1528 time to fit residues: 3261.1926 Evaluate side-chains 1049 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 978 time to evaluate : 12.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1062 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 3024 ASN Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3439 MET Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 1249 MET Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2448 ASP Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3024 ASN Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain B residue 3978 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 844 ARG Chi-restraints excluded: chain C residue 1062 TYR Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3024 ASN Chi-restraints excluded: chain C residue 3315 LEU Chi-restraints excluded: chain C residue 3653 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 844 ARG Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3024 ASN Chi-restraints excluded: chain D residue 3439 MET Chi-restraints excluded: chain D residue 3525 ARG Chi-restraints excluded: chain D residue 3653 GLU Chi-restraints excluded: chain D residue 3739 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1507 optimal weight: 7.9990 chunk 1027 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 1347 optimal weight: 1.9990 chunk 746 optimal weight: 2.9990 chunk 1544 optimal weight: 0.9990 chunk 1250 optimal weight: 40.0000 chunk 2 optimal weight: 9.9990 chunk 923 optimal weight: 3.9990 chunk 1624 optimal weight: 0.9990 chunk 456 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 ASN ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN I 42 GLN J 9 GLN B 79 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3318 HIS B3955 GLN B3975 GLN C 79 GLN ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 ASN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3095 ASN ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 153444 Z= 0.164 Angle : 0.572 15.345 207256 Z= 0.289 Chirality : 0.040 0.196 22756 Planarity : 0.004 0.072 26676 Dihedral : 5.610 88.307 20576 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.67 % Favored : 96.18 % Rotamer: Outliers : 0.71 % Allowed : 8.63 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.06), residues: 18624 helix: 1.96 (0.05), residues: 9920 sheet: -0.29 (0.12), residues: 1892 loop : -0.35 (0.08), residues: 6812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D2773 HIS 0.009 0.001 HIS B3732 PHE 0.036 0.001 PHE B4048 TYR 0.023 0.001 TYR I 139 ARG 0.011 0.000 ARG B2835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1001 time to evaluate : 13.145 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 893 TRP cc_start: 0.9031 (t-100) cc_final: 0.8283 (t-100) REVERT: A 1062 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: A 1501 ASN cc_start: 0.6403 (m110) cc_final: 0.6141 (m110) REVERT: A 2175 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8456 (ttm) REVERT: A 2187 ILE cc_start: 0.8384 (mm) cc_final: 0.8057 (pp) REVERT: A 2688 MET cc_start: 0.5779 (pp-130) cc_final: 0.5293 (ppp) REVERT: A 2734 MET cc_start: 0.8406 (mmm) cc_final: 0.8153 (mmm) REVERT: A 2844 MET cc_start: 0.8300 (ppp) cc_final: 0.7567 (tmm) REVERT: A 2848 TYR cc_start: 0.7469 (m-10) cc_final: 0.7206 (m-10) REVERT: A 3072 MET cc_start: 0.8517 (tpp) cc_final: 0.8250 (tpt) REVERT: A 3074 ASN cc_start: 0.7603 (m110) cc_final: 0.7384 (m110) REVERT: A 3162 PHE cc_start: 0.8834 (t80) cc_final: 0.8526 (t80) REVERT: A 3200 ASN cc_start: 0.8436 (m-40) cc_final: 0.8074 (m-40) REVERT: A 3231 MET cc_start: 0.6139 (tmt) cc_final: 0.5886 (tmm) REVERT: A 3250 TRP cc_start: 0.8524 (t-100) cc_final: 0.8322 (t-100) REVERT: A 3264 CYS cc_start: 0.7774 (m) cc_final: 0.7151 (m) REVERT: A 3283 ILE cc_start: 0.8693 (tt) cc_final: 0.8478 (pt) REVERT: A 3348 MET cc_start: 0.3130 (pmm) cc_final: 0.2185 (pmm) REVERT: A 3359 PHE cc_start: 0.8808 (m-80) cc_final: 0.8352 (m-80) REVERT: A 3398 MET cc_start: 0.8332 (mtm) cc_final: 0.8043 (mtp) REVERT: A 3981 MET cc_start: 0.8552 (tmm) cc_final: 0.8196 (tmm) REVERT: A 4256 MET cc_start: 0.7790 (mtp) cc_final: 0.7471 (mtt) REVERT: A 4567 TYR cc_start: 0.6637 (p90) cc_final: 0.5923 (p90) REVERT: G 3 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7449 (t) REVERT: H 19 LYS cc_start: 0.8531 (mmpt) cc_final: 0.8283 (mmmt) REVERT: I 1 MET cc_start: 0.7043 (ptp) cc_final: 0.6672 (tpt) REVERT: I 73 MET cc_start: 0.6194 (mpp) cc_final: 0.5125 (mpp) REVERT: I 110 MET cc_start: 0.3522 (tpt) cc_final: 0.3279 (tpt) REVERT: J 9 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8018 (pp30) REVERT: K 37 MET cc_start: 0.6902 (pmm) cc_final: 0.6688 (pmm) REVERT: K 50 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7289 (tp-100) REVERT: L 1 MET cc_start: 0.7319 (ttm) cc_final: 0.6946 (tpt) REVERT: L 110 MET cc_start: 0.5808 (tpt) cc_final: 0.5519 (tpp) REVERT: B 349 MET cc_start: 0.8692 (tpt) cc_final: 0.8484 (tpp) REVERT: B 1501 ASN cc_start: 0.6426 (m110) cc_final: 0.6147 (m110) REVERT: B 2187 ILE cc_start: 0.8380 (mm) cc_final: 0.8034 (pp) REVERT: B 2688 MET cc_start: 0.5764 (pp-130) cc_final: 0.5206 (ppp) REVERT: B 2734 MET cc_start: 0.8393 (mmm) cc_final: 0.8137 (mmm) REVERT: B 2844 MET cc_start: 0.8311 (ppp) cc_final: 0.7449 (tmm) REVERT: B 2848 TYR cc_start: 0.7614 (m-10) cc_final: 0.7355 (m-10) REVERT: B 2890 GLN cc_start: 0.8813 (mm110) cc_final: 0.8578 (mp10) REVERT: B 3074 ASN cc_start: 0.7669 (m110) cc_final: 0.7436 (m110) REVERT: B 3162 PHE cc_start: 0.8880 (t80) cc_final: 0.8551 (t80) REVERT: B 3200 ASN cc_start: 0.8402 (m-40) cc_final: 0.8072 (m-40) REVERT: B 3264 CYS cc_start: 0.7612 (m) cc_final: 0.6989 (m) REVERT: B 3273 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8366 (mtp) REVERT: B 3323 MET cc_start: 0.7110 (mpp) cc_final: 0.6882 (mpp) REVERT: B 3348 MET cc_start: 0.3131 (pmm) cc_final: 0.2176 (pmm) REVERT: B 3359 PHE cc_start: 0.8809 (m-80) cc_final: 0.8360 (m-80) REVERT: B 3398 MET cc_start: 0.8347 (mtm) cc_final: 0.8070 (mtp) REVERT: B 3981 MET cc_start: 0.8545 (tmm) cc_final: 0.8272 (tmm) REVERT: B 4109 MET cc_start: 0.8351 (mtp) cc_final: 0.7931 (mtp) REVERT: B 4256 MET cc_start: 0.7774 (mtp) cc_final: 0.7449 (mtt) REVERT: B 4274 MET cc_start: 0.6542 (pp-130) cc_final: 0.6219 (pp-130) REVERT: B 4567 TYR cc_start: 0.6635 (p90) cc_final: 0.5910 (p90) REVERT: C 78 LEU cc_start: 0.8408 (tp) cc_final: 0.8207 (tp) REVERT: C 349 MET cc_start: 0.8705 (tpt) cc_final: 0.8439 (tpp) REVERT: C 1501 ASN cc_start: 0.6450 (m110) cc_final: 0.6180 (m110) REVERT: C 2187 ILE cc_start: 0.8371 (mm) cc_final: 0.8037 (pp) REVERT: C 2688 MET cc_start: 0.5788 (pp-130) cc_final: 0.5385 (ppp) REVERT: C 2689 MET cc_start: 0.6959 (tmm) cc_final: 0.6458 (tmt) REVERT: C 2734 MET cc_start: 0.8377 (mmm) cc_final: 0.8150 (mmm) REVERT: C 2844 MET cc_start: 0.8317 (ppp) cc_final: 0.7563 (tmm) REVERT: C 2848 TYR cc_start: 0.7466 (m-10) cc_final: 0.7158 (m-10) REVERT: C 3074 ASN cc_start: 0.7635 (m110) cc_final: 0.7394 (m110) REVERT: C 3162 PHE cc_start: 0.8850 (t80) cc_final: 0.8535 (t80) REVERT: C 3200 ASN cc_start: 0.8409 (m-40) cc_final: 0.8057 (m-40) REVERT: C 3323 MET cc_start: 0.7368 (mmt) cc_final: 0.7107 (mmt) REVERT: C 3348 MET cc_start: 0.3088 (pmm) cc_final: 0.2190 (pmm) REVERT: C 3359 PHE cc_start: 0.8795 (m-80) cc_final: 0.8350 (m-80) REVERT: C 3398 MET cc_start: 0.8325 (mtm) cc_final: 0.7937 (mtp) REVERT: C 3981 MET cc_start: 0.8547 (tmm) cc_final: 0.8270 (tmm) REVERT: C 4256 MET cc_start: 0.7812 (mtp) cc_final: 0.7530 (mtt) REVERT: C 4567 TYR cc_start: 0.6648 (p90) cc_final: 0.5924 (p90) REVERT: D 349 MET cc_start: 0.8701 (tpt) cc_final: 0.8435 (tpp) REVERT: D 893 TRP cc_start: 0.9043 (t-100) cc_final: 0.8300 (t-100) REVERT: D 1300 MET cc_start: 0.8165 (mmp) cc_final: 0.7721 (mmt) REVERT: D 1501 ASN cc_start: 0.6381 (m110) cc_final: 0.6113 (m110) REVERT: D 2162 MET cc_start: 0.8697 (mmt) cc_final: 0.8254 (mmp) REVERT: D 2187 ILE cc_start: 0.8379 (mm) cc_final: 0.8038 (pp) REVERT: D 2688 MET cc_start: 0.5758 (pp-130) cc_final: 0.5405 (ppp) REVERT: D 2844 MET cc_start: 0.8334 (ppp) cc_final: 0.7595 (tmm) REVERT: D 2848 TYR cc_start: 0.7481 (m-10) cc_final: 0.7168 (m-10) REVERT: D 3072 MET cc_start: 0.8498 (tpp) cc_final: 0.8253 (tpt) REVERT: D 3074 ASN cc_start: 0.7614 (m110) cc_final: 0.7401 (m110) REVERT: D 3162 PHE cc_start: 0.8838 (t80) cc_final: 0.8532 (t80) REVERT: D 3200 ASN cc_start: 0.8442 (m-40) cc_final: 0.8078 (m-40) REVERT: D 3264 CYS cc_start: 0.7612 (m) cc_final: 0.6995 (m) REVERT: D 3348 MET cc_start: 0.3106 (pmm) cc_final: 0.2154 (pmm) REVERT: D 3359 PHE cc_start: 0.8779 (m-80) cc_final: 0.8350 (m-80) REVERT: D 3398 MET cc_start: 0.8325 (mtm) cc_final: 0.8040 (mtp) REVERT: D 3978 MET cc_start: 0.8943 (ttp) cc_final: 0.8726 (ttt) REVERT: D 3981 MET cc_start: 0.8567 (tmm) cc_final: 0.8198 (tmm) REVERT: D 4256 MET cc_start: 0.7812 (mtp) cc_final: 0.7526 (mtt) REVERT: D 4567 TYR cc_start: 0.6638 (p90) cc_final: 0.5907 (p90) outliers start: 108 outliers final: 46 residues processed: 1039 average time/residue: 2.1314 time to fit residues: 3255.9052 Evaluate side-chains 1034 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 982 time to evaluate : 12.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 1062 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 3024 ASN Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 9 GLN Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 1249 MET Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 3024 ASN Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3024 ASN Chi-restraints excluded: chain C residue 3504 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3024 ASN Chi-restraints excluded: chain D residue 3525 ARG Chi-restraints excluded: chain D residue 3739 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 608 optimal weight: 9.9990 chunk 1629 optimal weight: 10.0000 chunk 357 optimal weight: 0.9990 chunk 1062 optimal weight: 8.9990 chunk 446 optimal weight: 2.9990 chunk 1811 optimal weight: 2.9990 chunk 1503 optimal weight: 1.9990 chunk 838 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 599 optimal weight: 0.9990 chunk 950 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 ASN B2838 HIS A B2838 HIS B B2890 GLN B3178 HIS B3274 ASN ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3095 ASN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 153444 Z= 0.196 Angle : 0.587 13.007 207256 Z= 0.292 Chirality : 0.040 0.217 22756 Planarity : 0.004 0.071 26676 Dihedral : 5.443 80.439 20576 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Rotamer: Outliers : 0.72 % Allowed : 9.25 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.35 (0.06), residues: 18624 helix: 1.98 (0.05), residues: 9932 sheet: -0.25 (0.12), residues: 1892 loop : -0.34 (0.08), residues: 6800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D2773 HIS 0.008 0.001 HIS A3732 PHE 0.046 0.001 PHE D4016 TYR 0.023 0.001 TYR D2956 ARG 0.007 0.000 ARG D2835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 990 time to evaluate : 11.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 893 TRP cc_start: 0.9020 (t-100) cc_final: 0.8282 (t-100) REVERT: A 981 MET cc_start: 0.6118 (mpp) cc_final: 0.5438 (mpp) REVERT: A 1062 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: A 1501 ASN cc_start: 0.6419 (m110) cc_final: 0.6149 (m110) REVERT: A 2187 ILE cc_start: 0.8377 (mm) cc_final: 0.8029 (pp) REVERT: A 2688 MET cc_start: 0.5798 (pp-130) cc_final: 0.5311 (ppp) REVERT: A 2734 MET cc_start: 0.8389 (mmm) cc_final: 0.8164 (mmm) REVERT: A 2844 MET cc_start: 0.8274 (ppp) cc_final: 0.7613 (tmm) REVERT: A 2848 TYR cc_start: 0.7511 (m-10) cc_final: 0.7293 (m-10) REVERT: A 3072 MET cc_start: 0.8512 (tpp) cc_final: 0.8245 (tpt) REVERT: A 3074 ASN cc_start: 0.7678 (m110) cc_final: 0.7454 (m110) REVERT: A 3162 PHE cc_start: 0.8851 (t80) cc_final: 0.8535 (t80) REVERT: A 3200 ASN cc_start: 0.8450 (m-40) cc_final: 0.8084 (m-40) REVERT: A 3250 TRP cc_start: 0.8503 (t-100) cc_final: 0.8269 (t-100) REVERT: A 3264 CYS cc_start: 0.7808 (m) cc_final: 0.7187 (m) REVERT: A 3348 MET cc_start: 0.3182 (pmm) cc_final: 0.2186 (pmm) REVERT: A 3359 PHE cc_start: 0.8795 (m-80) cc_final: 0.8351 (m-80) REVERT: A 3375 ARG cc_start: 0.8591 (tmt170) cc_final: 0.8049 (tmt170) REVERT: A 3398 MET cc_start: 0.8330 (mtm) cc_final: 0.7952 (mtp) REVERT: A 3981 MET cc_start: 0.8572 (tmm) cc_final: 0.8180 (tmm) REVERT: A 4256 MET cc_start: 0.7792 (mtp) cc_final: 0.7476 (mtt) REVERT: A 4567 TYR cc_start: 0.6645 (p90) cc_final: 0.5917 (p90) REVERT: G 19 LYS cc_start: 0.8581 (mmpt) cc_final: 0.8321 (mmmt) REVERT: I 1 MET cc_start: 0.7100 (ptp) cc_final: 0.6707 (tpt) REVERT: J 1 MET cc_start: 0.7645 (ttm) cc_final: 0.7396 (ttm) REVERT: L 1 MET cc_start: 0.7439 (ttm) cc_final: 0.7044 (tpt) REVERT: L 110 MET cc_start: 0.5818 (tpt) cc_final: 0.5523 (ttm) REVERT: B 349 MET cc_start: 0.8718 (tpt) cc_final: 0.8478 (tpp) REVERT: B 893 TRP cc_start: 0.9040 (t-100) cc_final: 0.8335 (t-100) REVERT: B 981 MET cc_start: 0.6822 (pp-130) cc_final: 0.5747 (pmm) REVERT: B 1501 ASN cc_start: 0.6367 (m110) cc_final: 0.6092 (m110) REVERT: B 2187 ILE cc_start: 0.8373 (mm) cc_final: 0.8028 (pp) REVERT: B 2688 MET cc_start: 0.5846 (pp-130) cc_final: 0.5365 (ppp) REVERT: B 2734 MET cc_start: 0.8360 (mmm) cc_final: 0.8151 (mmm) REVERT: B 2844 MET cc_start: 0.8276 (ppp) cc_final: 0.7456 (tmm) REVERT: B 2848 TYR cc_start: 0.7639 (m-10) cc_final: 0.7332 (m-10) REVERT: B 2890 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8550 (mp10) REVERT: B 3074 ASN cc_start: 0.7676 (m110) cc_final: 0.7450 (m110) REVERT: B 3162 PHE cc_start: 0.8877 (t80) cc_final: 0.8544 (t80) REVERT: B 3200 ASN cc_start: 0.8424 (m-40) cc_final: 0.8101 (m-40) REVERT: B 3235 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6985 (pmm) REVERT: B 3273 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: B 3315 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (pp) REVERT: B 3323 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6712 (mpp) REVERT: B 3348 MET cc_start: 0.3113 (pmm) cc_final: 0.2129 (pmm) REVERT: B 3359 PHE cc_start: 0.8808 (m-80) cc_final: 0.8363 (m-80) REVERT: B 3398 MET cc_start: 0.8344 (mtm) cc_final: 0.7954 (mtp) REVERT: B 3978 MET cc_start: 0.8943 (ttp) cc_final: 0.8738 (ttt) REVERT: B 4256 MET cc_start: 0.7794 (mtp) cc_final: 0.7464 (mtt) REVERT: B 4567 TYR cc_start: 0.6649 (p90) cc_final: 0.5910 (p90) REVERT: B 4660 PHE cc_start: 0.8187 (t80) cc_final: 0.7915 (t80) REVERT: C 1064 LEU cc_start: 0.8326 (tm) cc_final: 0.8081 (pt) REVERT: C 1501 ASN cc_start: 0.6392 (m110) cc_final: 0.6136 (m-40) REVERT: C 2187 ILE cc_start: 0.8373 (mm) cc_final: 0.8038 (pp) REVERT: C 2688 MET cc_start: 0.5846 (pp-130) cc_final: 0.5498 (ppp) REVERT: C 2689 MET cc_start: 0.6926 (tmm) cc_final: 0.6708 (tmt) REVERT: C 2734 MET cc_start: 0.8401 (mmm) cc_final: 0.8159 (mmm) REVERT: C 2844 MET cc_start: 0.8294 (ppp) cc_final: 0.7536 (tmm) REVERT: C 2848 TYR cc_start: 0.7491 (m-10) cc_final: 0.7175 (m-10) REVERT: C 3074 ASN cc_start: 0.7663 (m110) cc_final: 0.7443 (m110) REVERT: C 3162 PHE cc_start: 0.8853 (t80) cc_final: 0.8529 (t80) REVERT: C 3200 ASN cc_start: 0.8434 (m-40) cc_final: 0.8077 (m-40) REVERT: C 3228 TYR cc_start: 0.3709 (OUTLIER) cc_final: 0.3406 (m-80) REVERT: C 3235 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7119 (pp-130) REVERT: C 3323 MET cc_start: 0.7353 (mmt) cc_final: 0.6906 (mmt) REVERT: C 3348 MET cc_start: 0.3170 (pmm) cc_final: 0.2233 (pmm) REVERT: C 3359 PHE cc_start: 0.8782 (m-80) cc_final: 0.8343 (m-80) REVERT: C 3398 MET cc_start: 0.8315 (mtm) cc_final: 0.7921 (mtp) REVERT: C 3819 MET cc_start: 0.1483 (pmt) cc_final: 0.1077 (pmt) REVERT: C 4256 MET cc_start: 0.7825 (mtp) cc_final: 0.7541 (mtt) REVERT: C 4567 TYR cc_start: 0.6653 (p90) cc_final: 0.5925 (p90) REVERT: D 893 TRP cc_start: 0.9030 (t-100) cc_final: 0.8286 (t-100) REVERT: D 1300 MET cc_start: 0.8169 (mmp) cc_final: 0.7735 (mmt) REVERT: D 1501 ASN cc_start: 0.6469 (m110) cc_final: 0.6186 (m110) REVERT: D 2187 ILE cc_start: 0.8371 (mm) cc_final: 0.8033 (pp) REVERT: D 2688 MET cc_start: 0.5820 (pp-130) cc_final: 0.5434 (ppp) REVERT: D 2734 MET cc_start: 0.8398 (mmm) cc_final: 0.8073 (mmm) REVERT: D 2835 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7847 (mmm160) REVERT: D 2844 MET cc_start: 0.8300 (ppp) cc_final: 0.7245 (tmm) REVERT: D 2848 TYR cc_start: 0.7503 (m-10) cc_final: 0.7193 (m-10) REVERT: D 3072 MET cc_start: 0.8503 (tpp) cc_final: 0.8242 (tpt) REVERT: D 3074 ASN cc_start: 0.7671 (m110) cc_final: 0.7453 (m110) REVERT: D 3162 PHE cc_start: 0.8844 (t80) cc_final: 0.8527 (t80) REVERT: D 3200 ASN cc_start: 0.8443 (m-40) cc_final: 0.8085 (m-40) REVERT: D 3348 MET cc_start: 0.3072 (pmm) cc_final: 0.2104 (pmm) REVERT: D 3359 PHE cc_start: 0.8785 (m-80) cc_final: 0.8353 (m-80) REVERT: D 3375 ARG cc_start: 0.8590 (tmt170) cc_final: 0.8070 (tmt170) REVERT: D 3398 MET cc_start: 0.8319 (mtm) cc_final: 0.7947 (mtp) REVERT: D 3819 MET cc_start: 0.1340 (pmt) cc_final: 0.0928 (pmt) REVERT: D 3978 MET cc_start: 0.8941 (ttp) cc_final: 0.8670 (ttt) REVERT: D 3981 MET cc_start: 0.8590 (tmm) cc_final: 0.8203 (tmm) REVERT: D 4256 MET cc_start: 0.7813 (mtp) cc_final: 0.7527 (mtt) REVERT: D 4567 TYR cc_start: 0.6641 (p90) cc_final: 0.5907 (p90) outliers start: 111 outliers final: 54 residues processed: 1032 average time/residue: 2.1150 time to fit residues: 3189.3160 Evaluate side-chains 1033 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 972 time to evaluate : 12.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 1062 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3504 GLU Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 9 GLN Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 1249 MET Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2448 ASP Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3024 ASN Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain B residue 3323 MET Chi-restraints excluded: chain B residue 3504 GLU Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3228 TYR Chi-restraints excluded: chain C residue 3235 MET Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3504 GLU Chi-restraints excluded: chain D residue 3525 ARG Chi-restraints excluded: chain D residue 3739 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1746 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 1031 optimal weight: 9.9990 chunk 1322 optimal weight: 2.9990 chunk 1024 optimal weight: 1.9990 chunk 1524 optimal weight: 9.9990 chunk 1011 optimal weight: 5.9990 chunk 1804 optimal weight: 0.9980 chunk 1129 optimal weight: 0.8980 chunk 1100 optimal weight: 0.9990 chunk 833 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 ASN ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4267 GLN L 9 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4267 GLN ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 HIS ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4049 HIS ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 934 GLN D3095 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4049 HIS ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4267 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 153444 Z= 0.176 Angle : 0.588 16.217 207256 Z= 0.291 Chirality : 0.040 0.200 22756 Planarity : 0.004 0.068 26676 Dihedral : 5.299 74.090 20576 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.77 % Favored : 96.08 % Rotamer: Outliers : 0.64 % Allowed : 9.55 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.41 (0.06), residues: 18624 helix: 2.03 (0.05), residues: 9920 sheet: -0.22 (0.12), residues: 1892 loop : -0.31 (0.08), residues: 6812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D3295 HIS 0.008 0.001 HIS A3732 PHE 0.038 0.001 PHE B4016 TYR 0.021 0.001 TYR K 139 ARG 0.012 0.000 ARG A2835 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 987 time to evaluate : 12.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 893 TRP cc_start: 0.9016 (t-100) cc_final: 0.8254 (t-100) REVERT: A 1501 ASN cc_start: 0.6430 (m110) cc_final: 0.6165 (m110) REVERT: A 2187 ILE cc_start: 0.8359 (mm) cc_final: 0.8012 (pp) REVERT: A 2688 MET cc_start: 0.5817 (pp-130) cc_final: 0.5357 (ppp) REVERT: A 2844 MET cc_start: 0.8249 (ppp) cc_final: 0.7577 (tmm) REVERT: A 2848 TYR cc_start: 0.7531 (m-10) cc_final: 0.7280 (m-10) REVERT: A 3072 MET cc_start: 0.8521 (tpp) cc_final: 0.8239 (tpt) REVERT: A 3074 ASN cc_start: 0.7632 (m110) cc_final: 0.7400 (m110) REVERT: A 3162 PHE cc_start: 0.8830 (t80) cc_final: 0.8507 (t80) REVERT: A 3200 ASN cc_start: 0.8442 (m-40) cc_final: 0.8082 (m-40) REVERT: A 3264 CYS cc_start: 0.7826 (m) cc_final: 0.7226 (m) REVERT: A 3314 LEU cc_start: 0.7891 (tm) cc_final: 0.7689 (tp) REVERT: A 3323 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6489 (mpp) REVERT: A 3348 MET cc_start: 0.3141 (pmm) cc_final: 0.2153 (pmm) REVERT: A 3359 PHE cc_start: 0.8802 (m-80) cc_final: 0.8327 (m-80) REVERT: A 3398 MET cc_start: 0.8334 (mtm) cc_final: 0.7919 (ttp) REVERT: A 3819 MET cc_start: 0.1295 (pmt) cc_final: 0.0878 (pmt) REVERT: A 4256 MET cc_start: 0.7784 (mtp) cc_final: 0.7464 (mtt) REVERT: A 4567 TYR cc_start: 0.6654 (p90) cc_final: 0.5908 (p90) REVERT: E 4 GLU cc_start: 0.7146 (pp20) cc_final: 0.6907 (pp20) REVERT: E 19 LYS cc_start: 0.8596 (mmpt) cc_final: 0.8359 (mmmt) REVERT: F 108 GLU cc_start: 0.7545 (mp0) cc_final: 0.7265 (mt-10) REVERT: J 1 MET cc_start: 0.7555 (ttm) cc_final: 0.7350 (ttm) REVERT: K 50 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7146 (tp-100) REVERT: K 110 MET cc_start: 0.4732 (tpt) cc_final: 0.4509 (tpt) REVERT: L 1 MET cc_start: 0.7330 (ttm) cc_final: 0.6990 (tpt) REVERT: L 110 MET cc_start: 0.5737 (tpt) cc_final: 0.5489 (ttm) REVERT: B 893 TRP cc_start: 0.9028 (t-100) cc_final: 0.8314 (t-100) REVERT: B 964 MET cc_start: 0.1327 (mpt) cc_final: 0.0651 (mmt) REVERT: B 981 MET cc_start: 0.6857 (pp-130) cc_final: 0.5754 (ptt) REVERT: B 1501 ASN cc_start: 0.6326 (m110) cc_final: 0.6060 (m110) REVERT: B 2187 ILE cc_start: 0.8364 (mm) cc_final: 0.8021 (pp) REVERT: B 2688 MET cc_start: 0.5941 (pp-130) cc_final: 0.5495 (ppp) REVERT: B 2844 MET cc_start: 0.8240 (ppp) cc_final: 0.7428 (tmm) REVERT: B 2848 TYR cc_start: 0.7647 (m-10) cc_final: 0.7342 (m-10) REVERT: B 3074 ASN cc_start: 0.7692 (m110) cc_final: 0.7474 (m110) REVERT: B 3162 PHE cc_start: 0.8861 (t80) cc_final: 0.8530 (t80) REVERT: B 3200 ASN cc_start: 0.8428 (m-40) cc_final: 0.8100 (m-40) REVERT: B 3231 MET cc_start: 0.6469 (tmm) cc_final: 0.6054 (tmm) REVERT: B 3273 MET cc_start: 0.8802 (ttm) cc_final: 0.8377 (mtp) REVERT: B 3314 LEU cc_start: 0.7906 (tm) cc_final: 0.7691 (tp) REVERT: B 3315 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8884 (pp) REVERT: B 3323 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6258 (mpp) REVERT: B 3348 MET cc_start: 0.3149 (pmm) cc_final: 0.2150 (pmm) REVERT: B 3359 PHE cc_start: 0.8782 (m-80) cc_final: 0.8376 (m-80) REVERT: B 3375 ARG cc_start: 0.8571 (tmt170) cc_final: 0.7997 (tmt170) REVERT: B 3398 MET cc_start: 0.8352 (mtm) cc_final: 0.7956 (mtp) REVERT: B 3819 MET cc_start: 0.1148 (pmt) cc_final: 0.0761 (pmt) REVERT: B 3978 MET cc_start: 0.8952 (ttp) cc_final: 0.8716 (ttt) REVERT: B 3981 MET cc_start: 0.8587 (tmm) cc_final: 0.8243 (tmm) REVERT: B 4256 MET cc_start: 0.7809 (mtp) cc_final: 0.7482 (mtt) REVERT: B 4274 MET cc_start: 0.6368 (pp-130) cc_final: 0.6167 (pp-130) REVERT: B 4567 TYR cc_start: 0.6649 (p90) cc_final: 0.5896 (p90) REVERT: B 4660 PHE cc_start: 0.8203 (t80) cc_final: 0.7993 (t80) REVERT: C 1300 MET cc_start: 0.8163 (mmp) cc_final: 0.7723 (mmt) REVERT: C 1501 ASN cc_start: 0.6403 (m110) cc_final: 0.6139 (m110) REVERT: C 2187 ILE cc_start: 0.8355 (mm) cc_final: 0.8022 (pp) REVERT: C 2688 MET cc_start: 0.5847 (pp-130) cc_final: 0.5506 (ppp) REVERT: C 2734 MET cc_start: 0.8393 (mmm) cc_final: 0.8144 (mmm) REVERT: C 2844 MET cc_start: 0.8264 (ppp) cc_final: 0.7291 (tmm) REVERT: C 2848 TYR cc_start: 0.7479 (m-10) cc_final: 0.7162 (m-10) REVERT: C 3074 ASN cc_start: 0.7679 (m110) cc_final: 0.7446 (m110) REVERT: C 3162 PHE cc_start: 0.8836 (t80) cc_final: 0.8511 (t80) REVERT: C 3200 ASN cc_start: 0.8430 (m-40) cc_final: 0.8068 (m-40) REVERT: C 3235 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6969 (pp-130) REVERT: C 3323 MET cc_start: 0.7754 (mmt) cc_final: 0.7440 (tpp) REVERT: C 3348 MET cc_start: 0.3108 (pmm) cc_final: 0.2116 (pmm) REVERT: C 3359 PHE cc_start: 0.8788 (m-80) cc_final: 0.8344 (m-80) REVERT: C 3398 MET cc_start: 0.8319 (mtm) cc_final: 0.8094 (mtm) REVERT: C 3981 MET cc_start: 0.8568 (tmm) cc_final: 0.8244 (tmm) REVERT: C 4256 MET cc_start: 0.7826 (mtp) cc_final: 0.7533 (mtt) REVERT: C 4567 TYR cc_start: 0.6605 (p90) cc_final: 0.5864 (p90) REVERT: D 893 TRP cc_start: 0.9017 (t-100) cc_final: 0.8265 (t-100) REVERT: D 1501 ASN cc_start: 0.6470 (m110) cc_final: 0.6203 (m110) REVERT: D 2187 ILE cc_start: 0.8351 (mm) cc_final: 0.8016 (pp) REVERT: D 2688 MET cc_start: 0.5857 (pp-130) cc_final: 0.5450 (ppp) REVERT: D 2734 MET cc_start: 0.8403 (mmm) cc_final: 0.8083 (mmm) REVERT: D 2844 MET cc_start: 0.8261 (ppp) cc_final: 0.7612 (tmm) REVERT: D 2848 TYR cc_start: 0.7517 (m-10) cc_final: 0.7233 (m-10) REVERT: D 3072 MET cc_start: 0.8495 (tpp) cc_final: 0.8228 (tpt) REVERT: D 3074 ASN cc_start: 0.7629 (m110) cc_final: 0.7404 (m110) REVERT: D 3162 PHE cc_start: 0.8833 (t80) cc_final: 0.8503 (t80) REVERT: D 3200 ASN cc_start: 0.8441 (m-40) cc_final: 0.8095 (m-40) REVERT: D 3323 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6515 (mpp) REVERT: D 3348 MET cc_start: 0.3105 (pmm) cc_final: 0.2104 (pmm) REVERT: D 3359 PHE cc_start: 0.8775 (m-80) cc_final: 0.8339 (m-80) REVERT: D 3375 ARG cc_start: 0.8562 (tmt170) cc_final: 0.8108 (tmt170) REVERT: D 3398 MET cc_start: 0.8302 (mtm) cc_final: 0.7906 (ttp) REVERT: D 3978 MET cc_start: 0.8935 (ttp) cc_final: 0.8658 (ttt) REVERT: D 3981 MET cc_start: 0.8581 (tmm) cc_final: 0.8200 (tmm) REVERT: D 4256 MET cc_start: 0.7809 (mtp) cc_final: 0.7513 (mtt) REVERT: D 4567 TYR cc_start: 0.6487 (p90) cc_final: 0.5773 (p90) outliers start: 98 outliers final: 57 residues processed: 1028 average time/residue: 2.1649 time to fit residues: 3270.4763 Evaluate side-chains 1039 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 976 time to evaluate : 12.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3024 ASN Chi-restraints excluded: chain A residue 3323 MET Chi-restraints excluded: chain A residue 3504 GLU Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3024 ASN Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain B residue 3323 MET Chi-restraints excluded: chain B residue 3504 GLU Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain C residue 706 TYR Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3024 ASN Chi-restraints excluded: chain C residue 3235 MET Chi-restraints excluded: chain C residue 3273 MET Chi-restraints excluded: chain C residue 3504 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3024 ASN Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3323 MET Chi-restraints excluded: chain D residue 3504 GLU Chi-restraints excluded: chain D residue 3525 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1116 optimal weight: 9.9990 chunk 720 optimal weight: 7.9990 chunk 1077 optimal weight: 50.0000 chunk 543 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 1147 optimal weight: 9.9990 chunk 1229 optimal weight: 7.9990 chunk 892 optimal weight: 30.0000 chunk 168 optimal weight: 0.1980 chunk 1418 optimal weight: 5.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2450 ASN ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3095 ASN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4267 GLN ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 153444 Z= 0.330 Angle : 0.627 61.600 207256 Z= 0.310 Chirality : 0.042 0.341 22756 Planarity : 0.004 0.191 26676 Dihedral : 5.289 74.024 20576 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 0.65 % Allowed : 9.81 % Favored : 89.54 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.37 (0.06), residues: 18624 helix: 1.99 (0.05), residues: 9924 sheet: -0.22 (0.12), residues: 1896 loop : -0.33 (0.08), residues: 6804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A3250 HIS 0.009 0.001 HIS A3732 PHE 0.046 0.002 PHE A3369 TYR 0.039 0.001 TYR D3228 ARG 0.016 0.000 ARG I 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 978 time to evaluate : 12.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 893 TRP cc_start: 0.9036 (t-100) cc_final: 0.8270 (t-100) REVERT: A 1062 TYR cc_start: 0.8089 (m-80) cc_final: 0.7073 (m-80) REVERT: A 1501 ASN cc_start: 0.6397 (m110) cc_final: 0.6114 (m110) REVERT: A 2187 ILE cc_start: 0.8362 (mm) cc_final: 0.8014 (pp) REVERT: A 2688 MET cc_start: 0.5825 (pp-130) cc_final: 0.5365 (ppp) REVERT: A 2844 MET cc_start: 0.8269 (ppp) cc_final: 0.7620 (tmm) REVERT: A 2848 TYR cc_start: 0.7546 (m-10) cc_final: 0.7297 (m-10) REVERT: A 3072 MET cc_start: 0.8523 (tpp) cc_final: 0.8258 (tpt) REVERT: A 3074 ASN cc_start: 0.7664 (m110) cc_final: 0.7427 (m110) REVERT: A 3162 PHE cc_start: 0.8847 (t80) cc_final: 0.8528 (t80) REVERT: A 3200 ASN cc_start: 0.8450 (m-40) cc_final: 0.8089 (m-40) REVERT: A 3250 TRP cc_start: 0.8265 (t-100) cc_final: 0.8061 (t-100) REVERT: A 3264 CYS cc_start: 0.7840 (m) cc_final: 0.7252 (m) REVERT: A 3314 LEU cc_start: 0.7895 (tm) cc_final: 0.7688 (tp) REVERT: A 3323 MET cc_start: 0.7033 (mpp) cc_final: 0.6195 (mpp) REVERT: A 3348 MET cc_start: 0.3151 (pmm) cc_final: 0.2166 (pmm) REVERT: A 3359 PHE cc_start: 0.8804 (m-80) cc_final: 0.8357 (m-80) REVERT: A 3375 ARG cc_start: 0.8593 (tmt170) cc_final: 0.7916 (tmt170) REVERT: A 3398 MET cc_start: 0.8340 (mtm) cc_final: 0.7921 (ttp) REVERT: A 3819 MET cc_start: 0.1255 (pmt) cc_final: 0.0886 (pmt) REVERT: A 3981 MET cc_start: 0.8614 (tmm) cc_final: 0.8178 (tmm) REVERT: A 4256 MET cc_start: 0.7786 (mtp) cc_final: 0.7468 (mtt) REVERT: A 4567 TYR cc_start: 0.6658 (p90) cc_final: 0.5917 (p90) REVERT: E 19 LYS cc_start: 0.8597 (mmpt) cc_final: 0.8367 (mmmt) REVERT: F 108 GLU cc_start: 0.7553 (mp0) cc_final: 0.7275 (mt-10) REVERT: K 50 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7182 (tp-100) REVERT: L 1 MET cc_start: 0.7334 (ttm) cc_final: 0.6999 (tpt) REVERT: L 13 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: L 110 MET cc_start: 0.5757 (tpt) cc_final: 0.5516 (ttm) REVERT: B 678 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7325 (ttp) REVERT: B 964 MET cc_start: 0.1332 (mpt) cc_final: 0.0766 (mmt) REVERT: B 1077 VAL cc_start: 0.6590 (OUTLIER) cc_final: 0.6379 (m) REVERT: B 1501 ASN cc_start: 0.6335 (m110) cc_final: 0.6046 (m110) REVERT: B 2175 MET cc_start: 0.8442 (ttm) cc_final: 0.8187 (ttm) REVERT: B 2187 ILE cc_start: 0.8367 (mm) cc_final: 0.8022 (pp) REVERT: B 2688 MET cc_start: 0.5948 (pp-130) cc_final: 0.5513 (ppp) REVERT: B 2844 MET cc_start: 0.8246 (ppp) cc_final: 0.7482 (tmm) REVERT: B 2848 TYR cc_start: 0.7665 (m-10) cc_final: 0.7376 (m-10) REVERT: B 3074 ASN cc_start: 0.7695 (m110) cc_final: 0.7473 (m110) REVERT: B 3162 PHE cc_start: 0.8867 (t80) cc_final: 0.8535 (t80) REVERT: B 3200 ASN cc_start: 0.8434 (m-40) cc_final: 0.8106 (m-40) REVERT: B 3273 MET cc_start: 0.8811 (ttm) cc_final: 0.8371 (mtp) REVERT: B 3314 LEU cc_start: 0.7909 (tm) cc_final: 0.7696 (tp) REVERT: B 3315 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8889 (pp) REVERT: B 3323 MET cc_start: 0.7100 (mpp) cc_final: 0.6075 (mpp) REVERT: B 3348 MET cc_start: 0.3150 (pmm) cc_final: 0.2150 (pmm) REVERT: B 3359 PHE cc_start: 0.8788 (m-80) cc_final: 0.8378 (m-80) REVERT: B 3398 MET cc_start: 0.8357 (mtm) cc_final: 0.7956 (mtp) REVERT: B 3819 MET cc_start: 0.1252 (pmt) cc_final: 0.0875 (pmt) REVERT: B 3978 MET cc_start: 0.8953 (ttp) cc_final: 0.8704 (ttt) REVERT: B 3981 MET cc_start: 0.8595 (tmm) cc_final: 0.8249 (tmm) REVERT: B 4256 MET cc_start: 0.7811 (mtp) cc_final: 0.7487 (mtt) REVERT: B 4274 MET cc_start: 0.6367 (pp-130) cc_final: 0.6089 (pp-130) REVERT: B 4567 TYR cc_start: 0.6652 (p90) cc_final: 0.5903 (p90) REVERT: B 4660 PHE cc_start: 0.8204 (t80) cc_final: 0.7987 (t80) REVERT: C 1077 VAL cc_start: 0.6433 (OUTLIER) cc_final: 0.6232 (m) REVERT: C 1300 MET cc_start: 0.8171 (mmp) cc_final: 0.7736 (mmt) REVERT: C 1501 ASN cc_start: 0.6408 (m110) cc_final: 0.6139 (m-40) REVERT: C 2187 ILE cc_start: 0.8358 (mm) cc_final: 0.8025 (pp) REVERT: C 2688 MET cc_start: 0.5907 (pp-130) cc_final: 0.5550 (ppp) REVERT: C 2689 MET cc_start: 0.7263 (tmm) cc_final: 0.6794 (tmt) REVERT: C 2734 MET cc_start: 0.8398 (mmm) cc_final: 0.8148 (mmm) REVERT: C 2844 MET cc_start: 0.8279 (ppp) cc_final: 0.7603 (tmm) REVERT: C 2848 TYR cc_start: 0.7490 (m-10) cc_final: 0.7166 (m-10) REVERT: C 3074 ASN cc_start: 0.7689 (m110) cc_final: 0.7459 (m110) REVERT: C 3162 PHE cc_start: 0.8845 (t80) cc_final: 0.8518 (t80) REVERT: C 3200 ASN cc_start: 0.8435 (m-40) cc_final: 0.8074 (m-40) REVERT: C 3235 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6957 (pp-130) REVERT: C 3348 MET cc_start: 0.3111 (pmm) cc_final: 0.2118 (pmm) REVERT: C 3359 PHE cc_start: 0.8789 (m-80) cc_final: 0.8342 (m-80) REVERT: C 3398 MET cc_start: 0.8330 (mtm) cc_final: 0.8055 (mtm) REVERT: C 3797 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.7777 (mtt) REVERT: C 3819 MET cc_start: 0.1581 (pmt) cc_final: 0.1113 (pmt) REVERT: C 3981 MET cc_start: 0.8574 (tmm) cc_final: 0.8252 (tmm) REVERT: C 4256 MET cc_start: 0.7829 (mtp) cc_final: 0.7537 (mtt) REVERT: C 4567 TYR cc_start: 0.6611 (p90) cc_final: 0.5875 (p90) REVERT: D 678 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7318 (ttp) REVERT: D 893 TRP cc_start: 0.9043 (t-100) cc_final: 0.8273 (t-100) REVERT: D 1064 LEU cc_start: 0.8288 (tm) cc_final: 0.8063 (pt) REVERT: D 1501 ASN cc_start: 0.6448 (m110) cc_final: 0.6153 (m110) REVERT: D 2187 ILE cc_start: 0.8355 (mm) cc_final: 0.8019 (pp) REVERT: D 2688 MET cc_start: 0.5868 (pp-130) cc_final: 0.5458 (ppp) REVERT: D 2734 MET cc_start: 0.8420 (mmm) cc_final: 0.8079 (mmm) REVERT: D 2844 MET cc_start: 0.8275 (ppp) cc_final: 0.7594 (tmm) REVERT: D 2848 TYR cc_start: 0.7531 (m-10) cc_final: 0.7278 (m-10) REVERT: D 3072 MET cc_start: 0.8495 (tpp) cc_final: 0.8234 (tpt) REVERT: D 3074 ASN cc_start: 0.7663 (m110) cc_final: 0.7432 (m110) REVERT: D 3162 PHE cc_start: 0.8838 (t80) cc_final: 0.8511 (t80) REVERT: D 3200 ASN cc_start: 0.8447 (m-40) cc_final: 0.8102 (m-40) REVERT: D 3323 MET cc_start: 0.7016 (mpp) cc_final: 0.6164 (mpp) REVERT: D 3348 MET cc_start: 0.3114 (pmm) cc_final: 0.2117 (pmm) REVERT: D 3359 PHE cc_start: 0.8778 (m-80) cc_final: 0.8337 (m-80) REVERT: D 3375 ARG cc_start: 0.8568 (tmt170) cc_final: 0.7938 (tmt170) REVERT: D 3398 MET cc_start: 0.8309 (mtm) cc_final: 0.7915 (ttp) REVERT: D 3819 MET cc_start: 0.1546 (pmt) cc_final: 0.1049 (pmt) REVERT: D 3978 MET cc_start: 0.8938 (ttp) cc_final: 0.8693 (ttt) REVERT: D 3981 MET cc_start: 0.8583 (tmm) cc_final: 0.8201 (tmm) REVERT: D 4256 MET cc_start: 0.7811 (mtp) cc_final: 0.7517 (mtt) REVERT: D 4567 TYR cc_start: 0.6493 (p90) cc_final: 0.5784 (p90) outliers start: 99 outliers final: 62 residues processed: 1029 average time/residue: 2.1786 time to fit residues: 3292.2020 Evaluate side-chains 1044 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 973 time to evaluate : 12.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2596 VAL Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3504 GLU Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain A residue 3978 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 13 PHE Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 2448 ASP Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3024 ASN Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain B residue 3504 GLU Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain B residue 3650 GLU Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3235 MET Chi-restraints excluded: chain C residue 3273 MET Chi-restraints excluded: chain C residue 3504 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 3797 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3504 GLU Chi-restraints excluded: chain D residue 3525 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1641 optimal weight: 6.9990 chunk 1728 optimal weight: 9.9990 chunk 1577 optimal weight: 4.9990 chunk 1681 optimal weight: 1.9990 chunk 1012 optimal weight: 9.9990 chunk 732 optimal weight: 9.9990 chunk 1320 optimal weight: 0.8980 chunk 515 optimal weight: 4.9990 chunk 1519 optimal weight: 50.0000 chunk 1590 optimal weight: 5.9990 chunk 1675 optimal weight: 0.0770 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 ASN ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3095 ASN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3095 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 153444 Z= 0.330 Angle : 0.627 61.600 207256 Z= 0.310 Chirality : 0.042 0.341 22756 Planarity : 0.004 0.191 26676 Dihedral : 5.289 74.024 20576 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 0.49 % Allowed : 10.00 % Favored : 89.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.37 (0.06), residues: 18624 helix: 1.99 (0.05), residues: 9924 sheet: -0.22 (0.12), residues: 1896 loop : -0.33 (0.08), residues: 6804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A3250 HIS 0.009 0.001 HIS A3732 PHE 0.046 0.002 PHE A3369 TYR 0.039 0.001 TYR D3228 ARG 0.016 0.000 ARG I 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 973 time to evaluate : 12.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 893 TRP cc_start: 0.9047 (t-100) cc_final: 0.8270 (t-100) REVERT: A 1062 TYR cc_start: 0.8089 (m-80) cc_final: 0.7073 (m-80) REVERT: A 1501 ASN cc_start: 0.6375 (m110) cc_final: 0.6114 (m110) REVERT: A 2187 ILE cc_start: 0.8362 (mm) cc_final: 0.8014 (pp) REVERT: A 2688 MET cc_start: 0.5825 (pp-130) cc_final: 0.5365 (ppp) REVERT: A 2844 MET cc_start: 0.8270 (ppp) cc_final: 0.7620 (tmm) REVERT: A 2848 TYR cc_start: 0.7546 (m-10) cc_final: 0.7297 (m-10) REVERT: A 3072 MET cc_start: 0.8523 (tpp) cc_final: 0.8258 (tpt) REVERT: A 3074 ASN cc_start: 0.7664 (m110) cc_final: 0.7427 (m110) REVERT: A 3162 PHE cc_start: 0.8847 (t80) cc_final: 0.8528 (t80) REVERT: A 3200 ASN cc_start: 0.8450 (m-40) cc_final: 0.8089 (m-40) REVERT: A 3250 TRP cc_start: 0.8265 (t-100) cc_final: 0.8061 (t-100) REVERT: A 3264 CYS cc_start: 0.7842 (m) cc_final: 0.7252 (m) REVERT: A 3314 LEU cc_start: 0.7892 (tm) cc_final: 0.7688 (tp) REVERT: A 3323 MET cc_start: 0.6283 (mpp) cc_final: 0.5962 (mpp) REVERT: A 3348 MET cc_start: 0.3151 (pmm) cc_final: 0.2166 (pmm) REVERT: A 3359 PHE cc_start: 0.8804 (m-80) cc_final: 0.8357 (m-80) REVERT: A 3369 PHE cc_start: 0.6978 (t80) cc_final: 0.6715 (t80) REVERT: A 3375 ARG cc_start: 0.8593 (tmt170) cc_final: 0.7916 (tmt170) REVERT: A 3398 MET cc_start: 0.8341 (mtm) cc_final: 0.7921 (ttp) REVERT: A 3819 MET cc_start: 0.1254 (pmt) cc_final: 0.0886 (pmt) REVERT: A 3981 MET cc_start: 0.8614 (tmm) cc_final: 0.8178 (tmm) REVERT: A 4256 MET cc_start: 0.7786 (mtp) cc_final: 0.7469 (mtt) REVERT: A 4567 TYR cc_start: 0.6658 (p90) cc_final: 0.5917 (p90) REVERT: E 19 LYS cc_start: 0.8597 (mmpt) cc_final: 0.8367 (mmmt) REVERT: F 108 GLU cc_start: 0.7553 (mp0) cc_final: 0.7275 (mt-10) REVERT: K 50 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7182 (tp-100) REVERT: L 1 MET cc_start: 0.7333 (ttm) cc_final: 0.6999 (tpt) REVERT: L 13 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: L 110 MET cc_start: 0.5756 (tpt) cc_final: 0.5536 (ttm) REVERT: B 678 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7325 (ttp) REVERT: B 964 MET cc_start: 0.1356 (mpt) cc_final: 0.0766 (mmt) REVERT: B 1077 VAL cc_start: 0.6590 (OUTLIER) cc_final: 0.6379 (m) REVERT: B 1501 ASN cc_start: 0.6317 (m110) cc_final: 0.6046 (m110) REVERT: B 2175 MET cc_start: 0.8442 (ttm) cc_final: 0.8187 (ttm) REVERT: B 2187 ILE cc_start: 0.8368 (mm) cc_final: 0.8022 (pp) REVERT: B 2688 MET cc_start: 0.5949 (pp-130) cc_final: 0.5513 (ppp) REVERT: B 2844 MET cc_start: 0.8246 (ppp) cc_final: 0.7482 (tmm) REVERT: B 2848 TYR cc_start: 0.7665 (m-10) cc_final: 0.7376 (m-10) REVERT: B 3074 ASN cc_start: 0.7695 (m110) cc_final: 0.7473 (m110) REVERT: B 3162 PHE cc_start: 0.8867 (t80) cc_final: 0.8535 (t80) REVERT: B 3200 ASN cc_start: 0.8434 (m-40) cc_final: 0.8106 (m-40) REVERT: B 3273 MET cc_start: 0.8810 (ttm) cc_final: 0.8371 (mtp) REVERT: B 3314 LEU cc_start: 0.7908 (tm) cc_final: 0.7696 (tp) REVERT: B 3315 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8890 (pp) REVERT: B 3348 MET cc_start: 0.3149 (pmm) cc_final: 0.2150 (pmm) REVERT: B 3359 PHE cc_start: 0.8787 (m-80) cc_final: 0.8378 (m-80) REVERT: B 3398 MET cc_start: 0.8358 (mtm) cc_final: 0.7953 (mtp) REVERT: B 3819 MET cc_start: 0.1252 (pmt) cc_final: 0.0875 (pmt) REVERT: B 3978 MET cc_start: 0.8953 (ttp) cc_final: 0.8704 (ttt) REVERT: B 3981 MET cc_start: 0.8595 (tmm) cc_final: 0.8249 (tmm) REVERT: B 4256 MET cc_start: 0.7811 (mtp) cc_final: 0.7487 (mtt) REVERT: B 4274 MET cc_start: 0.6366 (pp-130) cc_final: 0.6089 (pp-130) REVERT: B 4567 TYR cc_start: 0.6652 (p90) cc_final: 0.5903 (p90) REVERT: B 4660 PHE cc_start: 0.8204 (t80) cc_final: 0.7987 (t80) REVERT: C 1300 MET cc_start: 0.8172 (mmp) cc_final: 0.7736 (mmt) REVERT: C 1501 ASN cc_start: 0.6407 (m110) cc_final: 0.6139 (m-40) REVERT: C 2187 ILE cc_start: 0.8358 (mm) cc_final: 0.8025 (pp) REVERT: C 2688 MET cc_start: 0.5908 (pp-130) cc_final: 0.5550 (ppp) REVERT: C 2689 MET cc_start: 0.7262 (tmm) cc_final: 0.6794 (tmt) REVERT: C 2734 MET cc_start: 0.8398 (mmm) cc_final: 0.8148 (mmm) REVERT: C 2844 MET cc_start: 0.8279 (ppp) cc_final: 0.7603 (tmm) REVERT: C 2848 TYR cc_start: 0.7490 (m-10) cc_final: 0.7166 (m-10) REVERT: C 3074 ASN cc_start: 0.7688 (m110) cc_final: 0.7459 (m110) REVERT: C 3162 PHE cc_start: 0.8844 (t80) cc_final: 0.8518 (t80) REVERT: C 3200 ASN cc_start: 0.8435 (m-40) cc_final: 0.8074 (m-40) REVERT: C 3235 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6957 (pp-130) REVERT: C 3348 MET cc_start: 0.3111 (pmm) cc_final: 0.2118 (pmm) REVERT: C 3359 PHE cc_start: 0.8789 (m-80) cc_final: 0.8342 (m-80) REVERT: C 3398 MET cc_start: 0.8260 (mtm) cc_final: 0.8055 (mtm) REVERT: C 3797 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.7777 (mtt) REVERT: C 3819 MET cc_start: 0.1581 (pmt) cc_final: 0.1113 (pmt) REVERT: C 3981 MET cc_start: 0.8584 (tmm) cc_final: 0.8252 (tmm) REVERT: C 4256 MET cc_start: 0.7829 (mtp) cc_final: 0.7537 (mtt) REVERT: C 4567 TYR cc_start: 0.6611 (p90) cc_final: 0.5875 (p90) REVERT: D 678 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7318 (ttp) REVERT: D 893 TRP cc_start: 0.9049 (t-100) cc_final: 0.8273 (t-100) REVERT: D 1064 LEU cc_start: 0.8287 (tm) cc_final: 0.8063 (pt) REVERT: D 1501 ASN cc_start: 0.6429 (m110) cc_final: 0.6153 (m110) REVERT: D 2187 ILE cc_start: 0.8355 (mm) cc_final: 0.8019 (pp) REVERT: D 2688 MET cc_start: 0.5867 (pp-130) cc_final: 0.5458 (ppp) REVERT: D 2734 MET cc_start: 0.8420 (mmm) cc_final: 0.8079 (mmm) REVERT: D 2844 MET cc_start: 0.8275 (ppp) cc_final: 0.7594 (tmm) REVERT: D 2848 TYR cc_start: 0.7531 (m-10) cc_final: 0.7278 (m-10) REVERT: D 3072 MET cc_start: 0.8495 (tpp) cc_final: 0.8234 (tpt) REVERT: D 3074 ASN cc_start: 0.7663 (m110) cc_final: 0.7432 (m110) REVERT: D 3162 PHE cc_start: 0.8838 (t80) cc_final: 0.8511 (t80) REVERT: D 3200 ASN cc_start: 0.8447 (m-40) cc_final: 0.8102 (m-40) REVERT: D 3323 MET cc_start: 0.6240 (mpp) cc_final: 0.5883 (mpp) REVERT: D 3348 MET cc_start: 0.3115 (pmm) cc_final: 0.2117 (pmm) REVERT: D 3359 PHE cc_start: 0.8778 (m-80) cc_final: 0.8337 (m-80) REVERT: D 3369 PHE cc_start: 0.6866 (t80) cc_final: 0.6614 (t80) REVERT: D 3375 ARG cc_start: 0.8570 (tmt170) cc_final: 0.7938 (tmt170) REVERT: D 3398 MET cc_start: 0.8310 (mtm) cc_final: 0.7915 (ttp) REVERT: D 3819 MET cc_start: 0.1548 (pmt) cc_final: 0.1049 (pmt) REVERT: D 3978 MET cc_start: 0.8938 (ttp) cc_final: 0.8693 (ttt) REVERT: D 3981 MET cc_start: 0.8583 (tmm) cc_final: 0.8201 (tmm) REVERT: D 4256 MET cc_start: 0.7812 (mtp) cc_final: 0.7517 (mtt) REVERT: D 4567 TYR cc_start: 0.6494 (p90) cc_final: 0.5784 (p90) outliers start: 72 outliers final: 62 residues processed: 1012 average time/residue: 2.2051 time to fit residues: 3277.2660 Evaluate side-chains 1043 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 973 time to evaluate : 12.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2596 VAL Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3504 GLU Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain A residue 3978 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 13 PHE Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 2448 ASP Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3024 ASN Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain B residue 3504 GLU Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain B residue 3650 GLU Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3235 MET Chi-restraints excluded: chain C residue 3273 MET Chi-restraints excluded: chain C residue 3504 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 3797 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3504 GLU Chi-restraints excluded: chain D residue 3525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1104 optimal weight: 8.9990 chunk 1777 optimal weight: 4.9990 chunk 1085 optimal weight: 20.0000 chunk 843 optimal weight: 7.9990 chunk 1235 optimal weight: 4.9990 chunk 1864 optimal weight: 0.4980 chunk 1716 optimal weight: 6.9990 chunk 1485 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 1147 optimal weight: 1.9990 chunk 910 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 ASN ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3095 ASN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3095 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 153444 Z= 0.330 Angle : 0.627 61.600 207256 Z= 0.310 Chirality : 0.042 0.341 22756 Planarity : 0.004 0.191 26676 Dihedral : 5.289 74.024 20576 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 0.48 % Allowed : 10.00 % Favored : 89.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.37 (0.06), residues: 18624 helix: 1.99 (0.05), residues: 9924 sheet: -0.22 (0.12), residues: 1896 loop : -0.33 (0.08), residues: 6804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A3250 HIS 0.009 0.001 HIS A3732 PHE 0.046 0.002 PHE A3369 TYR 0.039 0.001 TYR D3228 ARG 0.016 0.000 ARG I 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37248 Ramachandran restraints generated. 18624 Oldfield, 0 Emsley, 18624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 973 time to evaluate : 12.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 893 TRP cc_start: 0.9047 (t-100) cc_final: 0.8270 (t-100) REVERT: A 1062 TYR cc_start: 0.8089 (m-80) cc_final: 0.7073 (m-80) REVERT: A 1501 ASN cc_start: 0.6375 (m110) cc_final: 0.6114 (m110) REVERT: A 2187 ILE cc_start: 0.8362 (mm) cc_final: 0.8014 (pp) REVERT: A 2688 MET cc_start: 0.5825 (pp-130) cc_final: 0.5365 (ppp) REVERT: A 2844 MET cc_start: 0.8270 (ppp) cc_final: 0.7620 (tmm) REVERT: A 2848 TYR cc_start: 0.7546 (m-10) cc_final: 0.7297 (m-10) REVERT: A 3072 MET cc_start: 0.8523 (tpp) cc_final: 0.8258 (tpt) REVERT: A 3074 ASN cc_start: 0.7664 (m110) cc_final: 0.7427 (m110) REVERT: A 3162 PHE cc_start: 0.8847 (t80) cc_final: 0.8528 (t80) REVERT: A 3200 ASN cc_start: 0.8450 (m-40) cc_final: 0.8089 (m-40) REVERT: A 3250 TRP cc_start: 0.8265 (t-100) cc_final: 0.8061 (t-100) REVERT: A 3264 CYS cc_start: 0.7842 (m) cc_final: 0.7252 (m) REVERT: A 3314 LEU cc_start: 0.7892 (tm) cc_final: 0.7688 (tp) REVERT: A 3323 MET cc_start: 0.6283 (mpp) cc_final: 0.5962 (mpp) REVERT: A 3348 MET cc_start: 0.3151 (pmm) cc_final: 0.2166 (pmm) REVERT: A 3359 PHE cc_start: 0.8804 (m-80) cc_final: 0.8357 (m-80) REVERT: A 3369 PHE cc_start: 0.6978 (t80) cc_final: 0.6715 (t80) REVERT: A 3375 ARG cc_start: 0.8593 (tmt170) cc_final: 0.7916 (tmt170) REVERT: A 3398 MET cc_start: 0.8341 (mtm) cc_final: 0.7921 (ttp) REVERT: A 3819 MET cc_start: 0.1254 (pmt) cc_final: 0.0886 (pmt) REVERT: A 3981 MET cc_start: 0.8614 (tmm) cc_final: 0.8178 (tmm) REVERT: A 4256 MET cc_start: 0.7786 (mtp) cc_final: 0.7469 (mtt) REVERT: A 4567 TYR cc_start: 0.6658 (p90) cc_final: 0.5917 (p90) REVERT: E 19 LYS cc_start: 0.8597 (mmpt) cc_final: 0.8367 (mmmt) REVERT: F 108 GLU cc_start: 0.7553 (mp0) cc_final: 0.7275 (mt-10) REVERT: K 50 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7182 (tp-100) REVERT: L 1 MET cc_start: 0.7333 (ttm) cc_final: 0.6999 (tpt) REVERT: L 13 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: L 110 MET cc_start: 0.5756 (tpt) cc_final: 0.5536 (ttm) REVERT: B 678 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7325 (ttp) REVERT: B 964 MET cc_start: 0.1356 (mpt) cc_final: 0.0766 (mmt) REVERT: B 1077 VAL cc_start: 0.6590 (OUTLIER) cc_final: 0.6379 (m) REVERT: B 1501 ASN cc_start: 0.6317 (m110) cc_final: 0.6046 (m110) REVERT: B 2175 MET cc_start: 0.8442 (ttm) cc_final: 0.8187 (ttm) REVERT: B 2187 ILE cc_start: 0.8368 (mm) cc_final: 0.8022 (pp) REVERT: B 2688 MET cc_start: 0.5949 (pp-130) cc_final: 0.5513 (ppp) REVERT: B 2844 MET cc_start: 0.8246 (ppp) cc_final: 0.7482 (tmm) REVERT: B 2848 TYR cc_start: 0.7665 (m-10) cc_final: 0.7376 (m-10) REVERT: B 3074 ASN cc_start: 0.7695 (m110) cc_final: 0.7473 (m110) REVERT: B 3162 PHE cc_start: 0.8867 (t80) cc_final: 0.8535 (t80) REVERT: B 3200 ASN cc_start: 0.8434 (m-40) cc_final: 0.8106 (m-40) REVERT: B 3273 MET cc_start: 0.8810 (ttm) cc_final: 0.8371 (mtp) REVERT: B 3314 LEU cc_start: 0.7908 (tm) cc_final: 0.7696 (tp) REVERT: B 3315 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8890 (pp) REVERT: B 3348 MET cc_start: 0.3149 (pmm) cc_final: 0.2150 (pmm) REVERT: B 3359 PHE cc_start: 0.8787 (m-80) cc_final: 0.8378 (m-80) REVERT: B 3398 MET cc_start: 0.8357 (mtm) cc_final: 0.7952 (mtp) REVERT: B 3819 MET cc_start: 0.1252 (pmt) cc_final: 0.0875 (pmt) REVERT: B 3978 MET cc_start: 0.8953 (ttp) cc_final: 0.8704 (ttt) REVERT: B 3981 MET cc_start: 0.8595 (tmm) cc_final: 0.8249 (tmm) REVERT: B 4256 MET cc_start: 0.7811 (mtp) cc_final: 0.7487 (mtt) REVERT: B 4274 MET cc_start: 0.6367 (pp-130) cc_final: 0.6089 (pp-130) REVERT: B 4567 TYR cc_start: 0.6652 (p90) cc_final: 0.5903 (p90) REVERT: B 4660 PHE cc_start: 0.8204 (t80) cc_final: 0.7987 (t80) REVERT: C 1300 MET cc_start: 0.8172 (mmp) cc_final: 0.7736 (mmt) REVERT: C 1501 ASN cc_start: 0.6407 (m110) cc_final: 0.6139 (m-40) REVERT: C 2187 ILE cc_start: 0.8358 (mm) cc_final: 0.8025 (pp) REVERT: C 2688 MET cc_start: 0.5908 (pp-130) cc_final: 0.5550 (ppp) REVERT: C 2689 MET cc_start: 0.7262 (tmm) cc_final: 0.6794 (tmt) REVERT: C 2734 MET cc_start: 0.8398 (mmm) cc_final: 0.8148 (mmm) REVERT: C 2844 MET cc_start: 0.8279 (ppp) cc_final: 0.7603 (tmm) REVERT: C 2848 TYR cc_start: 0.7490 (m-10) cc_final: 0.7166 (m-10) REVERT: C 3074 ASN cc_start: 0.7688 (m110) cc_final: 0.7459 (m110) REVERT: C 3162 PHE cc_start: 0.8844 (t80) cc_final: 0.8518 (t80) REVERT: C 3200 ASN cc_start: 0.8435 (m-40) cc_final: 0.8074 (m-40) REVERT: C 3235 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6957 (pp-130) REVERT: C 3348 MET cc_start: 0.3111 (pmm) cc_final: 0.2118 (pmm) REVERT: C 3359 PHE cc_start: 0.8789 (m-80) cc_final: 0.8342 (m-80) REVERT: C 3398 MET cc_start: 0.8260 (mtm) cc_final: 0.8055 (mtm) REVERT: C 3797 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.7777 (mtt) REVERT: C 3819 MET cc_start: 0.1581 (pmt) cc_final: 0.1113 (pmt) REVERT: C 3981 MET cc_start: 0.8584 (tmm) cc_final: 0.8252 (tmm) REVERT: C 4256 MET cc_start: 0.7829 (mtp) cc_final: 0.7537 (mtt) REVERT: C 4567 TYR cc_start: 0.6611 (p90) cc_final: 0.5875 (p90) REVERT: D 678 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7318 (ttp) REVERT: D 893 TRP cc_start: 0.9049 (t-100) cc_final: 0.8273 (t-100) REVERT: D 1064 LEU cc_start: 0.8287 (tm) cc_final: 0.8063 (pt) REVERT: D 1501 ASN cc_start: 0.6429 (m110) cc_final: 0.6153 (m110) REVERT: D 2187 ILE cc_start: 0.8355 (mm) cc_final: 0.8019 (pp) REVERT: D 2688 MET cc_start: 0.5867 (pp-130) cc_final: 0.5458 (ppp) REVERT: D 2734 MET cc_start: 0.8420 (mmm) cc_final: 0.8079 (mmm) REVERT: D 2844 MET cc_start: 0.8275 (ppp) cc_final: 0.7594 (tmm) REVERT: D 2848 TYR cc_start: 0.7531 (m-10) cc_final: 0.7278 (m-10) REVERT: D 3072 MET cc_start: 0.8495 (tpp) cc_final: 0.8234 (tpt) REVERT: D 3074 ASN cc_start: 0.7663 (m110) cc_final: 0.7432 (m110) REVERT: D 3162 PHE cc_start: 0.8838 (t80) cc_final: 0.8511 (t80) REVERT: D 3200 ASN cc_start: 0.8447 (m-40) cc_final: 0.8102 (m-40) REVERT: D 3323 MET cc_start: 0.6240 (mpp) cc_final: 0.5883 (mpp) REVERT: D 3348 MET cc_start: 0.3115 (pmm) cc_final: 0.2117 (pmm) REVERT: D 3359 PHE cc_start: 0.8778 (m-80) cc_final: 0.8337 (m-80) REVERT: D 3369 PHE cc_start: 0.6866 (t80) cc_final: 0.6614 (t80) REVERT: D 3375 ARG cc_start: 0.8570 (tmt170) cc_final: 0.7938 (tmt170) REVERT: D 3398 MET cc_start: 0.8310 (mtm) cc_final: 0.7915 (ttp) REVERT: D 3819 MET cc_start: 0.1548 (pmt) cc_final: 0.1049 (pmt) REVERT: D 3978 MET cc_start: 0.8938 (ttp) cc_final: 0.8693 (ttt) REVERT: D 3981 MET cc_start: 0.8583 (tmm) cc_final: 0.8201 (tmm) REVERT: D 4256 MET cc_start: 0.7812 (mtp) cc_final: 0.7517 (mtt) REVERT: D 4567 TYR cc_start: 0.6494 (p90) cc_final: 0.5784 (p90) outliers start: 71 outliers final: 62 residues processed: 1011 average time/residue: 2.1934 time to fit residues: 3260.1477 Evaluate side-chains 1043 residues out of total 16468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 973 time to evaluate : 12.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2596 VAL Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2861 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3273 MET Chi-restraints excluded: chain A residue 3504 GLU Chi-restraints excluded: chain A residue 3525 ARG Chi-restraints excluded: chain A residue 3978 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 13 PHE Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 2448 ASP Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2861 GLU Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3024 ASN Chi-restraints excluded: chain B residue 3095 ASN Chi-restraints excluded: chain B residue 3315 LEU Chi-restraints excluded: chain B residue 3504 GLU Chi-restraints excluded: chain B residue 3525 ARG Chi-restraints excluded: chain B residue 3650 GLU Chi-restraints excluded: chain B residue 3739 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2861 GLU Chi-restraints excluded: chain C residue 3235 MET Chi-restraints excluded: chain C residue 3273 MET Chi-restraints excluded: chain C residue 3504 GLU Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 3797 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2861 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3504 GLU Chi-restraints excluded: chain D residue 3525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1872 random chunks: chunk 1179 optimal weight: 0.9990 chunk 1581 optimal weight: 6.9990 chunk 454 optimal weight: 0.5980 chunk 1369 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 412 optimal weight: 10.0000 chunk 1487 optimal weight: 0.5980 chunk 622 optimal weight: 0.3980 chunk 1527 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 ASN ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3095 ASN ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3095 ASN ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.060530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044595 restraints weight = 1206506.832| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.46 r_work: 0.2958 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 153444 Z= 0.330 Angle : 0.627 61.600 207256 Z= 0.310 Chirality : 0.042 0.341 22756 Planarity : 0.004 0.191 26676 Dihedral : 5.289 74.024 20576 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 0.48 % Allowed : 10.00 % Favored : 89.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.37 (0.06), residues: 18624 helix: 1.99 (0.05), residues: 9924 sheet: -0.22 (0.12), residues: 1896 loop : -0.33 (0.08), residues: 6804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A3250 HIS 0.009 0.001 HIS A3732 PHE 0.046 0.002 PHE A3369 TYR 0.039 0.001 TYR D3228 ARG 0.016 0.000 ARG I 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 55698.73 seconds wall clock time: 966 minutes 20.50 seconds (57980.50 seconds total)