Starting phenix.real_space_refine on Mon Mar 11 18:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gky_9518/03_2024/5gky_9518.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gky_9518/03_2024/5gky_9518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gky_9518/03_2024/5gky_9518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gky_9518/03_2024/5gky_9518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gky_9518/03_2024/5gky_9518.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gky_9518/03_2024/5gky_9518.pdb" } resolution = 3.8 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= 0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 644 5.16 5 C 70556 2.51 5 N 19316 2.21 5 O 20516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A ARG 728": "NH1" <-> "NH2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1584": "NH1" <-> "NH2" Residue "A ARG 1618": "NH1" <-> "NH2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A TYR 1712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1820": "NH1" <-> "NH2" Residue "A ARG 2330": "NH1" <-> "NH2" Residue "A ARG 2552": "NH1" <-> "NH2" Residue "A ARG 3672": "NH1" <-> "NH2" Residue "A ARG 3984": "NH1" <-> "NH2" Residue "A ARG 4188": "NH1" <-> "NH2" Residue "A ARG 4192": "NH1" <-> "NH2" Residue "A ARG 4202": "NH1" <-> "NH2" Residue "A ARG 4563": "NH1" <-> "NH2" Residue "A ARG 4673": "NH1" <-> "NH2" Residue "A TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4860": "NH1" <-> "NH2" Residue "A ARG 4892": "NH1" <-> "NH2" Residue "A PHE 4920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 531": "NH1" <-> "NH2" Residue "C ARG 728": "NH1" <-> "NH2" Residue "C ARG 1110": "NH1" <-> "NH2" Residue "C PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1584": "NH1" <-> "NH2" Residue "C ARG 1618": "NH1" <-> "NH2" Residue "C ARG 1680": "NH1" <-> "NH2" Residue "C TYR 1712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1725": "NH1" <-> "NH2" Residue "C ARG 1820": "NH1" <-> "NH2" Residue "C ARG 2330": "NH1" <-> "NH2" Residue "C ARG 2552": "NH1" <-> "NH2" Residue "C ARG 3672": "NH1" <-> "NH2" Residue "C ARG 3984": "NH1" <-> "NH2" Residue "C ARG 4188": "NH1" <-> "NH2" Residue "C ARG 4192": "NH1" <-> "NH2" Residue "C ARG 4202": "NH1" <-> "NH2" Residue "C ARG 4563": "NH1" <-> "NH2" Residue "C ARG 4673": "NH1" <-> "NH2" Residue "C TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4860": "NH1" <-> "NH2" Residue "C ARG 4892": "NH1" <-> "NH2" Residue "C PHE 4920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 257": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 531": "NH1" <-> "NH2" Residue "E ARG 728": "NH1" <-> "NH2" Residue "E ARG 1110": "NH1" <-> "NH2" Residue "E PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1584": "NH1" <-> "NH2" Residue "E ARG 1618": "NH1" <-> "NH2" Residue "E ARG 1680": "NH1" <-> "NH2" Residue "E TYR 1712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1820": "NH1" <-> "NH2" Residue "E ARG 2330": "NH1" <-> "NH2" Residue "E ARG 2552": "NH1" <-> "NH2" Residue "E ARG 3672": "NH1" <-> "NH2" Residue "E ARG 3984": "NH1" <-> "NH2" Residue "E ARG 4188": "NH1" <-> "NH2" Residue "E ARG 4192": "NH1" <-> "NH2" Residue "E ARG 4202": "NH1" <-> "NH2" Residue "E ARG 4563": "NH1" <-> "NH2" Residue "E ARG 4673": "NH1" <-> "NH2" Residue "E TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E PHE 4920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 257": "NH1" <-> "NH2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 531": "NH1" <-> "NH2" Residue "G ARG 728": "NH1" <-> "NH2" Residue "G PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1110": "NH1" <-> "NH2" Residue "G PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1584": "NH1" <-> "NH2" Residue "G ARG 1618": "NH1" <-> "NH2" Residue "G ARG 1680": "NH1" <-> "NH2" Residue "G TYR 1712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 1820": "NH1" <-> "NH2" Residue "G ARG 2330": "NH1" <-> "NH2" Residue "G ARG 2552": "NH1" <-> "NH2" Residue "G GLU 2925": "OE1" <-> "OE2" Residue "G ARG 3672": "NH1" <-> "NH2" Residue "G ARG 3984": "NH1" <-> "NH2" Residue "G ARG 4188": "NH1" <-> "NH2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4202": "NH1" <-> "NH2" Residue "G TYR 4560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G ARG 4673": "NH1" <-> "NH2" Residue "G TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 13": "NH1" <-> "NH2" Time to flip residues: 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 111036 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 26926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2073 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 Conformer: "B" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2073 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 bond proxies already assigned to first conformer: 27376 Chain: "B" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 26926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2072 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 Conformer: "B" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2072 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 bond proxies already assigned to first conformer: 27376 Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 26926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2072 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 Conformer: "B" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2072 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 bond proxies already assigned to first conformer: 27376 Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 26926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2074 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 Conformer: "B" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 80 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2522 Unresolved non-hydrogen angles: 3241 Unresolved non-hydrogen dihedrals: 2074 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1410 bond proxies already assigned to first conformer: 27376 Chain: "H" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26287 SG CYS A4958 190.607 166.245 87.376 1.00125.36 S ATOM 26312 SG CYS A4961 188.703 166.266 90.308 1.00 62.24 S ATOM 54045 SG CYS C4958 166.253 168.512 87.373 1.00125.35 S ATOM 54070 SG CYS C4961 166.263 170.418 90.308 1.00 62.84 S ATOM 81803 SG CYS E4958 168.515 192.871 87.375 1.00125.22 S ATOM 81828 SG CYS E4961 170.419 192.856 90.311 1.00 62.69 S ATOM A07DL SG CYS G4958 192.824 190.549 87.320 1.00120.46 S ATOM A07EA SG CYS G4961 192.826 188.683 90.290 1.00 59.41 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AGLU A2925 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A2925 " occ=0.50 residue: pdb=" N HIS B 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS B 87 " occ=0.99 residue: pdb=" N AGLU C2925 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU C2925 " occ=0.50 residue: pdb=" N HIS D 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS D 87 " occ=0.99 residue: pdb=" N AGLU E2925 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU E2925 " occ=0.50 residue: pdb=" N HIS F 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS F 87 " occ=0.99 residue: pdb=" N AGLU G2925 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU G2925 " occ=0.50 residue: pdb=" N HIS H 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS H 87 " occ=0.99 Time building chain proxies: 78.56, per 1000 atoms: 0.71 Number of scatterers: 111036 At special positions: 0 Unit cell: (360.46, 360.46, 207.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 644 16.00 O 20516 8.00 N 19316 7.00 C 70556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 33.26 Conformation dependent library (CDL) restraints added in 29.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4961 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4958 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4961 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4958 " pdb=" ZN E6000 " pdb="ZN ZN E6000 " - pdb=" NE2 HIS E4978 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4961 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4958 " pdb=" ZN G6000 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4978 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4961 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4958 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4983 " Number of angles added : 2 28848 Ramachandran restraints generated. 14424 Oldfield, 0 Emsley, 14424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28296 Finding SS restraints... Secondary structure from input PDB file: 671 helices and 108 sheets defined 58.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.94 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.640A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 65' Processing helix chain 'A' and resid 77 through 82 removed outlier: 4.286A pdb=" N MET A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 82' Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.037A pdb=" N VAL A 252 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.644A pdb=" N THR A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.882A pdb=" N ALA A 387 " --> pdb=" O MET A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 423 removed outlier: 4.527A pdb=" N GLN A 413 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.697A pdb=" N SER A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 480 Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 508 through 530 removed outlier: 4.716A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 4.094A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.634A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 579 through 594 removed outlier: 3.731A pdb=" N ILE A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 4.034A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 810 through 816 removed outlier: 3.555A pdb=" N VAL A 815 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 891 removed outlier: 3.884A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLN A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 920 Processing helix chain 'A' and resid 921 through 936 removed outlier: 4.044A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1002 Processing helix chain 'A' and resid 1023 through 1027 removed outlier: 4.084A pdb=" N LEU A1027 " --> pdb=" O TYR A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1049 removed outlier: 4.279A pdb=" N SER A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN A1035 " --> pdb=" O THR A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1082 Processing helix chain 'A' and resid 1225 through 1229 Processing helix chain 'A' and resid 1530 through 1534 removed outlier: 3.551A pdb=" N GLY A1533 " --> pdb=" O THR A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1585 removed outlier: 3.661A pdb=" N LYS A1585 " --> pdb=" O LEU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1654 removed outlier: 3.825A pdb=" N SER A1654 " --> pdb=" O LEU A1651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1651 through 1654' Processing helix chain 'A' and resid 1657 through 1674 Processing helix chain 'A' and resid 1681 through 1690 removed outlier: 3.532A pdb=" N LEU A1685 " --> pdb=" O VAL A1681 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1700 Processing helix chain 'A' and resid 1704 through 1718 Processing helix chain 'A' and resid 1719 through 1732 removed outlier: 4.181A pdb=" N ALA A1723 " --> pdb=" O HIS A1719 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A1729 " --> pdb=" O ARG A1725 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1769 removed outlier: 3.893A pdb=" N THR A1768 " --> pdb=" O VAL A1765 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR A1769 " --> pdb=" O GLY A1766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1765 through 1769' Processing helix chain 'A' and resid 1803 through 1824 Processing helix chain 'A' and resid 1833 through 1851 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1856 through 1867 Processing helix chain 'A' and resid 1925 through 1929 Processing helix chain 'A' and resid 1934 through 1975 removed outlier: 4.403A pdb=" N LYS A1968 " --> pdb=" O ARG A1964 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1971 " --> pdb=" O ASP A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2043 Processing helix chain 'A' and resid 2059 through 2071 removed outlier: 3.733A pdb=" N LEU A2063 " --> pdb=" O LEU A2059 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU A2068 " --> pdb=" O ARG A2064 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2110 removed outlier: 4.245A pdb=" N SER A2099 " --> pdb=" O GLN A2095 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A2110 " --> pdb=" O ALA A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2129 removed outlier: 3.741A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2141 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2148 through 2166 removed outlier: 3.645A pdb=" N THR A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A2157 " --> pdb=" O MET A2153 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS A2158 " --> pdb=" O SER A2154 " (cutoff:3.500A) Processing helix chain 'A' and resid 2174 through 2188 Processing helix chain 'A' and resid 2189 through 2194 Processing helix chain 'A' and resid 2194 through 2202 removed outlier: 3.552A pdb=" N MET A2198 " --> pdb=" O HIS A2194 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2215 Processing helix chain 'A' and resid 2228 through 2242 Processing helix chain 'A' and resid 2243 through 2252 removed outlier: 3.570A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) Processing helix chain 'A' and resid 2253 through 2260 Processing helix chain 'A' and resid 2272 through 2281 Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2304 removed outlier: 3.838A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2326 through 2341 removed outlier: 3.930A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2358 removed outlier: 4.190A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2385 removed outlier: 4.090A pdb=" N GLU A2381 " --> pdb=" O LEU A2377 " (cutoff:3.500A) Processing helix chain 'A' and resid 2420 through 2433 Processing helix chain 'A' and resid 2434 through 2436 No H-bonds generated for 'chain 'A' and resid 2434 through 2436' Processing helix chain 'A' and resid 2450 through 2459 removed outlier: 3.925A pdb=" N ARG A2454 " --> pdb=" O ALA A2450 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A2455 " --> pdb=" O LEU A2451 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2475 removed outlier: 3.558A pdb=" N ILE A2470 " --> pdb=" O LEU A2466 " (cutoff:3.500A) Proline residue: A2473 - end of helix Processing helix chain 'A' and resid 2495 through 2509 removed outlier: 3.510A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2521 Processing helix chain 'A' and resid 2525 through 2534 removed outlier: 3.827A pdb=" N ALA A2533 " --> pdb=" O ASP A2529 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A2534 " --> pdb=" O MET A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2557 removed outlier: 3.608A pdb=" N ASN A2551 " --> pdb=" O ALA A2547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A2556 " --> pdb=" O ARG A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2557 through 2562 removed outlier: 4.092A pdb=" N LEU A2561 " --> pdb=" O ALA A2557 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A2562 " --> pdb=" O VAL A2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2557 through 2562' Processing helix chain 'A' and resid 2568 through 2586 Processing helix chain 'A' and resid 2592 through 2609 removed outlier: 3.774A pdb=" N ALA A2609 " --> pdb=" O ASP A2605 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2634 Proline residue: A2631 - end of helix removed outlier: 3.755A pdb=" N ASN A2634 " --> pdb=" O VAL A2630 " (cutoff:3.500A) Processing helix chain 'A' and resid 2639 through 2660 Proline residue: A2658 - end of helix Processing helix chain 'A' and resid 2668 through 2686 removed outlier: 3.532A pdb=" N LEU A2686 " --> pdb=" O ILE A2682 " (cutoff:3.500A) Processing helix chain 'A' and resid 2692 through 2710 Proline residue: A2701 - end of helix Processing helix chain 'A' and resid 2748 through 2773 removed outlier: 3.673A pdb=" N ASP A2752 " --> pdb=" O PRO A2748 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A2753 " --> pdb=" O GLU A2749 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A2773 " --> pdb=" O ASP A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2782 through 2785 Processing helix chain 'A' and resid 2793 through 2797 Processing helix chain 'A' and resid 2798 through 2819 removed outlier: 4.214A pdb=" N TYR A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) Proline residue: A2808 - end of helix Processing helix chain 'A' and resid 2861 through 2865 Processing helix chain 'A' and resid 2868 through 2898 Processing helix chain 'A' and resid 2907 through 2911 Processing helix chain 'A' and resid 2912 through 2934 removed outlier: 3.732A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) Processing helix chain 'A' and resid 3018 through 3038 Processing helix chain 'A' and resid 3044 through 3061 Processing helix chain 'A' and resid 3069 through 3090 Proline residue: A3085 - end of helix removed outlier: 3.803A pdb=" N VAL A3088 " --> pdb=" O GLY A3084 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A3090 " --> pdb=" O GLU A3086 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3114 Processing helix chain 'A' and resid 3132 through 3134 No H-bonds generated for 'chain 'A' and resid 3132 through 3134' Processing helix chain 'A' and resid 3135 through 3152 Processing helix chain 'A' and resid 3159 through 3177 Processing helix chain 'A' and resid 3185 through 3198 Processing helix chain 'A' and resid 3205 through 3216 Processing helix chain 'A' and resid 3274 through 3288 Proline residue: A3282 - end of helix Processing helix chain 'A' and resid 3295 through 3300 Processing helix chain 'A' and resid 3301 through 3311 Processing helix chain 'A' and resid 3318 through 3337 Processing helix chain 'A' and resid 3350 through 3363 Proline residue: A3360 - end of helix Processing helix chain 'A' and resid 3368 through 3397 removed outlier: 3.704A pdb=" N VAL A3373 " --> pdb=" O ALA A3369 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A3397 " --> pdb=" O LEU A3393 " (cutoff:3.500A) Processing helix chain 'A' and resid 3403 through 3407 Processing helix chain 'A' and resid 3407 through 3424 Processing helix chain 'A' and resid 3428 through 3435 removed outlier: 3.536A pdb=" N PHE A3435 " --> pdb=" O ALA A3431 " (cutoff:3.500A) Processing helix chain 'A' and resid 3439 through 3455 Processing helix chain 'A' and resid 3458 through 3469 Processing helix chain 'A' and resid 3479 through 3491 removed outlier: 3.861A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A3485 " --> pdb=" O ALA A3481 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A3487 " --> pdb=" O ASP A3483 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A3489 " --> pdb=" O GLN A3485 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A3490 " --> pdb=" O SER A3486 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3503 Processing helix chain 'A' and resid 3516 through 3526 removed outlier: 3.545A pdb=" N ALA A3526 " --> pdb=" O LEU A3522 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3543 Processing helix chain 'A' and resid 3550 through 3570 Proline residue: A3567 - end of helix Processing helix chain 'A' and resid 3646 through 3660 Processing helix chain 'A' and resid 3667 through 3679 removed outlier: 4.162A pdb=" N ASP A3671 " --> pdb=" O HIS A3667 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A3672 " --> pdb=" O SER A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3710 Processing helix chain 'A' and resid 3719 through 3731 Processing helix chain 'A' and resid 3751 through 3772 removed outlier: 3.678A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3786 Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3823 Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 3.757A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) Processing helix chain 'A' and resid 3844 through 3851 Processing helix chain 'A' and resid 3878 through 3893 removed outlier: 3.589A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3906 Processing helix chain 'A' and resid 3914 through 3938 Processing helix chain 'A' and resid 3949 through 3970 Processing helix chain 'A' and resid 3973 through 3982 Processing helix chain 'A' and resid 3984 through 4003 removed outlier: 4.034A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) Processing helix chain 'A' and resid 4004 through 4008 removed outlier: 5.125A pdb=" N SER A4007 " --> pdb=" O ALA A4004 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER A4008 " --> pdb=" O GLN A4005 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4004 through 4008' Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.547A pdb=" N GLU A4015 " --> pdb=" O GLU A4011 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 removed outlier: 3.546A pdb=" N MET A4044 " --> pdb=" O ILE A4040 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 4.019A pdb=" N ILE A4058 " --> pdb=" O ASN A4054 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A4062 " --> pdb=" O ILE A4058 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4080 removed outlier: 3.829A pdb=" N PHE A4077 " --> pdb=" O GLY A4073 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) Processing helix chain 'A' and resid 4091 through 4097 removed outlier: 3.842A pdb=" N LYS A4095 " --> pdb=" O LYS A4091 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4100 No H-bonds generated for 'chain 'A' and resid 4098 through 4100' Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4136 through 4154 removed outlier: 3.713A pdb=" N GLY A4140 " --> pdb=" O ALA A4136 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4166 Processing helix chain 'A' and resid 4167 through 4175 removed outlier: 4.014A pdb=" N LEU A4171 " --> pdb=" O ALA A4167 " (cutoff:3.500A) Processing helix chain 'A' and resid 4200 through 4205 removed outlier: 3.872A pdb=" N TRP A4205 " --> pdb=" O ASN A4201 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4223 removed outlier: 4.164A pdb=" N GLU A4212 " --> pdb=" O PRO A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4228 through 4250 removed outlier: 4.481A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE A4234 " --> pdb=" O LYS A4230 " (cutoff:3.500A) Processing helix chain 'A' and resid 4546 through 4558 removed outlier: 3.574A pdb=" N LYS A4550 " --> pdb=" O VAL A4546 " (cutoff:3.500A) Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4663 removed outlier: 3.545A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) Processing helix chain 'A' and resid 4664 through 4683 removed outlier: 3.993A pdb=" N LEU A4668 " --> pdb=" O LEU A4664 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4703 removed outlier: 3.688A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) Processing helix chain 'A' and resid 4704 through 4708 removed outlier: 3.803A pdb=" N ASN A4707 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4729 Processing helix chain 'A' and resid 4734 through 4741 Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 4.231A pdb=" N ILE A4771 " --> pdb=" O TRP A4767 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4786 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 4.133A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 removed outlier: 3.891A pdb=" N ALA A4811 " --> pdb=" O PHE A4808 " (cutoff:3.500A) Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 3.782A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.694A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4857 removed outlier: 3.637A pdb=" N ASN A4857 " --> pdb=" O VAL A4853 " (cutoff:3.500A) Processing helix chain 'A' and resid 4858 through 4863 removed outlier: 4.519A pdb=" N LYS A4861 " --> pdb=" O PHE A4858 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A4863 " --> pdb=" O ARG A4860 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4889 Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 3.906A pdb=" N ILE A4901 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4908 through 4924 removed outlier: 3.824A pdb=" N TYR A4912 " --> pdb=" O GLU A4908 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) Processing helix chain 'A' and resid 4927 through 4956 Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 4.206A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4974 through 4979 Processing helix chain 'A' and resid 4985 through 4997 removed outlier: 3.910A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.639A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 65' Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.282A pdb=" N MET C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 82' Processing helix chain 'C' and resid 249 through 254 removed outlier: 4.028A pdb=" N VAL C 252 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.647A pdb=" N THR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.874A pdb=" N ALA C 387 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 423 removed outlier: 4.523A pdb=" N GLN C 413 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 452 removed outlier: 3.699A pdb=" N SER C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 480 Processing helix chain 'C' and resid 482 through 495 Processing helix chain 'C' and resid 508 through 530 removed outlier: 4.717A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 529 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 540 removed outlier: 4.090A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 552 Processing helix chain 'C' and resid 557 through 570 removed outlier: 3.636A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 Processing helix chain 'C' and resid 579 through 594 removed outlier: 3.727A pdb=" N ILE C 583 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 608 removed outlier: 4.026A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 810 through 816 removed outlier: 3.558A pdb=" N VAL C 815 " --> pdb=" O HIS C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 891 removed outlier: 3.889A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 890 " --> pdb=" O ARG C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 920 Processing helix chain 'C' and resid 921 through 936 removed outlier: 4.045A pdb=" N GLY C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1002 Processing helix chain 'C' and resid 1023 through 1027 removed outlier: 4.082A pdb=" N LEU C1027 " --> pdb=" O TYR C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1049 removed outlier: 4.273A pdb=" N SER C1034 " --> pdb=" O ALA C1030 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C1035 " --> pdb=" O THR C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1082 Processing helix chain 'C' and resid 1225 through 1229 Processing helix chain 'C' and resid 1530 through 1534 removed outlier: 3.557A pdb=" N GLY C1533 " --> pdb=" O THR C1530 " (cutoff:3.500A) Processing helix chain 'C' and resid 1580 through 1585 removed outlier: 3.654A pdb=" N LYS C1585 " --> pdb=" O LEU C1581 " (cutoff:3.500A) Processing helix chain 'C' and resid 1651 through 1654 removed outlier: 3.823A pdb=" N SER C1654 " --> pdb=" O LEU C1651 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1651 through 1654' Processing helix chain 'C' and resid 1657 through 1674 Processing helix chain 'C' and resid 1681 through 1690 removed outlier: 3.535A pdb=" N LEU C1685 " --> pdb=" O VAL C1681 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C1690 " --> pdb=" O CYS C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1700 Processing helix chain 'C' and resid 1704 through 1718 Processing helix chain 'C' and resid 1719 through 1732 removed outlier: 4.184A pdb=" N ALA C1723 " --> pdb=" O HIS C1719 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C1729 " --> pdb=" O ARG C1725 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1765 through 1769 removed outlier: 3.889A pdb=" N THR C1768 " --> pdb=" O VAL C1765 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR C1769 " --> pdb=" O GLY C1766 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1765 through 1769' Processing helix chain 'C' and resid 1803 through 1824 Processing helix chain 'C' and resid 1833 through 1851 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1856 through 1867 Processing helix chain 'C' and resid 1925 through 1929 Processing helix chain 'C' and resid 1934 through 1975 removed outlier: 4.403A pdb=" N LYS C1968 " --> pdb=" O ARG C1964 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA C1971 " --> pdb=" O ASP C1967 " (cutoff:3.500A) Processing helix chain 'C' and resid 2034 through 2043 Processing helix chain 'C' and resid 2059 through 2071 removed outlier: 3.731A pdb=" N LEU C2063 " --> pdb=" O LEU C2059 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU C2068 " --> pdb=" O ARG C2064 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2110 removed outlier: 4.248A pdb=" N SER C2099 " --> pdb=" O GLN C2095 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C2110 " --> pdb=" O ALA C2106 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2129 removed outlier: 3.736A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) Processing helix chain 'C' and resid 2129 through 2141 Proline residue: C2139 - end of helix Processing helix chain 'C' and resid 2148 through 2166 removed outlier: 3.645A pdb=" N THR C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C2157 " --> pdb=" O MET C2153 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS C2158 " --> pdb=" O SER C2154 " (cutoff:3.500A) Processing helix chain 'C' and resid 2174 through 2188 Processing helix chain 'C' and resid 2189 through 2194 Processing helix chain 'C' and resid 2194 through 2202 removed outlier: 3.554A pdb=" N MET C2198 " --> pdb=" O HIS C2194 " (cutoff:3.500A) Processing helix chain 'C' and resid 2202 through 2215 Processing helix chain 'C' and resid 2228 through 2242 Processing helix chain 'C' and resid 2243 through 2252 removed outlier: 3.571A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2260 Processing helix chain 'C' and resid 2272 through 2281 Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2304 removed outlier: 3.840A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2326 through 2341 removed outlier: 3.926A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2358 removed outlier: 4.193A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2385 removed outlier: 4.089A pdb=" N GLU C2381 " --> pdb=" O LEU C2377 " (cutoff:3.500A) Processing helix chain 'C' and resid 2420 through 2433 Processing helix chain 'C' and resid 2434 through 2436 No H-bonds generated for 'chain 'C' and resid 2434 through 2436' Processing helix chain 'C' and resid 2450 through 2459 removed outlier: 3.924A pdb=" N ARG C2454 " --> pdb=" O ALA C2450 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C2455 " --> pdb=" O LEU C2451 " (cutoff:3.500A) Processing helix chain 'C' and resid 2466 through 2475 removed outlier: 3.559A pdb=" N ILE C2470 " --> pdb=" O LEU C2466 " (cutoff:3.500A) Proline residue: C2473 - end of helix Processing helix chain 'C' and resid 2495 through 2509 removed outlier: 3.510A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) Processing helix chain 'C' and resid 2515 through 2521 Processing helix chain 'C' and resid 2525 through 2534 removed outlier: 3.821A pdb=" N ALA C2533 " --> pdb=" O ASP C2529 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C2534 " --> pdb=" O MET C2530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2557 removed outlier: 3.606A pdb=" N ASN C2551 " --> pdb=" O ALA C2547 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C2556 " --> pdb=" O ARG C2552 " (cutoff:3.500A) Processing helix chain 'C' and resid 2557 through 2562 removed outlier: 4.082A pdb=" N LEU C2561 " --> pdb=" O ALA C2557 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C2562 " --> pdb=" O VAL C2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2557 through 2562' Processing helix chain 'C' and resid 2568 through 2586 Processing helix chain 'C' and resid 2592 through 2609 removed outlier: 3.776A pdb=" N ALA C2609 " --> pdb=" O ASP C2605 " (cutoff:3.500A) Processing helix chain 'C' and resid 2616 through 2634 Proline residue: C2631 - end of helix removed outlier: 3.736A pdb=" N ASN C2634 " --> pdb=" O VAL C2630 " (cutoff:3.500A) Processing helix chain 'C' and resid 2639 through 2660 Proline residue: C2658 - end of helix Processing helix chain 'C' and resid 2668 through 2686 removed outlier: 3.533A pdb=" N LEU C2686 " --> pdb=" O ILE C2682 " (cutoff:3.500A) Processing helix chain 'C' and resid 2692 through 2710 Proline residue: C2701 - end of helix Processing helix chain 'C' and resid 2748 through 2773 removed outlier: 3.674A pdb=" N ASP C2752 " --> pdb=" O PRO C2748 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C2753 " --> pdb=" O GLU C2749 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C2754 " --> pdb=" O LYS C2750 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C2773 " --> pdb=" O ASP C2769 " (cutoff:3.500A) Processing helix chain 'C' and resid 2782 through 2785 Processing helix chain 'C' and resid 2793 through 2797 Processing helix chain 'C' and resid 2798 through 2819 removed outlier: 4.215A pdb=" N TYR C2805 " --> pdb=" O ASP C2801 " (cutoff:3.500A) Proline residue: C2808 - end of helix Processing helix chain 'C' and resid 2861 through 2865 Processing helix chain 'C' and resid 2868 through 2898 Processing helix chain 'C' and resid 2907 through 2911 Processing helix chain 'C' and resid 2912 through 2934 removed outlier: 3.732A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) Processing helix chain 'C' and resid 3018 through 3038 Processing helix chain 'C' and resid 3044 through 3061 Processing helix chain 'C' and resid 3069 through 3090 Proline residue: C3085 - end of helix removed outlier: 3.804A pdb=" N VAL C3088 " --> pdb=" O GLY C3084 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA C3090 " --> pdb=" O GLU C3086 " (cutoff:3.500A) Processing helix chain 'C' and resid 3096 through 3115 Processing helix chain 'C' and resid 3132 through 3134 No H-bonds generated for 'chain 'C' and resid 3132 through 3134' Processing helix chain 'C' and resid 3135 through 3152 Processing helix chain 'C' and resid 3159 through 3177 Processing helix chain 'C' and resid 3185 through 3198 Processing helix chain 'C' and resid 3205 through 3217 removed outlier: 3.975A pdb=" N SER C3217 " --> pdb=" O TYR C3213 " (cutoff:3.500A) Processing helix chain 'C' and resid 3274 through 3288 Proline residue: C3282 - end of helix Processing helix chain 'C' and resid 3295 through 3300 Processing helix chain 'C' and resid 3301 through 3311 Processing helix chain 'C' and resid 3318 through 3338 Processing helix chain 'C' and resid 3350 through 3363 Proline residue: C3360 - end of helix Processing helix chain 'C' and resid 3368 through 3397 removed outlier: 3.703A pdb=" N VAL C3373 " --> pdb=" O ALA C3369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C3397 " --> pdb=" O LEU C3393 " (cutoff:3.500A) Processing helix chain 'C' and resid 3403 through 3407 Processing helix chain 'C' and resid 3407 through 3424 Processing helix chain 'C' and resid 3428 through 3435 removed outlier: 3.533A pdb=" N PHE C3435 " --> pdb=" O ALA C3431 " (cutoff:3.500A) Processing helix chain 'C' and resid 3439 through 3455 Processing helix chain 'C' and resid 3458 through 3469 Processing helix chain 'C' and resid 3479 through 3491 removed outlier: 3.860A pdb=" N ALA C3484 " --> pdb=" O LYS C3480 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C3485 " --> pdb=" O ALA C3481 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C3487 " --> pdb=" O ASP C3483 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C3488 " --> pdb=" O ALA C3484 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C3489 " --> pdb=" O GLN C3485 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP C3490 " --> pdb=" O SER C3486 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C3491 " --> pdb=" O GLY C3487 " (cutoff:3.500A) Processing helix chain 'C' and resid 3495 through 3503 Processing helix chain 'C' and resid 3516 through 3526 removed outlier: 3.537A pdb=" N ALA C3526 " --> pdb=" O LEU C3522 " (cutoff:3.500A) Processing helix chain 'C' and resid 3538 through 3543 Processing helix chain 'C' and resid 3550 through 3570 Proline residue: C3567 - end of helix Processing helix chain 'C' and resid 3646 through 3660 Processing helix chain 'C' and resid 3667 through 3679 removed outlier: 4.164A pdb=" N ASP C3671 " --> pdb=" O HIS C3667 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG C3672 " --> pdb=" O SER C3668 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3710 Processing helix chain 'C' and resid 3719 through 3731 Processing helix chain 'C' and resid 3751 through 3772 removed outlier: 3.629A pdb=" N MET C3758 " --> pdb=" O GLU C3754 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3786 Processing helix chain 'C' and resid 3791 through 3806 Processing helix chain 'C' and resid 3809 through 3823 Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 3.763A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) Processing helix chain 'C' and resid 3844 through 3851 Processing helix chain 'C' and resid 3878 through 3893 removed outlier: 3.591A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3906 Processing helix chain 'C' and resid 3914 through 3938 Processing helix chain 'C' and resid 3949 through 3970 Processing helix chain 'C' and resid 3973 through 3982 Processing helix chain 'C' and resid 3984 through 4003 removed outlier: 4.034A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) Processing helix chain 'C' and resid 4004 through 4008 removed outlier: 5.143A pdb=" N SER C4007 " --> pdb=" O ALA C4004 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER C4008 " --> pdb=" O GLN C4005 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4004 through 4008' Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.553A pdb=" N GLU C4015 " --> pdb=" O GLU C4011 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 removed outlier: 3.549A pdb=" N MET C4044 " --> pdb=" O ILE C4040 " (cutoff:3.500A) Processing helix chain 'C' and resid 4051 through 4062 removed outlier: 4.019A pdb=" N ILE C4058 " --> pdb=" O ASN C4054 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C4062 " --> pdb=" O ILE C4058 " (cutoff:3.500A) Processing helix chain 'C' and resid 4073 through 4080 removed outlier: 3.831A pdb=" N PHE C4077 " --> pdb=" O GLY C4073 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C4080 " --> pdb=" O ALA C4076 " (cutoff:3.500A) Processing helix chain 'C' and resid 4091 through 4097 removed outlier: 3.841A pdb=" N LYS C4095 " --> pdb=" O LYS C4091 " (cutoff:3.500A) Processing helix chain 'C' and resid 4098 through 4100 No H-bonds generated for 'chain 'C' and resid 4098 through 4100' Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4136 through 4154 removed outlier: 3.709A pdb=" N GLY C4140 " --> pdb=" O ALA C4136 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4166 Processing helix chain 'C' and resid 4167 through 4175 removed outlier: 4.019A pdb=" N LEU C4171 " --> pdb=" O ALA C4167 " (cutoff:3.500A) Processing helix chain 'C' and resid 4200 through 4205 removed outlier: 3.871A pdb=" N TRP C4205 " --> pdb=" O ASN C4201 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4223 removed outlier: 4.166A pdb=" N GLU C4212 " --> pdb=" O PRO C4208 " (cutoff:3.500A) Processing helix chain 'C' and resid 4228 through 4251 removed outlier: 4.484A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE C4234 " --> pdb=" O LYS C4230 " (cutoff:3.500A) Processing helix chain 'C' and resid 4546 through 4558 removed outlier: 3.567A pdb=" N LYS C4550 " --> pdb=" O VAL C4546 " (cutoff:3.500A) Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4663 removed outlier: 3.539A pdb=" N TRP C4644 " --> pdb=" O GLU C4640 " (cutoff:3.500A) Processing helix chain 'C' and resid 4664 through 4683 removed outlier: 3.995A pdb=" N LEU C4668 " --> pdb=" O LEU C4664 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4703 removed outlier: 3.683A pdb=" N GLN C4700 " --> pdb=" O ASP C4696 " (cutoff:3.500A) Processing helix chain 'C' and resid 4704 through 4708 removed outlier: 3.807A pdb=" N ASN C4707 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4729 Processing helix chain 'C' and resid 4734 through 4741 Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 4.226A pdb=" N ILE C4771 " --> pdb=" O TRP C4767 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4786 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 4.128A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4814 removed outlier: 3.522A pdb=" N ALA C4810 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C4811 " --> pdb=" O PHE C4808 " (cutoff:3.500A) Processing helix chain 'C' and resid 4815 through 4820 Processing helix chain 'C' and resid 4820 through 4832 removed outlier: 3.734A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4857 removed outlier: 3.648A pdb=" N ASN C4857 " --> pdb=" O VAL C4853 " (cutoff:3.500A) Processing helix chain 'C' and resid 4858 through 4863 removed outlier: 4.524A pdb=" N LYS C4861 " --> pdb=" O PHE C4858 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C4863 " --> pdb=" O ARG C4860 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4889 Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 3.510A pdb=" N GLU C4900 " --> pdb=" O ILE C4897 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C4901 " --> pdb=" O GLY C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4908 through 4924 removed outlier: 3.824A pdb=" N TYR C4912 " --> pdb=" O GLU C4908 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) Processing helix chain 'C' and resid 4927 through 4956 Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 4.197A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4974 through 4979 Processing helix chain 'C' and resid 4985 through 4997 removed outlier: 3.906A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C4996 " --> pdb=" O LEU C4992 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 56 through 63 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.642A pdb=" N CYS E 65 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 65' Processing helix chain 'E' and resid 77 through 82 removed outlier: 4.215A pdb=" N MET E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 82' Processing helix chain 'E' and resid 249 through 254 removed outlier: 4.022A pdb=" N VAL E 252 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 308 through 313 removed outlier: 3.648A pdb=" N THR E 312 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.876A pdb=" N ALA E 387 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 423 removed outlier: 4.524A pdb=" N GLN E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY E 423 " --> pdb=" O ASP E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 452 removed outlier: 3.695A pdb=" N SER E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 480 Processing helix chain 'E' and resid 482 through 495 Processing helix chain 'E' and resid 508 through 530 removed outlier: 4.716A pdb=" N SER E 514 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 520 " --> pdb=" O LYS E 516 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 529 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 540 removed outlier: 4.091A pdb=" N CYS E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 552 Processing helix chain 'E' and resid 557 through 570 removed outlier: 3.638A pdb=" N LEU E 561 " --> pdb=" O SER E 557 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU E 570 " --> pdb=" O CYS E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 578 Processing helix chain 'E' and resid 579 through 594 removed outlier: 3.730A pdb=" N ILE E 583 " --> pdb=" O GLN E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 608 removed outlier: 4.032A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 624 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 810 through 816 removed outlier: 3.553A pdb=" N VAL E 815 " --> pdb=" O HIS E 812 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 891 removed outlier: 3.892A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU E 888 " --> pdb=" O LEU E 884 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN E 889 " --> pdb=" O THR E 885 " (cutoff:3.500A) Processing helix chain 'E' and resid 917 through 920 Processing helix chain 'E' and resid 921 through 936 removed outlier: 4.043A pdb=" N GLY E 936 " --> pdb=" O LEU E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 1002 Processing helix chain 'E' and resid 1023 through 1027 removed outlier: 4.090A pdb=" N LEU E1027 " --> pdb=" O TYR E1024 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1049 removed outlier: 4.274A pdb=" N SER E1034 " --> pdb=" O ALA E1030 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN E1035 " --> pdb=" O THR E1031 " (cutoff:3.500A) Processing helix chain 'E' and resid 1079 through 1082 Processing helix chain 'E' and resid 1225 through 1229 Processing helix chain 'E' and resid 1530 through 1534 removed outlier: 3.556A pdb=" N GLY E1533 " --> pdb=" O THR E1530 " (cutoff:3.500A) Processing helix chain 'E' and resid 1580 through 1585 removed outlier: 3.670A pdb=" N LYS E1585 " --> pdb=" O LEU E1581 " (cutoff:3.500A) Processing helix chain 'E' and resid 1651 through 1654 removed outlier: 3.827A pdb=" N SER E1654 " --> pdb=" O LEU E1651 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1651 through 1654' Processing helix chain 'E' and resid 1657 through 1674 Processing helix chain 'E' and resid 1681 through 1690 removed outlier: 3.531A pdb=" N LEU E1685 " --> pdb=" O VAL E1681 " (cutoff:3.500A) Processing helix chain 'E' and resid 1690 through 1700 Processing helix chain 'E' and resid 1704 through 1718 Processing helix chain 'E' and resid 1719 through 1732 removed outlier: 4.179A pdb=" N ALA E1723 " --> pdb=" O HIS E1719 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER E1729 " --> pdb=" O ARG E1725 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1765 through 1769 removed outlier: 3.895A pdb=" N THR E1768 " --> pdb=" O VAL E1765 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR E1769 " --> pdb=" O GLY E1766 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1765 through 1769' Processing helix chain 'E' and resid 1803 through 1824 Processing helix chain 'E' and resid 1833 through 1851 Proline residue: E1840 - end of helix Processing helix chain 'E' and resid 1856 through 1867 Processing helix chain 'E' and resid 1925 through 1929 Processing helix chain 'E' and resid 1934 through 1975 removed outlier: 4.403A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA E1971 " --> pdb=" O ASP E1967 " (cutoff:3.500A) Processing helix chain 'E' and resid 2034 through 2043 Processing helix chain 'E' and resid 2059 through 2071 removed outlier: 3.732A pdb=" N LEU E2063 " --> pdb=" O LEU E2059 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU E2068 " --> pdb=" O ARG E2064 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2110 removed outlier: 4.236A pdb=" N SER E2099 " --> pdb=" O GLN E2095 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP E2109 " --> pdb=" O TRP E2105 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR E2110 " --> pdb=" O ALA E2106 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2129 removed outlier: 3.736A pdb=" N VAL E2117 " --> pdb=" O SER E2113 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2141 Proline residue: E2139 - end of helix Processing helix chain 'E' and resid 2148 through 2166 removed outlier: 3.645A pdb=" N THR E2152 " --> pdb=" O SER E2148 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E2157 " --> pdb=" O MET E2153 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS E2158 " --> pdb=" O SER E2154 " (cutoff:3.500A) Processing helix chain 'E' and resid 2174 through 2188 Processing helix chain 'E' and resid 2189 through 2194 Processing helix chain 'E' and resid 2194 through 2202 removed outlier: 3.555A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2215 Processing helix chain 'E' and resid 2228 through 2242 Processing helix chain 'E' and resid 2243 through 2252 removed outlier: 3.566A pdb=" N SER E2249 " --> pdb=" O GLN E2245 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2260 Processing helix chain 'E' and resid 2272 through 2281 Processing helix chain 'E' and resid 2283 through 2290 Processing helix chain 'E' and resid 2291 through 2304 removed outlier: 3.841A pdb=" N LEU E2295 " --> pdb=" O GLN E2291 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2341 removed outlier: 3.933A pdb=" N VAL E2341 " --> pdb=" O PHE E2337 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2358 removed outlier: 4.188A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) Processing helix chain 'E' and resid 2377 through 2385 removed outlier: 4.090A pdb=" N GLU E2381 " --> pdb=" O LEU E2377 " (cutoff:3.500A) Processing helix chain 'E' and resid 2420 through 2433 Processing helix chain 'E' and resid 2434 through 2436 No H-bonds generated for 'chain 'E' and resid 2434 through 2436' Processing helix chain 'E' and resid 2450 through 2459 removed outlier: 3.920A pdb=" N ARG E2454 " --> pdb=" O ALA E2450 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E2455 " --> pdb=" O LEU E2451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2466 through 2475 removed outlier: 3.557A pdb=" N ILE E2470 " --> pdb=" O LEU E2466 " (cutoff:3.500A) Proline residue: E2473 - end of helix Processing helix chain 'E' and resid 2495 through 2509 removed outlier: 3.512A pdb=" N LYS E2499 " --> pdb=" O VAL E2495 " (cutoff:3.500A) Processing helix chain 'E' and resid 2515 through 2521 Processing helix chain 'E' and resid 2525 through 2534 removed outlier: 3.822A pdb=" N ALA E2533 " --> pdb=" O ASP E2529 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E2534 " --> pdb=" O MET E2530 " (cutoff:3.500A) Processing helix chain 'E' and resid 2545 through 2557 removed outlier: 3.608A pdb=" N ASN E2551 " --> pdb=" O ALA E2547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E2556 " --> pdb=" O ARG E2552 " (cutoff:3.500A) Processing helix chain 'E' and resid 2557 through 2562 removed outlier: 4.088A pdb=" N LEU E2561 " --> pdb=" O ALA E2557 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE E2562 " --> pdb=" O VAL E2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2557 through 2562' Processing helix chain 'E' and resid 2568 through 2586 Processing helix chain 'E' and resid 2592 through 2609 removed outlier: 3.770A pdb=" N ALA E2609 " --> pdb=" O ASP E2605 " (cutoff:3.500A) Processing helix chain 'E' and resid 2616 through 2634 Proline residue: E2631 - end of helix removed outlier: 3.772A pdb=" N ASN E2634 " --> pdb=" O VAL E2630 " (cutoff:3.500A) Processing helix chain 'E' and resid 2639 through 2660 Proline residue: E2658 - end of helix Processing helix chain 'E' and resid 2668 through 2686 removed outlier: 3.525A pdb=" N LEU E2686 " --> pdb=" O ILE E2682 " (cutoff:3.500A) Processing helix chain 'E' and resid 2692 through 2710 Proline residue: E2701 - end of helix Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 3.673A pdb=" N ASP E2752 " --> pdb=" O PRO E2748 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E2770 " --> pdb=" O TRP E2766 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN E2773 " --> pdb=" O ASP E2769 " (cutoff:3.500A) Processing helix chain 'E' and resid 2782 through 2785 Processing helix chain 'E' and resid 2793 through 2797 Processing helix chain 'E' and resid 2798 through 2819 removed outlier: 4.215A pdb=" N TYR E2805 " --> pdb=" O ASP E2801 " (cutoff:3.500A) Proline residue: E2808 - end of helix Processing helix chain 'E' and resid 2861 through 2865 Processing helix chain 'E' and resid 2868 through 2898 Processing helix chain 'E' and resid 2907 through 2911 Processing helix chain 'E' and resid 2912 through 2934 removed outlier: 3.732A pdb=" N ARG E2918 " --> pdb=" O LYS E2914 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS E2922 " --> pdb=" O ARG E2918 " (cutoff:3.500A) Processing helix chain 'E' and resid 3018 through 3038 Processing helix chain 'E' and resid 3044 through 3061 Processing helix chain 'E' and resid 3069 through 3090 Proline residue: E3085 - end of helix removed outlier: 3.805A pdb=" N VAL E3088 " --> pdb=" O GLY E3084 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA E3090 " --> pdb=" O GLU E3086 " (cutoff:3.500A) Processing helix chain 'E' and resid 3096 through 3114 Processing helix chain 'E' and resid 3132 through 3134 No H-bonds generated for 'chain 'E' and resid 3132 through 3134' Processing helix chain 'E' and resid 3135 through 3152 Processing helix chain 'E' and resid 3159 through 3177 Processing helix chain 'E' and resid 3185 through 3198 Processing helix chain 'E' and resid 3205 through 3216 Processing helix chain 'E' and resid 3274 through 3288 Proline residue: E3282 - end of helix Processing helix chain 'E' and resid 3295 through 3300 Processing helix chain 'E' and resid 3301 through 3311 Processing helix chain 'E' and resid 3318 through 3337 Processing helix chain 'E' and resid 3350 through 3363 Proline residue: E3360 - end of helix Processing helix chain 'E' and resid 3368 through 3397 removed outlier: 3.702A pdb=" N VAL E3373 " --> pdb=" O ALA E3369 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E3397 " --> pdb=" O LEU E3393 " (cutoff:3.500A) Processing helix chain 'E' and resid 3403 through 3407 Processing helix chain 'E' and resid 3407 through 3424 Processing helix chain 'E' and resid 3428 through 3435 removed outlier: 3.535A pdb=" N PHE E3435 " --> pdb=" O ALA E3431 " (cutoff:3.500A) Processing helix chain 'E' and resid 3439 through 3455 Processing helix chain 'E' and resid 3458 through 3469 Processing helix chain 'E' and resid 3479 through 3491 removed outlier: 3.857A pdb=" N ALA E3484 " --> pdb=" O LYS E3480 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E3485 " --> pdb=" O ALA E3481 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY E3487 " --> pdb=" O ASP E3483 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY E3488 " --> pdb=" O ALA E3484 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E3489 " --> pdb=" O GLN E3485 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E3490 " --> pdb=" O SER E3486 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN E3491 " --> pdb=" O GLY E3487 " (cutoff:3.500A) Processing helix chain 'E' and resid 3495 through 3503 Processing helix chain 'E' and resid 3516 through 3526 removed outlier: 3.548A pdb=" N ALA E3526 " --> pdb=" O LEU E3522 " (cutoff:3.500A) Processing helix chain 'E' and resid 3538 through 3543 Processing helix chain 'E' and resid 3550 through 3570 Proline residue: E3567 - end of helix Processing helix chain 'E' and resid 3646 through 3660 Processing helix chain 'E' and resid 3667 through 3679 removed outlier: 4.166A pdb=" N ASP E3671 " --> pdb=" O HIS E3667 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG E3672 " --> pdb=" O SER E3668 " (cutoff:3.500A) Processing helix chain 'E' and resid 3696 through 3710 Processing helix chain 'E' and resid 3719 through 3731 Processing helix chain 'E' and resid 3751 through 3772 removed outlier: 3.674A pdb=" N MET E3758 " --> pdb=" O GLU E3754 " (cutoff:3.500A) Processing helix chain 'E' and resid 3774 through 3786 Processing helix chain 'E' and resid 3791 through 3806 Processing helix chain 'E' and resid 3809 through 3823 Processing helix chain 'E' and resid 3826 through 3839 removed outlier: 3.761A pdb=" N GLN E3830 " --> pdb=" O VAL E3826 " (cutoff:3.500A) Processing helix chain 'E' and resid 3844 through 3851 Processing helix chain 'E' and resid 3878 through 3893 removed outlier: 3.588A pdb=" N CYS E3892 " --> pdb=" O LEU E3888 " (cutoff:3.500A) Processing helix chain 'E' and resid 3896 through 3906 Processing helix chain 'E' and resid 3914 through 3938 Processing helix chain 'E' and resid 3949 through 3970 Processing helix chain 'E' and resid 3973 through 3982 Processing helix chain 'E' and resid 3984 through 4003 removed outlier: 4.032A pdb=" N ALA E3988 " --> pdb=" O ARG E3984 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) Processing helix chain 'E' and resid 4004 through 4008 removed outlier: 5.108A pdb=" N SER E4007 " --> pdb=" O ALA E4004 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER E4008 " --> pdb=" O GLN E4005 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4004 through 4008' Processing helix chain 'E' and resid 4009 through 4031 removed outlier: 3.550A pdb=" N GLU E4015 " --> pdb=" O GLU E4011 " (cutoff:3.500A) Processing helix chain 'E' and resid 4038 through 4051 removed outlier: 3.549A pdb=" N MET E4044 " --> pdb=" O ILE E4040 " (cutoff:3.500A) Processing helix chain 'E' and resid 4051 through 4062 removed outlier: 4.015A pdb=" N ILE E4058 " --> pdb=" O ASN E4054 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E4062 " --> pdb=" O ILE E4058 " (cutoff:3.500A) Processing helix chain 'E' and resid 4073 through 4080 removed outlier: 3.829A pdb=" N PHE E4077 " --> pdb=" O GLY E4073 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E4080 " --> pdb=" O ALA E4076 " (cutoff:3.500A) Processing helix chain 'E' and resid 4091 through 4097 removed outlier: 3.838A pdb=" N LYS E4095 " --> pdb=" O LYS E4091 " (cutoff:3.500A) Processing helix chain 'E' and resid 4098 through 4100 No H-bonds generated for 'chain 'E' and resid 4098 through 4100' Processing helix chain 'E' and resid 4104 through 4115 Processing helix chain 'E' and resid 4136 through 4154 removed outlier: 3.705A pdb=" N GLY E4140 " --> pdb=" O ALA E4136 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4166 Processing helix chain 'E' and resid 4167 through 4175 removed outlier: 4.014A pdb=" N LEU E4171 " --> pdb=" O ALA E4167 " (cutoff:3.500A) Processing helix chain 'E' and resid 4200 through 4205 removed outlier: 3.875A pdb=" N TRP E4205 " --> pdb=" O ASN E4201 " (cutoff:3.500A) Processing helix chain 'E' and resid 4208 through 4223 removed outlier: 4.165A pdb=" N GLU E4212 " --> pdb=" O PRO E4208 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4250 removed outlier: 4.492A pdb=" N GLU E4232 " --> pdb=" O ALA E4228 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) Processing helix chain 'E' and resid 4546 through 4557 removed outlier: 3.572A pdb=" N LYS E4550 " --> pdb=" O VAL E4546 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4578 Processing helix chain 'E' and resid 4638 through 4663 removed outlier: 3.547A pdb=" N TRP E4644 " --> pdb=" O GLU E4640 " (cutoff:3.500A) Processing helix chain 'E' and resid 4664 through 4683 removed outlier: 3.992A pdb=" N LEU E4668 " --> pdb=" O LEU E4664 " (cutoff:3.500A) Processing helix chain 'E' and resid 4696 through 4703 removed outlier: 3.686A pdb=" N GLN E4700 " --> pdb=" O ASP E4696 " (cutoff:3.500A) Processing helix chain 'E' and resid 4704 through 4708 removed outlier: 3.804A pdb=" N ASN E4707 " --> pdb=" O LEU E4704 " (cutoff:3.500A) Processing helix chain 'E' and resid 4719 through 4729 Processing helix chain 'E' and resid 4734 through 4741 Processing helix chain 'E' and resid 4766 through 4771 removed outlier: 4.233A pdb=" N ILE E4771 " --> pdb=" O TRP E4767 " (cutoff:3.500A) Processing helix chain 'E' and resid 4773 through 4786 Processing helix chain 'E' and resid 4786 through 4805 removed outlier: 4.132A pdb=" N HIS E4803 " --> pdb=" O SER E4799 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E4804 " --> pdb=" O LEU E4800 " (cutoff:3.500A) Processing helix chain 'E' and resid 4806 through 4814 removed outlier: 3.881A pdb=" N ALA E4811 " --> pdb=" O PHE E4808 " (cutoff:3.500A) Processing helix chain 'E' and resid 4815 through 4820 Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.734A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN E4833 " --> pdb=" O SER E4829 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4857 removed outlier: 3.641A pdb=" N ASN E4857 " --> pdb=" O VAL E4853 " (cutoff:3.500A) Processing helix chain 'E' and resid 4858 through 4863 removed outlier: 4.539A pdb=" N LYS E4861 " --> pdb=" O PHE E4858 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR E4863 " --> pdb=" O ARG E4860 " (cutoff:3.500A) Processing helix chain 'E' and resid 4878 through 4889 Processing helix chain 'E' and resid 4896 through 4901 removed outlier: 3.510A pdb=" N GLU E4900 " --> pdb=" O ILE E4897 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE E4901 " --> pdb=" O GLY E4898 " (cutoff:3.500A) Processing helix chain 'E' and resid 4908 through 4924 removed outlier: 3.819A pdb=" N TYR E4912 " --> pdb=" O GLU E4908 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL E4914 " --> pdb=" O GLU E4910 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL E4915 " --> pdb=" O LEU E4911 " (cutoff:3.500A) Processing helix chain 'E' and resid 4927 through 4956 Processing helix chain 'E' and resid 4964 through 4969 removed outlier: 4.205A pdb=" N PHE E4968 " --> pdb=" O GLY E4964 " (cutoff:3.500A) Processing helix chain 'E' and resid 4974 through 4979 Processing helix chain 'E' and resid 4985 through 4997 removed outlier: 3.905A pdb=" N MET E4989 " --> pdb=" O LEU E4985 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E4996 " --> pdb=" O LEU E4992 " (cutoff:3.500A) Processing helix chain 'E' and resid 5004 through 5017 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 56 through 63 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.640A pdb=" N CYS G 65 " --> pdb=" O ASP G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 65' Processing helix chain 'G' and resid 77 through 82 removed outlier: 4.278A pdb=" N MET G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 77 through 82' Processing helix chain 'G' and resid 249 through 254 removed outlier: 4.034A pdb=" N VAL G 252 " --> pdb=" O GLY G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 Processing helix chain 'G' and resid 308 through 313 removed outlier: 3.647A pdb=" N THR G 312 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.883A pdb=" N ALA G 387 " --> pdb=" O MET G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 423 removed outlier: 4.513A pdb=" N GLN G 413 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 420 " --> pdb=" O LYS G 416 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 422 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY G 423 " --> pdb=" O ASP G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 452 removed outlier: 3.702A pdb=" N SER G 444 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 480 Processing helix chain 'G' and resid 482 through 495 Processing helix chain 'G' and resid 508 through 530 removed outlier: 4.720A pdb=" N SER G 514 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN G 520 " --> pdb=" O LYS G 516 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 529 " --> pdb=" O LEU G 525 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE G 530 " --> pdb=" O LEU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 540 removed outlier: 4.114A pdb=" N CYS G 537 " --> pdb=" O ASN G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 552 Processing helix chain 'G' and resid 557 through 570 removed outlier: 3.638A pdb=" N LEU G 561 " --> pdb=" O SER G 557 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU G 570 " --> pdb=" O CYS G 566 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 578 Processing helix chain 'G' and resid 579 through 594 removed outlier: 3.730A pdb=" N ILE G 583 " --> pdb=" O GLN G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 608 removed outlier: 4.036A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 624 Processing helix chain 'G' and resid 625 through 629 Processing helix chain 'G' and resid 810 through 816 removed outlier: 3.549A pdb=" N VAL G 815 " --> pdb=" O HIS G 812 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 891 removed outlier: 3.889A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU G 888 " --> pdb=" O LEU G 884 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLN G 889 " --> pdb=" O THR G 885 " (cutoff:3.500A) Processing helix chain 'G' and resid 917 through 920 Processing helix chain 'G' and resid 921 through 936 removed outlier: 4.047A pdb=" N GLY G 936 " --> pdb=" O LEU G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 978 through 1002 Processing helix chain 'G' and resid 1023 through 1027 removed outlier: 4.084A pdb=" N LEU G1027 " --> pdb=" O TYR G1024 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1049 removed outlier: 4.276A pdb=" N SER G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN G1035 " --> pdb=" O THR G1031 " (cutoff:3.500A) Processing helix chain 'G' and resid 1079 through 1082 Processing helix chain 'G' and resid 1225 through 1229 Processing helix chain 'G' and resid 1530 through 1534 removed outlier: 3.553A pdb=" N GLY G1533 " --> pdb=" O THR G1530 " (cutoff:3.500A) Processing helix chain 'G' and resid 1580 through 1585 removed outlier: 3.676A pdb=" N LYS G1585 " --> pdb=" O LEU G1581 " (cutoff:3.500A) Processing helix chain 'G' and resid 1651 through 1654 removed outlier: 3.825A pdb=" N SER G1654 " --> pdb=" O LEU G1651 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1651 through 1654' Processing helix chain 'G' and resid 1657 through 1674 Processing helix chain 'G' and resid 1681 through 1690 removed outlier: 3.522A pdb=" N LEU G1685 " --> pdb=" O VAL G1681 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP G1690 " --> pdb=" O CYS G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1690 through 1700 Processing helix chain 'G' and resid 1704 through 1718 Processing helix chain 'G' and resid 1719 through 1732 removed outlier: 4.180A pdb=" N ALA G1723 " --> pdb=" O HIS G1719 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER G1729 " --> pdb=" O ARG G1725 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET G1730 " --> pdb=" O SER G1726 " (cutoff:3.500A) Processing helix chain 'G' and resid 1765 through 1769 removed outlier: 3.888A pdb=" N THR G1768 " --> pdb=" O VAL G1765 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR G1769 " --> pdb=" O GLY G1766 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1765 through 1769' Processing helix chain 'G' and resid 1803 through 1824 Processing helix chain 'G' and resid 1833 through 1851 Proline residue: G1840 - end of helix Processing helix chain 'G' and resid 1856 through 1867 Processing helix chain 'G' and resid 1925 through 1929 Processing helix chain 'G' and resid 1934 through 1975 removed outlier: 4.373A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA G1971 " --> pdb=" O ASP G1967 " (cutoff:3.500A) Processing helix chain 'G' and resid 2034 through 2043 Processing helix chain 'G' and resid 2059 through 2071 removed outlier: 3.731A pdb=" N LEU G2063 " --> pdb=" O LEU G2059 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU G2068 " --> pdb=" O ARG G2064 " (cutoff:3.500A) Processing helix chain 'G' and resid 2094 through 2110 removed outlier: 4.239A pdb=" N SER G2099 " --> pdb=" O GLN G2095 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP G2109 " --> pdb=" O TRP G2105 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR G2110 " --> pdb=" O ALA G2106 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2129 removed outlier: 3.741A pdb=" N VAL G2117 " --> pdb=" O SER G2113 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2141 Proline residue: G2139 - end of helix Processing helix chain 'G' and resid 2148 through 2166 removed outlier: 3.649A pdb=" N THR G2152 " --> pdb=" O SER G2148 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU G2157 " --> pdb=" O MET G2153 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS G2158 " --> pdb=" O SER G2154 " (cutoff:3.500A) Processing helix chain 'G' and resid 2174 through 2188 Processing helix chain 'G' and resid 2189 through 2194 Processing helix chain 'G' and resid 2194 through 2202 removed outlier: 3.556A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2215 Processing helix chain 'G' and resid 2228 through 2242 Processing helix chain 'G' and resid 2243 through 2252 removed outlier: 3.571A pdb=" N SER G2249 " --> pdb=" O GLN G2245 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2260 Processing helix chain 'G' and resid 2272 through 2281 Processing helix chain 'G' and resid 2283 through 2290 Processing helix chain 'G' and resid 2291 through 2304 removed outlier: 3.822A pdb=" N LEU G2295 " --> pdb=" O GLN G2291 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2341 removed outlier: 3.932A pdb=" N VAL G2341 " --> pdb=" O PHE G2337 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2358 removed outlier: 4.184A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) Processing helix chain 'G' and resid 2377 through 2385 removed outlier: 4.090A pdb=" N GLU G2381 " --> pdb=" O LEU G2377 " (cutoff:3.500A) Processing helix chain 'G' and resid 2420 through 2433 Processing helix chain 'G' and resid 2434 through 2436 No H-bonds generated for 'chain 'G' and resid 2434 through 2436' Processing helix chain 'G' and resid 2450 through 2459 removed outlier: 3.920A pdb=" N ARG G2454 " --> pdb=" O ALA G2450 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G2455 " --> pdb=" O LEU G2451 " (cutoff:3.500A) Processing helix chain 'G' and resid 2466 through 2475 removed outlier: 3.560A pdb=" N ILE G2470 " --> pdb=" O LEU G2466 " (cutoff:3.500A) Proline residue: G2473 - end of helix Processing helix chain 'G' and resid 2495 through 2509 removed outlier: 3.512A pdb=" N LYS G2499 " --> pdb=" O VAL G2495 " (cutoff:3.500A) Processing helix chain 'G' and resid 2515 through 2521 Processing helix chain 'G' and resid 2525 through 2534 removed outlier: 3.826A pdb=" N ALA G2533 " --> pdb=" O ASP G2529 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G2534 " --> pdb=" O MET G2530 " (cutoff:3.500A) Processing helix chain 'G' and resid 2545 through 2557 removed outlier: 3.606A pdb=" N ASN G2551 " --> pdb=" O ALA G2547 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU G2556 " --> pdb=" O ARG G2552 " (cutoff:3.500A) Processing helix chain 'G' and resid 2557 through 2562 removed outlier: 4.086A pdb=" N LEU G2561 " --> pdb=" O ALA G2557 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE G2562 " --> pdb=" O VAL G2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2557 through 2562' Processing helix chain 'G' and resid 2568 through 2586 Processing helix chain 'G' and resid 2592 through 2609 removed outlier: 3.780A pdb=" N ALA G2609 " --> pdb=" O ASP G2605 " (cutoff:3.500A) Processing helix chain 'G' and resid 2616 through 2634 Proline residue: G2631 - end of helix removed outlier: 3.778A pdb=" N ASN G2634 " --> pdb=" O VAL G2630 " (cutoff:3.500A) Processing helix chain 'G' and resid 2639 through 2660 Proline residue: G2658 - end of helix Processing helix chain 'G' and resid 2668 through 2686 removed outlier: 3.520A pdb=" N LEU G2686 " --> pdb=" O ILE G2682 " (cutoff:3.500A) Processing helix chain 'G' and resid 2692 through 2710 Proline residue: G2701 - end of helix Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 3.715A pdb=" N ASP G2752 " --> pdb=" O PRO G2748 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS G2770 " --> pdb=" O TRP G2766 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN G2773 " --> pdb=" O ASP G2769 " (cutoff:3.500A) Processing helix chain 'G' and resid 2782 through 2785 Processing helix chain 'G' and resid 2793 through 2797 Processing helix chain 'G' and resid 2798 through 2819 removed outlier: 4.214A pdb=" N TYR G2805 " --> pdb=" O ASP G2801 " (cutoff:3.500A) Proline residue: G2808 - end of helix Processing helix chain 'G' and resid 2861 through 2865 removed outlier: 3.522A pdb=" N GLY G2864 " --> pdb=" O ASP G2861 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2898 Processing helix chain 'G' and resid 2907 through 2911 Processing helix chain 'G' and resid 2912 through 2934 removed outlier: 3.601A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS G2922 " --> pdb=" O ARG G2918 " (cutoff:3.500A) Processing helix chain 'G' and resid 3018 through 3038 removed outlier: 3.501A pdb=" N VAL G3024 " --> pdb=" O THR G3020 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G3025 " --> pdb=" O PRO G3021 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU G3035 " --> pdb=" O ALA G3031 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET G3038 " --> pdb=" O LYS G3034 " (cutoff:3.500A) Processing helix chain 'G' and resid 3044 through 3061 removed outlier: 3.712A pdb=" N ASP G3060 " --> pdb=" O LEU G3056 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA G3061 " --> pdb=" O PHE G3057 " (cutoff:3.500A) Processing helix chain 'G' and resid 3069 through 3090 removed outlier: 4.167A pdb=" N ARG G3073 " --> pdb=" O HIS G3069 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G3075 " --> pdb=" O LEU G3071 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY G3084 " --> pdb=" O VAL G3080 " (cutoff:3.500A) Proline residue: G3085 - end of helix removed outlier: 3.593A pdb=" N VAL G3088 " --> pdb=" O GLY G3084 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA G3090 " --> pdb=" O GLU G3086 " (cutoff:3.500A) Processing helix chain 'G' and resid 3096 through 3115 removed outlier: 3.566A pdb=" N ARG G3111 " --> pdb=" O VAL G3107 " (cutoff:3.500A) Processing helix chain 'G' and resid 3132 through 3134 No H-bonds generated for 'chain 'G' and resid 3132 through 3134' Processing helix chain 'G' and resid 3135 through 3152 removed outlier: 3.679A pdb=" N ILE G3147 " --> pdb=" O LEU G3143 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA G3148 " --> pdb=" O PHE G3144 " (cutoff:3.500A) Processing helix chain 'G' and resid 3159 through 3176 removed outlier: 3.572A pdb=" N VAL G3163 " --> pdb=" O ASP G3159 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER G3164 " --> pdb=" O ASP G3160 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G3174 " --> pdb=" O CYS G3170 " (cutoff:3.500A) Processing helix chain 'G' and resid 3185 through 3200 removed outlier: 3.604A pdb=" N ARG G3196 " --> pdb=" O GLU G3192 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU G3197 " --> pdb=" O CYS G3193 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA G3198 " --> pdb=" O LEU G3194 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA G3200 " --> pdb=" O ARG G3196 " (cutoff:3.500A) Processing helix chain 'G' and resid 3205 through 3216 Processing helix chain 'G' and resid 3274 through 3288 removed outlier: 3.849A pdb=" N CYS G3278 " --> pdb=" O LEU G3274 " (cutoff:3.500A) Proline residue: G3282 - end of helix Processing helix chain 'G' and resid 3295 through 3300 removed outlier: 3.774A pdb=" N GLY G3299 " --> pdb=" O ALA G3295 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA G3300 " --> pdb=" O LEU G3296 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3295 through 3300' Processing helix chain 'G' and resid 3300 through 3312 removed outlier: 3.846A pdb=" N CYS G3304 " --> pdb=" O ALA G3300 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G3309 " --> pdb=" O THR G3305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP G3310 " --> pdb=" O ALA G3306 " (cutoff:3.500A) Processing helix chain 'G' and resid 3318 through 3338 removed outlier: 3.537A pdb=" N ILE G3322 " --> pdb=" O ASN G3318 " (cutoff:3.500A) Processing helix chain 'G' and resid 3348 through 3363 removed outlier: 3.503A pdb=" N LEU G3354 " --> pdb=" O ARG G3350 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS G3355 " --> pdb=" O PRO G3351 " (cutoff:3.500A) Proline residue: G3360 - end of helix Processing helix chain 'G' and resid 3368 through 3397 removed outlier: 3.512A pdb=" N VAL G3373 " --> pdb=" O ALA G3369 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU G3376 " --> pdb=" O VAL G3372 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G3385 " --> pdb=" O LEU G3381 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G3397 " --> pdb=" O LEU G3393 " (cutoff:3.500A) Processing helix chain 'G' and resid 3402 through 3406 Processing helix chain 'G' and resid 3407 through 3424 Processing helix chain 'G' and resid 3428 through 3435 removed outlier: 3.842A pdb=" N GLU G3432 " --> pdb=" O ASN G3428 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G3433 " --> pdb=" O ALA G3429 " (cutoff:3.500A) Processing helix chain 'G' and resid 3439 through 3455 Processing helix chain 'G' and resid 3457 through 3469 removed outlier: 4.265A pdb=" N GLN G3461 " --> pdb=" O ASN G3457 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU G3463 " --> pdb=" O VAL G3459 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE G3464 " --> pdb=" O VAL G3460 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G3465 " --> pdb=" O GLN G3461 " (cutoff:3.500A) Processing helix chain 'G' and resid 3479 through 3491 removed outlier: 4.211A pdb=" N ALA G3484 " --> pdb=" O LYS G3480 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN G3485 " --> pdb=" O ALA G3481 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY G3487 " --> pdb=" O ASP G3483 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY G3488 " --> pdb=" O ALA G3484 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER G3489 " --> pdb=" O GLN G3485 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP G3490 " --> pdb=" O SER G3486 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN G3491 " --> pdb=" O GLY G3487 " (cutoff:3.500A) Processing helix chain 'G' and resid 3495 through 3504 removed outlier: 3.749A pdb=" N GLY G3500 " --> pdb=" O LYS G3496 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP G3501 " --> pdb=" O LYS G3497 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG G3502 " --> pdb=" O ARG G3498 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G3504 " --> pdb=" O GLY G3500 " (cutoff:3.500A) Processing helix chain 'G' and resid 3513 through 3515 No H-bonds generated for 'chain 'G' and resid 3513 through 3515' Processing helix chain 'G' and resid 3516 through 3526 removed outlier: 3.684A pdb=" N ILE G3520 " --> pdb=" O LYS G3516 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN G3523 " --> pdb=" O PRO G3519 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET G3524 " --> pdb=" O ILE G3520 " (cutoff:3.500A) Processing helix chain 'G' and resid 3538 through 3543 removed outlier: 4.002A pdb=" N LEU G3542 " --> pdb=" O THR G3538 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G3543 " --> pdb=" O ARG G3539 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3538 through 3543' Processing helix chain 'G' and resid 3550 through 3571 Proline residue: G3567 - end of helix removed outlier: 3.773A pdb=" N TRP G3571 " --> pdb=" O PRO G3567 " (cutoff:3.500A) Processing helix chain 'G' and resid 3646 through 3660 removed outlier: 3.792A pdb=" N LYS G3658 " --> pdb=" O LEU G3654 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G3659 " --> pdb=" O GLU G3655 " (cutoff:3.500A) Processing helix chain 'G' and resid 3668 through 3679 removed outlier: 3.787A pdb=" N ARG G3672 " --> pdb=" O SER G3668 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE G3674 " --> pdb=" O GLU G3670 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP G3675 " --> pdb=" O ASP G3671 " (cutoff:3.500A) Processing helix chain 'G' and resid 3696 through 3711 removed outlier: 3.764A pdb=" N THR G3711 " --> pdb=" O ARG G3707 " (cutoff:3.500A) Processing helix chain 'G' and resid 3719 through 3731 Processing helix chain 'G' and resid 3751 through 3772 removed outlier: 3.983A pdb=" N GLU G3755 " --> pdb=" O VAL G3751 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET G3758 " --> pdb=" O GLU G3754 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU G3770 " --> pdb=" O GLN G3766 " (cutoff:3.500A) Processing helix chain 'G' and resid 3774 through 3787 removed outlier: 3.986A pdb=" N SER G3784 " --> pdb=" O LEU G3780 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3804 removed outlier: 3.603A pdb=" N SER G3795 " --> pdb=" O GLY G3791 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G3800 " --> pdb=" O SER G3796 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3823 Processing helix chain 'G' and resid 3826 through 3839 removed outlier: 3.639A pdb=" N GLN G3830 " --> pdb=" O VAL G3826 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3851 removed outlier: 3.914A pdb=" N PHE G3847 " --> pdb=" O ASP G3843 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU G3848 " --> pdb=" O LEU G3844 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG G3849 " --> pdb=" O ASN G3845 " (cutoff:3.500A) Processing helix chain 'G' and resid 3878 through 3893 removed outlier: 3.606A pdb=" N ASP G3883 " --> pdb=" O GLU G3879 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG G3886 " --> pdb=" O GLN G3882 " (cutoff:3.500A) Processing helix chain 'G' and resid 3896 through 3906 removed outlier: 3.742A pdb=" N TYR G3902 " --> pdb=" O ASP G3898 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG G3904 " --> pdb=" O GLN G3900 " (cutoff:3.500A) Processing helix chain 'G' and resid 3914 through 3939 removed outlier: 3.692A pdb=" N VAL G3920 " --> pdb=" O ILE G3916 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY G3939 " --> pdb=" O TRP G3935 " (cutoff:3.500A) Processing helix chain 'G' and resid 3949 through 3969 Processing helix chain 'G' and resid 3973 through 3982 Processing helix chain 'G' and resid 3986 through 3997 removed outlier: 4.398A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) Processing helix chain 'G' and resid 3998 through 4003 Processing helix chain 'G' and resid 4004 through 4006 No H-bonds generated for 'chain 'G' and resid 4004 through 4006' Processing helix chain 'G' and resid 4009 through 4029 removed outlier: 3.692A pdb=" N ASP G4022 " --> pdb=" O ASP G4018 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL G4024 " --> pdb=" O GLN G4020 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G4027 " --> pdb=" O MET G4023 " (cutoff:3.500A) Processing helix chain 'G' and resid 4038 through 4051 removed outlier: 3.795A pdb=" N GLN G4043 " --> pdb=" O MET G4039 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET G4044 " --> pdb=" O ILE G4040 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G4045 " --> pdb=" O ALA G4041 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU G4048 " --> pdb=" O MET G4044 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4061 removed outlier: 3.807A pdb=" N MET G4057 " --> pdb=" O SER G4053 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE G4058 " --> pdb=" O ASN G4054 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G4059 " --> pdb=" O VAL G4055 " (cutoff:3.500A) Processing helix chain 'G' and resid 4062 through 4064 No H-bonds generated for 'chain 'G' and resid 4062 through 4064' Processing helix chain 'G' and resid 4073 through 4080 removed outlier: 3.907A pdb=" N PHE G4077 " --> pdb=" O GLY G4073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN G4078 " --> pdb=" O SER G4074 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR G4080 " --> pdb=" O ALA G4076 " (cutoff:3.500A) Processing helix chain 'G' and resid 4091 through 4097 removed outlier: 3.842A pdb=" N LYS G4095 " --> pdb=" O LYS G4091 " (cutoff:3.500A) Processing helix chain 'G' and resid 4098 through 4100 No H-bonds generated for 'chain 'G' and resid 4098 through 4100' Processing helix chain 'G' and resid 4104 through 4115 Processing helix chain 'G' and resid 4136 through 4154 removed outlier: 3.671A pdb=" N GLY G4140 " --> pdb=" O ALA G4136 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4166 removed outlier: 3.740A pdb=" N PHE G4163 " --> pdb=" O ARG G4159 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G4166 " --> pdb=" O ASN G4162 " (cutoff:3.500A) Processing helix chain 'G' and resid 4167 through 4175 removed outlier: 3.527A pdb=" N LEU G4171 " --> pdb=" O ALA G4167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR G4173 " --> pdb=" O SER G4169 " (cutoff:3.500A) Processing helix chain 'G' and resid 4200 through 4205 removed outlier: 3.833A pdb=" N TRP G4205 " --> pdb=" O ASN G4201 " (cutoff:3.500A) Processing helix chain 'G' and resid 4208 through 4223 removed outlier: 4.114A pdb=" N GLU G4212 " --> pdb=" O PRO G4208 " (cutoff:3.500A) Processing helix chain 'G' and resid 4227 through 4231 removed outlier: 3.804A pdb=" N MET G4231 " --> pdb=" O ALA G4228 " (cutoff:3.500A) Processing helix chain 'G' and resid 4232 through 4251 removed outlier: 3.636A pdb=" N ASP G4240 " --> pdb=" O SER G4236 " (cutoff:3.500A) Processing helix chain 'G' and resid 4546 through 4578 removed outlier: 3.526A pdb=" N ASN G4558 " --> pdb=" O TYR G4554 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR G4560 " --> pdb=" O SER G4556 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR G4561 " --> pdb=" O ARG G4557 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN G4574 " --> pdb=" O ALA G4570 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE G4576 " --> pdb=" O ALA G4572 " (cutoff:3.500A) Processing helix chain 'G' and resid 4638 through 4663 removed outlier: 3.505A pdb=" N LEU G4648 " --> pdb=" O TRP G4644 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE G4658 " --> pdb=" O ALA G4654 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY G4660 " --> pdb=" O LEU G4656 " (cutoff:3.500A) Processing helix chain 'G' and resid 4664 through 4683 removed outlier: 4.033A pdb=" N LEU G4668 " --> pdb=" O LEU G4664 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG G4679 " --> pdb=" O LYS G4675 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS G4680 " --> pdb=" O GLU G4676 " (cutoff:3.500A) Processing helix chain 'G' and resid 4696 through 4701 Processing helix chain 'G' and resid 4702 through 4707 removed outlier: 3.935A pdb=" N LEU G4706 " --> pdb=" O ASP G4702 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN G4707 " --> pdb=" O ARG G4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4702 through 4707' Processing helix chain 'G' and resid 4718 through 4729 removed outlier: 4.497A pdb=" N ARG G4722 " --> pdb=" O LYS G4718 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU G4725 " --> pdb=" O LYS G4721 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP G4726 " --> pdb=" O ARG G4722 " (cutoff:3.500A) Processing helix chain 'G' and resid 4734 through 4741 Processing helix chain 'G' and resid 4766 through 4771 removed outlier: 4.246A pdb=" N ILE G4771 " --> pdb=" O TRP G4767 " (cutoff:3.500A) Processing helix chain 'G' and resid 4772 through 4784 removed outlier: 3.995A pdb=" N GLN G4776 " --> pdb=" O ASP G4772 " (cutoff:3.500A) Processing helix chain 'G' and resid 4786 through 4805 removed outlier: 3.831A pdb=" N MET G4798 " --> pdb=" O TRP G4794 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS G4803 " --> pdb=" O SER G4799 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR G4804 " --> pdb=" O LEU G4800 " (cutoff:3.500A) Processing helix chain 'G' and resid 4806 through 4814 removed outlier: 3.624A pdb=" N ALA G4810 " --> pdb=" O PHE G4807 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G4811 " --> pdb=" O PHE G4808 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS G4812 " --> pdb=" O PHE G4809 " (cutoff:3.500A) Processing helix chain 'G' and resid 4815 through 4820 Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.679A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4857 removed outlier: 3.619A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) Processing helix chain 'G' and resid 4858 through 4863 removed outlier: 4.535A pdb=" N LYS G4861 " --> pdb=" O PHE G4858 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR G4863 " --> pdb=" O ARG G4860 " (cutoff:3.500A) Processing helix chain 'G' and resid 4878 through 4889 removed outlier: 3.588A pdb=" N MET G4887 " --> pdb=" O TYR G4883 " (cutoff:3.500A) Processing helix chain 'G' and resid 4889 through 4894 removed outlier: 4.601A pdb=" N GLY G4894 " --> pdb=" O GLY G4890 " (cutoff:3.500A) Processing helix chain 'G' and resid 4896 through 4901 removed outlier: 3.801A pdb=" N ILE G4901 " --> pdb=" O GLY G4898 " (cutoff:3.500A) Processing helix chain 'G' and resid 4908 through 4924 removed outlier: 4.319A pdb=" N TYR G4912 " --> pdb=" O GLU G4908 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) Processing helix chain 'G' and resid 4927 through 4955 removed outlier: 3.686A pdb=" N ILE G4936 " --> pdb=" O ILE G4932 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G4937 " --> pdb=" O GLN G4933 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP G4945 " --> pdb=" O GLY G4941 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4969 removed outlier: 4.231A pdb=" N PHE G4968 " --> pdb=" O GLY G4964 " (cutoff:3.500A) Processing helix chain 'G' and resid 4974 through 4979 Processing helix chain 'G' and resid 4986 through 4997 Processing helix chain 'G' and resid 5004 through 5017 Processing helix chain 'H' and resid 39 through 43 Processing helix chain 'H' and resid 56 through 66 removed outlier: 4.961A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.944A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.944A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 3.814A pdb=" N GLN A 71 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 230 through 233 removed outlier: 5.017A pdb=" N VAL A 245 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 376 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 290 through 292 Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 317 Processing sheet with id=AB1, first strand: chain 'A' and resid 635 through 639 Processing sheet with id=AB2, first strand: chain 'A' and resid 684 through 687 Processing sheet with id=AB3, first strand: chain 'A' and resid 762 through 766 removed outlier: 5.069A pdb=" N PHE A 757 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY A 766 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE A 755 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 756 " --> pdb=" O CYS A 747 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 713 through 714 removed outlier: 3.523A pdb=" N SER A 713 " --> pdb=" O TRP A 722 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP A 722 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 723 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 830 through 833 removed outlier: 5.345A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A1091 " --> pdb=" O ASN A1203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1136 through 1137 removed outlier: 3.513A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A1101 " --> pdb=" O SER A1193 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A1193 " --> pdb=" O ARG A1101 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A1238 " --> pdb=" O ASN A1610 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1245 through 1246 Processing sheet with id=AB8, first strand: chain 'A' and resid 1258 through 1260 Processing sheet with id=AB9, first strand: chain 'A' and resid 1295 through 1296 Processing sheet with id=AC1, first strand: chain 'A' and resid 1514 through 1517 removed outlier: 3.521A pdb=" N TYR A1435 " --> pdb=" O GLY A1517 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A1434 " --> pdb=" O ALA A1578 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1494 through 1496 removed outlier: 3.916A pdb=" N VAL A1450 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A1553 " --> pdb=" O TRP A1449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2776 through 2777 removed outlier: 5.558A pdb=" N SER A2776 " --> pdb=" O HIS A2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 2822 through 2824 Processing sheet with id=AC5, first strand: chain 'A' and resid 4178 through 4180 Processing sheet with id=AC6, first strand: chain 'A' and resid 4183 through 4184 Processing sheet with id=AC7, first strand: chain 'A' and resid 4580 through 4581 Processing sheet with id=AC8, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.994A pdb=" N THR B 75 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B 71 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 27 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY B 28 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.994A pdb=" N THR B 75 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B 71 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 23 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.954A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.954A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 71 through 73 removed outlier: 3.810A pdb=" N GLN C 71 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 117 through 120 Processing sheet with id=AD5, first strand: chain 'C' and resid 179 through 183 Processing sheet with id=AD6, first strand: chain 'C' and resid 280 through 283 Processing sheet with id=AD7, first strand: chain 'C' and resid 230 through 233 removed outlier: 5.005A pdb=" N VAL C 245 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 376 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 290 through 292 Processing sheet with id=AD9, first strand: chain 'C' and resid 315 through 317 Processing sheet with id=AE1, first strand: chain 'C' and resid 635 through 639 Processing sheet with id=AE2, first strand: chain 'C' and resid 684 through 687 Processing sheet with id=AE3, first strand: chain 'C' and resid 762 through 766 removed outlier: 5.073A pdb=" N PHE C 757 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY C 766 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ILE C 755 " --> pdb=" O GLY C 766 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C 756 " --> pdb=" O CYS C 747 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 713 through 714 removed outlier: 3.522A pdb=" N SER C 713 " --> pdb=" O TRP C 722 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 722 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 723 " --> pdb=" O VAL C 726 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 830 through 833 removed outlier: 5.343A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C1091 " --> pdb=" O ASN C1203 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1136 through 1137 removed outlier: 3.517A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG C1101 " --> pdb=" O SER C1193 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER C1193 " --> pdb=" O ARG C1101 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C1238 " --> pdb=" O ASN C1610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1245 through 1246 Processing sheet with id=AE8, first strand: chain 'C' and resid 1258 through 1260 Processing sheet with id=AE9, first strand: chain 'C' and resid 1295 through 1296 Processing sheet with id=AF1, first strand: chain 'C' and resid 1514 through 1517 removed outlier: 3.636A pdb=" N TYR C1434 " --> pdb=" O ALA C1578 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1494 through 1496 removed outlier: 3.915A pdb=" N VAL C1450 " --> pdb=" O TRP C1496 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C1553 " --> pdb=" O TRP C1449 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 2776 through 2777 removed outlier: 5.555A pdb=" N SER C2776 " --> pdb=" O HIS C2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 2822 through 2824 Processing sheet with id=AF5, first strand: chain 'C' and resid 4178 through 4180 Processing sheet with id=AF6, first strand: chain 'C' and resid 4183 through 4184 Processing sheet with id=AF7, first strand: chain 'C' and resid 4580 through 4581 Processing sheet with id=AF8, first strand: chain 'D' and resid 3 through 8 removed outlier: 3.991A pdb=" N THR D 75 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG D 71 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR D 27 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY D 28 " --> pdb=" O PHE D 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 3 through 8 removed outlier: 3.991A pdb=" N THR D 75 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG D 71 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL D 23 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.954A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.954A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 71 through 73 removed outlier: 3.812A pdb=" N GLN E 71 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 117 through 120 Processing sheet with id=AG5, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AG6, first strand: chain 'E' and resid 280 through 283 Processing sheet with id=AG7, first strand: chain 'E' and resid 230 through 233 removed outlier: 5.017A pdb=" N VAL E 245 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA E 376 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 290 through 292 Processing sheet with id=AG9, first strand: chain 'E' and resid 315 through 317 Processing sheet with id=AH1, first strand: chain 'E' and resid 635 through 639 Processing sheet with id=AH2, first strand: chain 'E' and resid 684 through 687 Processing sheet with id=AH3, first strand: chain 'E' and resid 762 through 766 removed outlier: 5.070A pdb=" N PHE E 757 " --> pdb=" O VAL E 764 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY E 766 " --> pdb=" O ILE E 755 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE E 755 " --> pdb=" O GLY E 766 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER E 756 " --> pdb=" O CYS E 747 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 713 through 714 removed outlier: 3.522A pdb=" N SER E 713 " --> pdb=" O TRP E 722 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP E 722 " --> pdb=" O SER E 713 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR E 723 " --> pdb=" O VAL E 726 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 830 through 833 removed outlier: 5.346A pdb=" N LEU E1202 " --> pdb=" O PRO E 837 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E1091 " --> pdb=" O ASN E1203 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 1136 through 1137 removed outlier: 3.520A pdb=" N VAL E1123 " --> pdb=" O TRP E1132 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E1101 " --> pdb=" O SER E1193 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER E1193 " --> pdb=" O ARG E1101 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E1238 " --> pdb=" O ASN E1610 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 1245 through 1246 Processing sheet with id=AH8, first strand: chain 'E' and resid 1258 through 1260 Processing sheet with id=AH9, first strand: chain 'E' and resid 1295 through 1296 Processing sheet with id=AI1, first strand: chain 'E' and resid 1514 through 1517 removed outlier: 3.639A pdb=" N TYR E1434 " --> pdb=" O ALA E1578 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 1494 through 1496 removed outlier: 3.915A pdb=" N VAL E1450 " --> pdb=" O TRP E1496 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E1553 " --> pdb=" O TRP E1449 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 2776 through 2777 removed outlier: 5.557A pdb=" N SER E2776 " --> pdb=" O HIS E2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'E' and resid 2822 through 2824 Processing sheet with id=AI5, first strand: chain 'E' and resid 4178 through 4180 Processing sheet with id=AI6, first strand: chain 'E' and resid 4183 through 4184 Processing sheet with id=AI7, first strand: chain 'E' and resid 4580 through 4581 Processing sheet with id=AI8, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.989A pdb=" N THR F 75 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY F 28 " --> pdb=" O PHE F 36 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.989A pdb=" N THR F 75 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL F 23 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 49 through 51 removed outlier: 4.942A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 49 through 51 removed outlier: 4.942A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 71 through 73 removed outlier: 3.813A pdb=" N GLN G 71 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AJ5, first strand: chain 'G' and resid 179 through 183 Processing sheet with id=AJ6, first strand: chain 'G' and resid 280 through 283 Processing sheet with id=AJ7, first strand: chain 'G' and resid 230 through 233 removed outlier: 5.003A pdb=" N VAL G 245 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 376 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'G' and resid 290 through 292 Processing sheet with id=AJ9, first strand: chain 'G' and resid 315 through 317 Processing sheet with id=AK1, first strand: chain 'G' and resid 635 through 639 Processing sheet with id=AK2, first strand: chain 'G' and resid 684 through 687 Processing sheet with id=AK3, first strand: chain 'G' and resid 762 through 766 removed outlier: 5.069A pdb=" N PHE G 757 " --> pdb=" O VAL G 764 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY G 766 " --> pdb=" O ILE G 755 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ILE G 755 " --> pdb=" O GLY G 766 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER G 756 " --> pdb=" O CYS G 747 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 713 through 714 removed outlier: 3.519A pdb=" N SER G 713 " --> pdb=" O TRP G 722 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP G 722 " --> pdb=" O SER G 713 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR G 723 " --> pdb=" O VAL G 726 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 830 through 833 removed outlier: 5.351A pdb=" N LEU G1202 " --> pdb=" O PRO G 837 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU G1091 " --> pdb=" O ASN G1203 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 1136 through 1137 removed outlier: 3.513A pdb=" N VAL G1123 " --> pdb=" O TRP G1132 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG G1101 " --> pdb=" O SER G1193 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER G1193 " --> pdb=" O ARG G1101 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE G1238 " --> pdb=" O ASN G1610 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 1245 through 1246 Processing sheet with id=AK8, first strand: chain 'G' and resid 1258 through 1260 Processing sheet with id=AK9, first strand: chain 'G' and resid 1295 through 1296 Processing sheet with id=AL1, first strand: chain 'G' and resid 1514 through 1517 removed outlier: 3.636A pdb=" N TYR G1434 " --> pdb=" O ALA G1578 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 1494 through 1496 removed outlier: 3.914A pdb=" N VAL G1450 " --> pdb=" O TRP G1496 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE G1553 " --> pdb=" O TRP G1449 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'G' and resid 2776 through 2777 removed outlier: 5.554A pdb=" N SER G2776 " --> pdb=" O HIS G2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL3 Processing sheet with id=AL4, first strand: chain 'G' and resid 4178 through 4180 removed outlier: 3.519A pdb=" N GLY G4179 " --> pdb=" O PHE G4195 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'G' and resid 4183 through 4184 Processing sheet with id=AL6, first strand: chain 'G' and resid 4580 through 4581 Processing sheet with id=AL7, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.893A pdb=" N THR H 75 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL H 23 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.893A pdb=" N THR H 75 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'H' and resid 27 through 29 removed outlier: 3.505A pdb=" N ASP H 37 " --> pdb=" O GLY H 28 " (cutoff:3.500A) 6269 hydrogen bonds defined for protein. 17812 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: 78.32 Time building geometry restraints manager: 36.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 18881 1.29 - 1.43: 29974 1.43 - 1.58: 63049 1.58 - 1.72: 87 1.72 - 1.86: 997 Bond restraints: 112988 Sorted by residual: bond pdb=" CD GLU A2853 " pdb=" OE1 GLU A2853 " ideal model delta sigma weight residual 1.249 1.449 -0.200 1.90e-02 2.77e+03 1.11e+02 bond pdb=" CD GLU E2853 " pdb=" OE1 GLU E2853 " ideal model delta sigma weight residual 1.249 1.449 -0.200 1.90e-02 2.77e+03 1.10e+02 bond pdb=" CD GLU G2853 " pdb=" OE1 GLU G2853 " ideal model delta sigma weight residual 1.249 1.444 -0.195 1.90e-02 2.77e+03 1.06e+02 bond pdb=" CD GLU C2853 " pdb=" OE1 GLU C2853 " ideal model delta sigma weight residual 1.249 1.443 -0.194 1.90e-02 2.77e+03 1.04e+02 bond pdb=" CA ILE A4181 " pdb=" C ILE A4181 " ideal model delta sigma weight residual 1.525 1.450 0.075 9.00e-03 1.23e+04 6.87e+01 ... (remaining 112983 not shown) Histogram of bond angle deviations from ideal: 91.53 - 100.82: 259 100.82 - 110.11: 25055 110.11 - 119.40: 69463 119.40 - 128.70: 57450 128.70 - 137.99: 853 Bond angle restraints: 153080 Sorted by residual: angle pdb=" C GLU C 915 " pdb=" N PRO C 916 " pdb=" CA PRO C 916 " ideal model delta sigma weight residual 119.84 137.99 -18.15 1.25e+00 6.40e-01 2.11e+02 angle pdb=" C GLU G 915 " pdb=" N PRO G 916 " pdb=" CA PRO G 916 " ideal model delta sigma weight residual 119.84 137.85 -18.01 1.25e+00 6.40e-01 2.07e+02 angle pdb=" C GLU E 915 " pdb=" N PRO E 916 " pdb=" CA PRO E 916 " ideal model delta sigma weight residual 119.84 137.83 -17.99 1.25e+00 6.40e-01 2.07e+02 angle pdb=" C GLU A 915 " pdb=" N PRO A 916 " pdb=" CA PRO A 916 " ideal model delta sigma weight residual 119.84 137.77 -17.93 1.25e+00 6.40e-01 2.06e+02 angle pdb=" C PRO A 805 " pdb=" N PRO A 806 " pdb=" CA PRO A 806 " ideal model delta sigma weight residual 119.90 131.86 -11.96 1.02e+00 9.61e-01 1.38e+02 ... (remaining 153075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.25: 66061 26.25 - 52.50: 1065 52.50 - 78.75: 71 78.75 - 105.01: 56 105.01 - 131.26: 28 Dihedral angle restraints: 67281 sinusoidal: 23813 harmonic: 43468 Sorted by residual: dihedral pdb=" CA ALA E1588 " pdb=" C ALA E1588 " pdb=" N PRO E1589 " pdb=" CA PRO E1589 " ideal model delta harmonic sigma weight residual -180.00 -48.74 -131.26 0 5.00e+00 4.00e-02 6.89e+02 dihedral pdb=" CA ALA A1588 " pdb=" C ALA A1588 " pdb=" N PRO A1589 " pdb=" CA PRO A1589 " ideal model delta harmonic sigma weight residual -180.00 -48.78 -131.22 0 5.00e+00 4.00e-02 6.89e+02 dihedral pdb=" CA ALA G1588 " pdb=" C ALA G1588 " pdb=" N PRO G1589 " pdb=" CA PRO G1589 " ideal model delta harmonic sigma weight residual -180.00 -48.87 -131.13 0 5.00e+00 4.00e-02 6.88e+02 ... (remaining 67278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 15753 0.154 - 0.308: 1632 0.308 - 0.462: 111 0.462 - 0.616: 13 0.616 - 0.770: 3 Chirality restraints: 17512 Sorted by residual: chirality pdb=" CG LEU A3884 " pdb=" CB LEU A3884 " pdb=" CD1 LEU A3884 " pdb=" CD2 LEU A3884 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CG LEU C3884 " pdb=" CB LEU C3884 " pdb=" CD1 LEU C3884 " pdb=" CD2 LEU C3884 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CG LEU E3884 " pdb=" CB LEU E3884 " pdb=" CD1 LEU E3884 " pdb=" CD2 LEU E3884 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 17509 not shown) Planarity restraints: 19832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G4849 " 0.115 2.00e-02 2.50e+03 6.22e-02 7.73e+01 pdb=" CG TYR G4849 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR G4849 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR G4849 " -0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR G4849 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR G4849 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR G4849 " 0.030 2.00e-02 2.50e+03 pdb=" OH TYR G4849 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A4849 " 0.105 2.00e-02 2.50e+03 6.13e-02 7.52e+01 pdb=" CG TYR A4849 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A4849 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A4849 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 TYR A4849 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR A4849 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A4849 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A4849 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C4849 " 0.102 2.00e-02 2.50e+03 5.85e-02 6.84e+01 pdb=" CG TYR C4849 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR C4849 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C4849 " -0.083 2.00e-02 2.50e+03 pdb=" CE1 TYR C4849 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR C4849 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR C4849 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C4849 " 0.061 2.00e-02 2.50e+03 ... (remaining 19829 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 475 2.41 - 3.03: 65913 3.03 - 3.66: 180166 3.66 - 4.28: 265230 4.28 - 4.90: 403982 Nonbonded interactions: 915766 Sorted by model distance: nonbonded pdb=" NH1 ARG G1808 " pdb=" OD2 ASP G1858 " model vdw 1.789 2.520 nonbonded pdb=" NH1 ARG E1808 " pdb=" OD2 ASP E1858 " model vdw 1.790 2.520 nonbonded pdb=" NH1 ARG A1808 " pdb=" OD2 ASP A1858 " model vdw 1.790 2.520 nonbonded pdb=" NH1 ARG C1808 " pdb=" OD2 ASP C1858 " model vdw 1.791 2.520 nonbonded pdb=" NH1 ARG A 683 " pdb=" O ASN A 705 " model vdw 1.974 2.520 ... (remaining 915761 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 12 through 2924 or resid 2926 through 5033 or resid 6000)) \ selection = (chain 'C' and (resid 12 through 2924 or resid 2926 through 5033 or resid 6000)) \ selection = (chain 'E' and (resid 12 through 2924 or resid 2926 through 5033 or resid 6000)) \ selection = (chain 'G' and (resid 12 through 2924 or resid 2926 through 5033 or resid 6000)) \ } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.070 Extract box with map and model: 14.380 Check model and map are aligned: 1.240 Set scattering table: 0.750 Process input model: 335.510 Find NCS groups from input model: 5.910 Set up NCS constraints: 0.670 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: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 362.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.017 0.200 112988 Z= 1.095 Angle : 1.699 18.149 153080 Z= 1.084 Chirality : 0.095 0.770 17512 Planarity : 0.009 0.116 19832 Dihedral : 11.295 131.258 38985 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 2.46 % Allowed : 5.75 % Favored : 91.78 % Rotamer: Outliers : 0.51 % Allowed : 1.69 % Favored : 97.80 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.90 % Twisted General : 0.17 % 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: -2.71 (0.06), residues: 14424 helix: -2.56 (0.03), residues: 7884 sheet: -3.39 (0.13), residues: 1096 loop : 0.27 (0.09), residues: 5444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.011 TRP G3986 HIS 0.037 0.006 HIS C4153 PHE 0.079 0.010 PHE G3899 TYR 0.115 0.010 TYR G4849 ARG 0.035 0.003 ARG G3849 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28848 Ramachandran restraints generated. 14424 Oldfield, 0 Emsley, 14424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28848 Ramachandran restraints generated. 14424 Oldfield, 0 Emsley, 14424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3160 residues out of total 13156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 3087 time to evaluate : 9.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable