Starting phenix.real_space_refine on Fri Dec 8 18:32:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8h_2807/12_2023/3j8h_2807.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8h_2807/12_2023/3j8h_2807.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/3j8h_2807/12_2023/3j8h_2807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8h_2807/12_2023/3j8h_2807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8h_2807/12_2023/3j8h_2807.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8h_2807/12_2023/3j8h_2807.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 70680 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 GLU 159": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A ARG 1584": "NH1" <-> "NH2" Residue "A ARG 1618": "NH1" <-> "NH2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1820": "NH1" <-> "NH2" Residue "A GLU 1857": "OE1" <-> "OE2" Residue "A GLU 1963": "OE1" <-> "OE2" Residue "A GLU 2449": "OE1" <-> "OE2" Residue "A ARG 2552": "NH1" <-> "NH2" Residue "A GLU 2925": "OE1" <-> "OE2" Residue "A ARG 3648": "NH1" <-> "NH2" Residue "A GLU 3670": "OE1" <-> "OE2" Residue "A ARG 3672": "NH1" <-> "NH2" Residue "A ARG 3984": "NH1" <-> "NH2" Residue "A ARG 4161": "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 GLU 4690": "OE1" <-> "OE2" Residue "A ARG 4892": "NH1" <-> "NH2" Residue "A GLU 4910": "OE1" <-> "OE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 844": "NH1" <-> "NH2" Residue "C ARG 1584": "NH1" <-> "NH2" Residue "C ARG 1618": "NH1" <-> "NH2" Residue "C ARG 1725": "NH1" <-> "NH2" Residue "C ARG 1820": "NH1" <-> "NH2" Residue "C GLU 1857": "OE1" <-> "OE2" Residue "C GLU 1963": "OE1" <-> "OE2" Residue "C GLU 2449": "OE1" <-> "OE2" Residue "C ARG 2552": "NH1" <-> "NH2" Residue "C GLU 2925": "OE1" <-> "OE2" Residue "C ARG 3648": "NH1" <-> "NH2" Residue "C GLU 3670": "OE1" <-> "OE2" Residue "C ARG 3672": "NH1" <-> "NH2" Residue "C ARG 3984": "NH1" <-> "NH2" Residue "C ARG 4161": "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 GLU 4690": "OE1" <-> "OE2" Residue "C ARG 4892": "NH1" <-> "NH2" Residue "C GLU 4910": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 844": "NH1" <-> "NH2" Residue "E ARG 1584": "NH1" <-> "NH2" Residue "E ARG 1618": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1820": "NH1" <-> "NH2" Residue "E GLU 1857": "OE1" <-> "OE2" Residue "E GLU 1963": "OE1" <-> "OE2" Residue "E GLU 2449": "OE1" <-> "OE2" Residue "E ARG 2552": "NH1" <-> "NH2" Residue "E GLU 2925": "OE1" <-> "OE2" Residue "E ARG 3648": "NH1" <-> "NH2" Residue "E GLU 3670": "OE1" <-> "OE2" Residue "E ARG 3672": "NH1" <-> "NH2" Residue "E ARG 3984": "NH1" <-> "NH2" Residue "E ARG 4161": "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 GLU 4690": "OE1" <-> "OE2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E GLU 4910": "OE1" <-> "OE2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "G GLU 159": "OE1" <-> "OE2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 844": "NH1" <-> "NH2" Residue "G ARG 1584": "NH1" <-> "NH2" Residue "G ARG 1618": "NH1" <-> "NH2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 1820": "NH1" <-> "NH2" Residue "G GLU 1857": "OE1" <-> "OE2" Residue "G GLU 1963": "OE1" <-> "OE2" Residue "G GLU 2449": "OE1" <-> "OE2" Residue "G ARG 2552": "NH1" <-> "NH2" Residue "G GLU 2925": "OE1" <-> "OE2" Residue "G ARG 3648": "NH1" <-> "NH2" Residue "G GLU 3670": "OE1" <-> "OE2" Residue "G ARG 3672": "NH1" <-> "NH2" Residue "G ARG 3984": "NH1" <-> "NH2" Residue "G ARG 4161": "NH1" <-> "NH2" Residue "G ARG 4188": "NH1" <-> "NH2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4202": "NH1" <-> "NH2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G GLU 4690": "OE1" <-> "OE2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G GLU 4910": "OE1" <-> "OE2" Residue "H ARG 13": "NH1" <-> "NH2" Time to flip residues: 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 111160 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 26957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 Conformer: "B" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 bond proxies already assigned to first conformer: 27406 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: 26957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 Conformer: "B" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 bond proxies already assigned to first conformer: 27406 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: 26957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 Conformer: "B" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 bond proxies already assigned to first conformer: 27406 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: 26957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 Conformer: "B" Number of residues, atoms: 3660, 26948 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 130, 'TRANS': 3524} Chain breaks: 81 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2631 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 20, 'UNK:plan-1': 568, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 15, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1009 bond proxies already assigned to first conformer: 27406 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 26318 SG CYS A4958 189.061 165.050 84.692 1.00 20.00 S ATOM 26343 SG CYS A4961 187.583 164.788 87.788 1.00 20.00 S ATOM 54107 SG CYS C4958 165.050 167.379 84.692 1.00 20.00 S ATOM 54132 SG CYS C4961 164.788 168.857 87.788 1.00 20.00 S ATOM 81896 SG CYS E4958 167.379 191.390 84.692 1.00 20.00 S ATOM 81921 SG CYS E4961 168.857 191.652 87.788 1.00 20.00 S ATOM A07H1 SG CYS G4958 191.390 189.061 84.692 1.00 20.00 S ATOM A07HQ SG CYS G4961 191.652 187.583 87.788 1.00 20.00 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: 77.46, per 1000 atoms: 0.70 Number of scatterers: 111160 At special positions: 0 Unit cell: (357.78, 357.78, 206.36, 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 70680 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: 30.32 Conformation dependent library (CDL) restraints added in 24.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4961 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4958 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4961 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4983 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4958 " pdb=" ZN E6000 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4961 " pdb="ZN ZN E6000 " - pdb=" NE2 HIS E4983 " pdb="ZN ZN E6000 " - pdb=" NE2 HIS E4978 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4958 " pdb=" ZN G6000 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4961 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4983 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4978 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4958 " Number of angles added : 8 24784 Ramachandran restraints generated. 12392 Oldfield, 0 Emsley, 12392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28544 Finding SS restraints... Secondary structure from input PDB file: 680 helices and 116 sheets defined 71.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.02 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.151A 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 75 through 84 removed outlier: 3.606A pdb=" N ASN A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.103A pdb=" N VAL A 252 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.808A pdb=" N ALA A 387 " --> pdb=" O MET A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.888A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 460 through 480 removed outlier: 3.642A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 508 through 513 Processing helix chain 'A' and resid 514 through 531 Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.878A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.956A pdb=" N ASP A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 570 removed outlier: 4.130A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 579 through 594 removed outlier: 3.627A pdb=" N ILE A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.521A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 812 through 816 removed outlier: 4.119A pdb=" N LEU A 816 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 888 removed outlier: 3.852A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 935 removed outlier: 4.561A pdb=" N TYR A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1002 Processing helix chain 'A' and resid 1028 through 1049 removed outlier: 4.379A pdb=" N SER A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 4.608A 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 1217 through 1222 removed outlier: 3.952A pdb=" N GLU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A1222 " --> pdb=" O GLY A1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1217 through 1222' Processing helix chain 'A' and resid 1225 through 1229 Processing helix chain 'A' and resid 1531 through 1534 Processing helix chain 'A' and resid 1579 through 1585 Processing helix chain 'A' and resid 1641 through 1645 removed outlier: 3.946A pdb=" N ASN A1645 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1654 Processing helix chain 'A' and resid 1656 through 1674 removed outlier: 3.933A pdb=" N GLN A1660 " --> pdb=" O ARG A1656 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS A1674 " --> pdb=" O TYR A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1690 removed outlier: 3.720A 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 1734 removed outlier: 4.638A pdb=" N ALA A1723 " --> pdb=" O HIS A1719 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A1729 " --> pdb=" O ARG A1725 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A1734 " --> pdb=" O MET A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 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 1855 through 1867 Processing helix chain 'A' and resid 1932 through 1974 removed outlier: 3.774A pdb=" N VAL A1966 " --> pdb=" O ALA A1962 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A1968 " --> pdb=" O ARG A1964 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2044 Processing helix chain 'A' and resid 2045 through 2047 No H-bonds generated for 'chain 'A' and resid 2045 through 2047' Processing helix chain 'A' and resid 2057 through 2057 No H-bonds generated for 'chain 'A' and resid 2057 through 2057' Processing helix chain 'A' and resid 2058 through 2071 Processing helix chain 'A' and resid 2094 through 2109 removed outlier: 3.582A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2129 removed outlier: 4.046A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2138 Processing helix chain 'A' and resid 2139 through 2141 No H-bonds generated for 'chain 'A' and resid 2139 through 2141' Processing helix chain 'A' and resid 2145 through 2147 No H-bonds generated for 'chain 'A' and resid 2145 through 2147' Processing helix chain 'A' and resid 2148 through 2167 removed outlier: 4.503A pdb=" N SER A2164 " --> pdb=" O GLY A2160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (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: 3.527A pdb=" N MET A2198 " --> pdb=" O HIS A2194 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A2202 " --> pdb=" O MET A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2216 removed outlier: 3.516A pdb=" N GLY A2216 " --> pdb=" O VAL A2212 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2242 Processing helix chain 'A' and resid 2243 through 2252 removed outlier: 3.618A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) Processing helix chain 'A' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N GLU A2259 " --> pdb=" O SER A2255 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2263 No H-bonds generated for 'chain 'A' and resid 2262 through 2263' Processing helix chain 'A' and resid 2271 through 2271 No H-bonds generated for 'chain 'A' and resid 2271 through 2271' Processing helix chain 'A' and resid 2272 through 2282 removed outlier: 4.673A pdb=" N ASP A2282 " --> pdb=" O ALA A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2305 removed outlier: 3.785A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2326 through 2340 removed outlier: 3.746A pdb=" N PHE A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2360 removed outlier: 4.361A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2385 Processing helix chain 'A' and resid 2420 through 2436 Processing helix chain 'A' and resid 2450 through 2459 Processing helix chain 'A' and resid 2466 through 2475 removed outlier: 3.603A pdb=" N UNK A2470 " --> pdb=" O UNK A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2510 removed outlier: 3.718A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2522 Processing helix chain 'A' and resid 2526 through 2534 removed outlier: 3.911A pdb=" N ALA A2534 " --> pdb=" O ASP A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2537 No H-bonds generated for 'chain 'A' and resid 2535 through 2537' Processing helix chain 'A' and resid 2545 through 2559 Processing helix chain 'A' and resid 2560 through 2562 No H-bonds generated for 'chain 'A' and resid 2560 through 2562' Processing helix chain 'A' and resid 2568 through 2586 Processing helix chain 'A' and resid 2592 through 2609 Processing helix chain 'A' and resid 2616 through 2634 removed outlier: 3.760A pdb=" N UNK A2634 " --> pdb=" O UNK A2630 " (cutoff:3.500A) Processing helix chain 'A' and resid 2639 through 2659 Processing helix chain 'A' and resid 2668 through 2686 removed outlier: 3.500A pdb=" N UNK A2686 " --> pdb=" O UNK A2682 " (cutoff:3.500A) Processing helix chain 'A' and resid 2692 through 2712 Processing helix chain 'A' and resid 2748 through 2773 removed outlier: 3.728A pdb=" N ASP A2752 " --> pdb=" O PRO A2748 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A2753 " --> pdb=" O GLU A2749 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A2773 " --> pdb=" O ASP A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2782 through 2786 Processing helix chain 'A' and resid 2793 through 2797 Processing helix chain 'A' and resid 2798 through 2819 removed outlier: 3.640A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.231A 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 2912 through 2934 removed outlier: 3.895A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A2929 " --> pdb=" O AGLU A2925 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3038 Processing helix chain 'A' and resid 3044 through 3061 Processing helix chain 'A' and resid 3069 through 3089 removed outlier: 3.697A pdb=" N UNK A3088 " --> pdb=" O UNK A3084 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3115 Processing helix chain 'A' and resid 3133 through 3152 removed outlier: 3.799A pdb=" N UNK A3137 " --> pdb=" O UNK A3133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK A3144 " --> pdb=" O UNK A3140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK A3151 " --> pdb=" O UNK A3147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNK A3152 " --> pdb=" O UNK A3148 " (cutoff:3.500A) Processing helix chain 'A' and resid 3159 through 3178 Processing helix chain 'A' and resid 3184 through 3199 Processing helix chain 'A' and resid 3205 through 3217 removed outlier: 3.938A pdb=" N UNK A3217 " --> pdb=" O UNK A3213 " (cutoff:3.500A) Processing helix chain 'A' and resid 3274 through 3289 Processing helix chain 'A' and resid 3295 through 3312 removed outlier: 3.912A pdb=" N UNK A3303 " --> pdb=" O UNK A3299 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N UNK A3304 " --> pdb=" O UNK A3300 " (cutoff:3.500A) Processing helix chain 'A' and resid 3318 through 3338 Processing helix chain 'A' and resid 3347 through 3362 Processing helix chain 'A' and resid 3369 through 3397 removed outlier: 3.504A pdb=" N UNK A3397 " --> pdb=" O UNK A3393 " (cutoff:3.500A) Processing helix chain 'A' and resid 3403 through 3424 removed outlier: 4.184A pdb=" N UNK A3408 " --> pdb=" O UNK A3404 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N UNK A3409 " --> pdb=" O UNK A3405 " (cutoff:3.500A) Processing helix chain 'A' and resid 3428 through 3435 removed outlier: 3.629A pdb=" N UNK A3435 " --> pdb=" O UNK A3431 " (cutoff:3.500A) Processing helix chain 'A' and resid 3437 through 3454 Processing helix chain 'A' and resid 3458 through 3469 Processing helix chain 'A' and resid 3479 through 3490 removed outlier: 3.788A pdb=" N UNK A3490 " --> pdb=" O UNK A3486 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3504 Processing helix chain 'A' and resid 3514 through 3526 Processing helix chain 'A' and resid 3538 through 3544 Processing helix chain 'A' and resid 3550 through 3570 Processing helix chain 'A' and resid 3646 through 3661 removed outlier: 3.889A pdb=" N ALA A3659 " --> pdb=" O GLU A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3665 through 3667 No H-bonds generated for 'chain 'A' and resid 3665 through 3667' Processing helix chain 'A' and resid 3668 through 3679 removed outlier: 3.969A pdb=" N ARG A3672 " --> pdb=" O SER A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3733 removed outlier: 3.907A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) Processing helix chain 'A' and resid 3751 through 3773 removed outlier: 3.868A pdb=" N ARG A3773 " --> pdb=" O ARG A3769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.961A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A3783 " --> pdb=" O VAL A3779 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 3.513A pdb=" N SER A3795 " --> pdb=" O GLY A3791 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A3800 " --> pdb=" O SER A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3823 Processing helix chain 'A' and resid 3826 through 3838 removed outlier: 3.582A pdb=" N THR A3838 " --> pdb=" O ALA A3834 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3852 removed outlier: 3.829A pdb=" N LYS A3852 " --> pdb=" O GLU A3848 " (cutoff:3.500A) Processing helix chain 'A' and resid 3878 through 3893 Processing helix chain 'A' and resid 3896 through 3906 Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 4.306A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3971 removed outlier: 3.969A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A3971 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3982 removed outlier: 3.533A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3984 through 4003 removed outlier: 4.030A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A3993 " --> pdb=" O VAL A3989 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) Processing helix chain 'A' and resid 4006 through 4032 removed outlier: 3.794A pdb=" N GLU A4011 " --> pdb=" O SER A4007 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU A4012 " --> pdb=" O SER A4008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A4013 " --> pdb=" O GLN A4009 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A4032 " --> pdb=" O LEU A4028 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.576A pdb=" N ASP A4063 " --> pdb=" O LEU A4059 " (cutoff:3.500A) Processing helix chain 'A' and resid 4072 through 4080 removed outlier: 3.783A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4099 removed outlier: 3.625A pdb=" N LYS A4095 " --> pdb=" O LYS A4091 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 3.567A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4130 removed outlier: 3.820A pdb=" N PHE A4128 " --> pdb=" O ASN A4124 " (cutoff:3.500A) Processing helix chain 'A' and resid 4136 through 4154 removed outlier: 3.747A pdb=" N GLY A4140 " --> pdb=" O ALA A4136 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4175 removed outlier: 5.348A pdb=" N SER A4169 " --> pdb=" O GLU A4165 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE A4170 " --> pdb=" O LEU A4166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR A4173 " --> pdb=" O SER A4169 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A4174 " --> pdb=" O ILE A4170 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4205 Processing helix chain 'A' and resid 4208 through 4223 removed outlier: 4.492A pdb=" N GLU A4212 " --> pdb=" O PRO A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4227 through 4250 removed outlier: 4.038A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A4234 " --> pdb=" O LYS A4230 " (cutoff:3.500A) Processing helix chain 'A' and resid 4546 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4663 removed outlier: 3.511A pdb=" N CYS A4663 " --> pdb=" O ILE A4659 " (cutoff:3.500A) Processing helix chain 'A' and resid 4664 through 4683 removed outlier: 3.894A pdb=" N LEU A4668 " --> pdb=" O LEU A4664 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4702 Processing helix chain 'A' and resid 4702 through 4707 removed outlier: 3.868A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4702 through 4707' Processing helix chain 'A' and resid 4719 through 4729 removed outlier: 3.699A pdb=" N LEU A4725 " --> pdb=" O LYS A4721 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4741 Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 3.742A 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 Processing helix chain 'A' and resid 4808 through 4819 removed outlier: 3.641A pdb=" N LEU A4813 " --> pdb=" O ALA A4810 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.617A pdb=" N ARG A4824 " --> pdb=" O VAL A4820 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A4825 " --> pdb=" O LYS A4821 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4858 removed outlier: 3.671A pdb=" N LEU A4837 " --> pdb=" O ASN A4833 " (cutoff:3.500A) Processing helix chain 'A' and resid 4859 through 4863 removed outlier: 3.565A 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: 3.740A pdb=" N ASP A4899 " --> pdb=" O GLY A4896 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A4901 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4907 through 4924 removed outlier: 3.604A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) Processing helix chain 'A' and resid 4927 through 4956 removed outlier: 3.625A pdb=" N ILE A4937 " --> pdb=" O GLN A4933 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 4.077A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 removed outlier: 4.052A pdb=" N THR A4977 " --> pdb=" O HIS A4973 " (cutoff:3.500A) Processing helix chain 'A' and resid 4985 through 4998 removed outlier: 3.675A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) Processing helix chain 'A' and resid 4999 through 5003 removed outlier: 3.723A pdb=" N HIS A5003 " --> pdb=" O GLU A5000 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5033 Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.567A pdb=" N VAL B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) 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: 4.151A 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 75 through 84 removed outlier: 3.606A pdb=" N ASN C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 249 through 254 removed outlier: 4.103A pdb=" N VAL C 252 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.808A pdb=" N ALA C 387 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.888A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 452 Processing helix chain 'C' and resid 460 through 480 removed outlier: 3.642A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 495 Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 514 through 531 Processing helix chain 'C' and resid 533 through 540 removed outlier: 3.878A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 552 removed outlier: 3.956A pdb=" N ASP C 552 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 570 removed outlier: 4.130A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 Processing helix chain 'C' and resid 579 through 594 removed outlier: 3.627A pdb=" N ILE C 583 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 608 removed outlier: 3.521A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 Processing helix chain 'C' and resid 626 through 629 Processing helix chain 'C' and resid 812 through 816 removed outlier: 4.119A pdb=" N LEU C 816 " --> pdb=" O GLU C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 888 removed outlier: 3.852A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 886 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 935 removed outlier: 4.561A pdb=" N TYR C 920 " --> pdb=" O PRO C 916 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 921 " --> pdb=" O GLU C 917 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET C 924 " --> pdb=" O TYR C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1002 Processing helix chain 'C' and resid 1028 through 1049 removed outlier: 4.379A pdb=" N SER C1034 " --> pdb=" O ALA C1030 " (cutoff:3.500A) removed outlier: 4.608A 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 1217 through 1222 removed outlier: 3.952A pdb=" N GLU C1221 " --> pdb=" O CYS C1217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C1222 " --> pdb=" O GLY C1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1222' Processing helix chain 'C' and resid 1225 through 1229 Processing helix chain 'C' and resid 1531 through 1534 Processing helix chain 'C' and resid 1579 through 1585 Processing helix chain 'C' and resid 1641 through 1645 removed outlier: 3.946A pdb=" N ASN C1645 " --> pdb=" O PRO C1642 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1654 Processing helix chain 'C' and resid 1656 through 1674 removed outlier: 3.933A pdb=" N GLN C1660 " --> pdb=" O ARG C1656 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS C1674 " --> pdb=" O TYR C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1690 removed outlier: 3.720A pdb=" N LEU C1685 " --> pdb=" O VAL C1681 " (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 1734 removed outlier: 4.638A pdb=" N ALA C1723 " --> pdb=" O HIS C1719 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER C1729 " --> pdb=" O ARG C1725 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C1734 " --> pdb=" O MET C1730 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 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 1855 through 1867 Processing helix chain 'C' and resid 1932 through 1974 removed outlier: 3.774A pdb=" N VAL C1966 " --> pdb=" O ALA C1962 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C1968 " --> pdb=" O ARG C1964 " (cutoff:3.500A) Processing helix chain 'C' and resid 2034 through 2044 Processing helix chain 'C' and resid 2045 through 2047 No H-bonds generated for 'chain 'C' and resid 2045 through 2047' Processing helix chain 'C' and resid 2057 through 2057 No H-bonds generated for 'chain 'C' and resid 2057 through 2057' Processing helix chain 'C' and resid 2058 through 2071 Processing helix chain 'C' and resid 2094 through 2109 removed outlier: 3.582A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2129 removed outlier: 4.046A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) Processing helix chain 'C' and resid 2129 through 2138 Processing helix chain 'C' and resid 2139 through 2141 No H-bonds generated for 'chain 'C' and resid 2139 through 2141' Processing helix chain 'C' and resid 2145 through 2147 No H-bonds generated for 'chain 'C' and resid 2145 through 2147' Processing helix chain 'C' and resid 2148 through 2167 removed outlier: 4.503A pdb=" N SER C2164 " --> pdb=" O GLY C2160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (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: 3.527A pdb=" N MET C2198 " --> pdb=" O HIS C2194 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C2202 " --> pdb=" O MET C2198 " (cutoff:3.500A) Processing helix chain 'C' and resid 2202 through 2216 removed outlier: 3.516A pdb=" N GLY C2216 " --> pdb=" O VAL C2212 " (cutoff:3.500A) Processing helix chain 'C' and resid 2227 through 2242 Processing helix chain 'C' and resid 2243 through 2252 removed outlier: 3.618A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N GLU C2259 " --> pdb=" O SER C2255 " (cutoff:3.500A) Processing helix chain 'C' and resid 2262 through 2263 No H-bonds generated for 'chain 'C' and resid 2262 through 2263' Processing helix chain 'C' and resid 2271 through 2271 No H-bonds generated for 'chain 'C' and resid 2271 through 2271' Processing helix chain 'C' and resid 2272 through 2282 removed outlier: 4.673A pdb=" N ASP C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2305 removed outlier: 3.785A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2326 through 2340 removed outlier: 3.746A pdb=" N PHE C2340 " --> pdb=" O ARG C2336 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2360 removed outlier: 4.361A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) Processing helix chain 'C' and resid 2376 through 2385 Processing helix chain 'C' and resid 2420 through 2436 Processing helix chain 'C' and resid 2450 through 2459 Processing helix chain 'C' and resid 2466 through 2475 removed outlier: 3.603A pdb=" N UNK C2470 " --> pdb=" O UNK C2466 " (cutoff:3.500A) Processing helix chain 'C' and resid 2495 through 2510 removed outlier: 3.718A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) Processing helix chain 'C' and resid 2515 through 2522 Processing helix chain 'C' and resid 2526 through 2534 removed outlier: 3.911A pdb=" N ALA C2534 " --> pdb=" O ASP C2530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2535 through 2537 No H-bonds generated for 'chain 'C' and resid 2535 through 2537' Processing helix chain 'C' and resid 2545 through 2559 Processing helix chain 'C' and resid 2560 through 2562 No H-bonds generated for 'chain 'C' and resid 2560 through 2562' Processing helix chain 'C' and resid 2568 through 2586 Processing helix chain 'C' and resid 2592 through 2609 Processing helix chain 'C' and resid 2616 through 2634 removed outlier: 3.760A pdb=" N UNK C2634 " --> pdb=" O UNK C2630 " (cutoff:3.500A) Processing helix chain 'C' and resid 2639 through 2659 Processing helix chain 'C' and resid 2668 through 2686 removed outlier: 3.500A pdb=" N UNK C2686 " --> pdb=" O UNK C2682 " (cutoff:3.500A) Processing helix chain 'C' and resid 2692 through 2712 Processing helix chain 'C' and resid 2748 through 2773 removed outlier: 3.728A pdb=" N ASP C2752 " --> pdb=" O PRO C2748 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C2753 " --> pdb=" O GLU C2749 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C2754 " --> pdb=" O LYS C2750 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C2773 " --> pdb=" O ASP C2769 " (cutoff:3.500A) Processing helix chain 'C' and resid 2782 through 2786 Processing helix chain 'C' and resid 2793 through 2797 Processing helix chain 'C' and resid 2798 through 2819 removed outlier: 3.640A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.231A 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 2912 through 2934 removed outlier: 3.895A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C2929 " --> pdb=" O AGLU C2925 " (cutoff:3.500A) Processing helix chain 'C' and resid 3017 through 3038 Processing helix chain 'C' and resid 3044 through 3061 Processing helix chain 'C' and resid 3069 through 3089 removed outlier: 3.697A pdb=" N UNK C3088 " --> pdb=" O UNK C3084 " (cutoff:3.500A) Processing helix chain 'C' and resid 3096 through 3115 Processing helix chain 'C' and resid 3133 through 3152 removed outlier: 3.799A pdb=" N UNK C3137 " --> pdb=" O UNK C3133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK C3144 " --> pdb=" O UNK C3140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK C3151 " --> pdb=" O UNK C3147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNK C3152 " --> pdb=" O UNK C3148 " (cutoff:3.500A) Processing helix chain 'C' and resid 3159 through 3178 Processing helix chain 'C' and resid 3184 through 3199 Processing helix chain 'C' and resid 3205 through 3217 removed outlier: 3.938A pdb=" N UNK C3217 " --> pdb=" O UNK C3213 " (cutoff:3.500A) Processing helix chain 'C' and resid 3274 through 3289 Processing helix chain 'C' and resid 3295 through 3312 removed outlier: 3.912A pdb=" N UNK C3303 " --> pdb=" O UNK C3299 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N UNK C3304 " --> pdb=" O UNK C3300 " (cutoff:3.500A) Processing helix chain 'C' and resid 3318 through 3338 Processing helix chain 'C' and resid 3347 through 3362 Processing helix chain 'C' and resid 3369 through 3397 removed outlier: 3.504A pdb=" N UNK C3397 " --> pdb=" O UNK C3393 " (cutoff:3.500A) Processing helix chain 'C' and resid 3403 through 3424 removed outlier: 4.184A pdb=" N UNK C3408 " --> pdb=" O UNK C3404 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N UNK C3409 " --> pdb=" O UNK C3405 " (cutoff:3.500A) Processing helix chain 'C' and resid 3428 through 3435 removed outlier: 3.629A pdb=" N UNK C3435 " --> pdb=" O UNK C3431 " (cutoff:3.500A) Processing helix chain 'C' and resid 3437 through 3454 Processing helix chain 'C' and resid 3458 through 3469 Processing helix chain 'C' and resid 3479 through 3490 removed outlier: 3.788A pdb=" N UNK C3490 " --> pdb=" O UNK C3486 " (cutoff:3.500A) Processing helix chain 'C' and resid 3495 through 3504 Processing helix chain 'C' and resid 3514 through 3526 Processing helix chain 'C' and resid 3538 through 3544 Processing helix chain 'C' and resid 3550 through 3570 Processing helix chain 'C' and resid 3646 through 3661 removed outlier: 3.889A pdb=" N ALA C3659 " --> pdb=" O GLU C3655 " (cutoff:3.500A) Processing helix chain 'C' and resid 3665 through 3667 No H-bonds generated for 'chain 'C' and resid 3665 through 3667' Processing helix chain 'C' and resid 3668 through 3679 removed outlier: 3.969A pdb=" N ARG C3672 " --> pdb=" O SER C3668 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3733 removed outlier: 3.907A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) Processing helix chain 'C' and resid 3751 through 3773 removed outlier: 3.868A pdb=" N ARG C3773 " --> pdb=" O ARG C3769 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 3.961A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C3783 " --> pdb=" O VAL C3779 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.513A pdb=" N SER C3795 " --> pdb=" O GLY C3791 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C3800 " --> pdb=" O SER C3796 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3823 Processing helix chain 'C' and resid 3826 through 3838 removed outlier: 3.582A pdb=" N THR C3838 " --> pdb=" O ALA C3834 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3852 removed outlier: 3.829A pdb=" N LYS C3852 " --> pdb=" O GLU C3848 " (cutoff:3.500A) Processing helix chain 'C' and resid 3878 through 3893 Processing helix chain 'C' and resid 3896 through 3906 Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 4.306A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3971 removed outlier: 3.969A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY C3971 " --> pdb=" O GLU C3967 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3982 removed outlier: 3.533A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3984 through 4003 removed outlier: 4.030A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C3993 " --> pdb=" O VAL C3989 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) Processing helix chain 'C' and resid 4006 through 4032 removed outlier: 3.794A pdb=" N GLU C4011 " --> pdb=" O SER C4007 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU C4012 " --> pdb=" O SER C4008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C4013 " --> pdb=" O GLN C4009 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C4032 " --> pdb=" O LEU C4028 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4051 through 4063 removed outlier: 3.576A pdb=" N ASP C4063 " --> pdb=" O LEU C4059 " (cutoff:3.500A) Processing helix chain 'C' and resid 4072 through 4080 removed outlier: 3.783A pdb=" N TYR C4080 " --> pdb=" O ALA C4076 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4099 removed outlier: 3.625A pdb=" N LYS C4095 " --> pdb=" O LYS C4091 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 3.567A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4130 removed outlier: 3.820A pdb=" N PHE C4128 " --> pdb=" O ASN C4124 " (cutoff:3.500A) Processing helix chain 'C' and resid 4136 through 4154 removed outlier: 3.747A pdb=" N GLY C4140 " --> pdb=" O ALA C4136 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4175 removed outlier: 5.348A pdb=" N SER C4169 " --> pdb=" O GLU C4165 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE C4170 " --> pdb=" O LEU C4166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR C4173 " --> pdb=" O SER C4169 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C4174 " --> pdb=" O ILE C4170 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4205 Processing helix chain 'C' and resid 4208 through 4223 removed outlier: 4.492A pdb=" N GLU C4212 " --> pdb=" O PRO C4208 " (cutoff:3.500A) Processing helix chain 'C' and resid 4227 through 4250 removed outlier: 4.038A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE C4234 " --> pdb=" O LYS C4230 " (cutoff:3.500A) Processing helix chain 'C' and resid 4546 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4663 removed outlier: 3.511A pdb=" N CYS C4663 " --> pdb=" O ILE C4659 " (cutoff:3.500A) Processing helix chain 'C' and resid 4664 through 4683 removed outlier: 3.894A pdb=" N LEU C4668 " --> pdb=" O LEU C4664 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4702 Processing helix chain 'C' and resid 4702 through 4707 removed outlier: 3.868A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4702 through 4707' Processing helix chain 'C' and resid 4719 through 4729 removed outlier: 3.699A pdb=" N LEU C4725 " --> pdb=" O LYS C4721 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C4726 " --> pdb=" O ARG C4722 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4741 Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 3.742A 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 Processing helix chain 'C' and resid 4808 through 4819 removed outlier: 3.641A pdb=" N LEU C4813 " --> pdb=" O ALA C4810 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.617A pdb=" N ARG C4824 " --> pdb=" O VAL C4820 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C4825 " --> pdb=" O LYS C4821 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4858 removed outlier: 3.671A pdb=" N LEU C4837 " --> pdb=" O ASN C4833 " (cutoff:3.500A) Processing helix chain 'C' and resid 4859 through 4863 removed outlier: 3.565A 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: 3.740A pdb=" N ASP C4899 " --> pdb=" O GLY C4896 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C4901 " --> pdb=" O GLY C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4907 through 4924 removed outlier: 3.604A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) Processing helix chain 'C' and resid 4927 through 4956 removed outlier: 3.625A pdb=" N ILE C4937 " --> pdb=" O GLN C4933 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 4.077A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 removed outlier: 4.052A pdb=" N THR C4977 " --> pdb=" O HIS C4973 " (cutoff:3.500A) Processing helix chain 'C' and resid 4985 through 4998 removed outlier: 3.675A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) Processing helix chain 'C' and resid 4999 through 5003 removed outlier: 3.723A pdb=" N HIS C5003 " --> pdb=" O GLU C5000 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5033 Processing helix chain 'D' and resid 40 through 43 Processing helix chain 'D' and resid 56 through 63 removed outlier: 3.567A pdb=" N VAL D 63 " --> pdb=" O TRP D 59 " (cutoff:3.500A) 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: 4.151A 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 75 through 84 removed outlier: 3.606A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 249 through 254 removed outlier: 4.103A pdb=" N VAL E 252 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 308 through 313 Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.808A pdb=" N ALA E 387 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 421 removed outlier: 3.888A pdb=" N PHE E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 452 Processing helix chain 'E' and resid 460 through 480 removed outlier: 3.642A pdb=" N GLU E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 495 Processing helix chain 'E' and resid 508 through 513 Processing helix chain 'E' and resid 514 through 531 Processing helix chain 'E' and resid 533 through 540 removed outlier: 3.878A pdb=" N CYS E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 552 removed outlier: 3.956A pdb=" N ASP E 552 " --> pdb=" O VAL E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 570 removed outlier: 4.130A pdb=" N ILE E 560 " --> pdb=" O ALA E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 578 Processing helix chain 'E' and resid 579 through 594 removed outlier: 3.627A pdb=" N ILE E 583 " --> pdb=" O GLN E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 608 removed outlier: 3.521A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 625 Processing helix chain 'E' and resid 626 through 629 Processing helix chain 'E' and resid 812 through 816 removed outlier: 4.119A pdb=" N LEU E 816 " --> pdb=" O GLU E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 888 removed outlier: 3.852A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 935 removed outlier: 4.561A pdb=" N TYR E 920 " --> pdb=" O PRO E 916 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN E 921 " --> pdb=" O GLU E 917 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET E 924 " --> pdb=" O TYR E 920 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 1002 Processing helix chain 'E' and resid 1028 through 1049 removed outlier: 4.379A pdb=" N SER E1034 " --> pdb=" O ALA E1030 " (cutoff:3.500A) removed outlier: 4.608A 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 1217 through 1222 removed outlier: 3.952A pdb=" N GLU E1221 " --> pdb=" O CYS E1217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY E1222 " --> pdb=" O GLY E1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1217 through 1222' Processing helix chain 'E' and resid 1225 through 1229 Processing helix chain 'E' and resid 1531 through 1534 Processing helix chain 'E' and resid 1579 through 1585 Processing helix chain 'E' and resid 1641 through 1645 removed outlier: 3.946A pdb=" N ASN E1645 " --> pdb=" O PRO E1642 " (cutoff:3.500A) Processing helix chain 'E' and resid 1649 through 1654 Processing helix chain 'E' and resid 1656 through 1674 removed outlier: 3.933A pdb=" N GLN E1660 " --> pdb=" O ARG E1656 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS E1674 " --> pdb=" O TYR E1670 " (cutoff:3.500A) Processing helix chain 'E' and resid 1681 through 1690 removed outlier: 3.720A 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 1734 removed outlier: 4.638A pdb=" N ALA E1723 " --> pdb=" O HIS E1719 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER E1729 " --> pdb=" O ARG E1725 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR E1734 " --> pdb=" O MET E1730 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1745 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 1855 through 1867 Processing helix chain 'E' and resid 1932 through 1974 removed outlier: 3.774A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP E1967 " --> pdb=" O GLU E1963 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) Processing helix chain 'E' and resid 2034 through 2044 Processing helix chain 'E' and resid 2045 through 2047 No H-bonds generated for 'chain 'E' and resid 2045 through 2047' Processing helix chain 'E' and resid 2057 through 2057 No H-bonds generated for 'chain 'E' and resid 2057 through 2057' Processing helix chain 'E' and resid 2058 through 2071 Processing helix chain 'E' and resid 2094 through 2109 removed outlier: 3.582A pdb=" N ASP E2109 " --> pdb=" O TRP E2105 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2129 removed outlier: 4.046A pdb=" N VAL E2117 " --> pdb=" O SER E2113 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2138 Processing helix chain 'E' and resid 2139 through 2141 No H-bonds generated for 'chain 'E' and resid 2139 through 2141' Processing helix chain 'E' and resid 2145 through 2147 No H-bonds generated for 'chain 'E' and resid 2145 through 2147' Processing helix chain 'E' and resid 2148 through 2167 removed outlier: 4.503A pdb=" N SER E2164 " --> pdb=" O GLY E2160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE E2167 " --> pdb=" O ARG E2163 " (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: 3.527A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E2202 " --> pdb=" O MET E2198 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.516A pdb=" N GLY E2216 " --> pdb=" O VAL E2212 " (cutoff:3.500A) Processing helix chain 'E' and resid 2227 through 2242 Processing helix chain 'E' and resid 2243 through 2252 removed outlier: 3.618A pdb=" N SER E2249 " --> pdb=" O GLN E2245 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N GLU E2259 " --> pdb=" O SER E2255 " (cutoff:3.500A) Processing helix chain 'E' and resid 2262 through 2263 No H-bonds generated for 'chain 'E' and resid 2262 through 2263' Processing helix chain 'E' and resid 2271 through 2271 No H-bonds generated for 'chain 'E' and resid 2271 through 2271' Processing helix chain 'E' and resid 2272 through 2282 removed outlier: 4.673A pdb=" N ASP E2282 " --> pdb=" O ALA E2278 " (cutoff:3.500A) Processing helix chain 'E' and resid 2283 through 2290 Processing helix chain 'E' and resid 2291 through 2305 removed outlier: 3.785A pdb=" N LEU E2295 " --> pdb=" O GLN E2291 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2340 removed outlier: 3.746A pdb=" N PHE E2340 " --> pdb=" O ARG E2336 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2360 removed outlier: 4.361A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) Processing helix chain 'E' and resid 2376 through 2385 Processing helix chain 'E' and resid 2420 through 2436 Processing helix chain 'E' and resid 2450 through 2459 Processing helix chain 'E' and resid 2466 through 2475 removed outlier: 3.603A pdb=" N UNK E2470 " --> pdb=" O UNK E2466 " (cutoff:3.500A) Processing helix chain 'E' and resid 2495 through 2510 removed outlier: 3.718A pdb=" N LYS E2499 " --> pdb=" O VAL E2495 " (cutoff:3.500A) Processing helix chain 'E' and resid 2515 through 2522 Processing helix chain 'E' and resid 2526 through 2534 removed outlier: 3.911A pdb=" N ALA E2534 " --> pdb=" O ASP E2530 " (cutoff:3.500A) Processing helix chain 'E' and resid 2535 through 2537 No H-bonds generated for 'chain 'E' and resid 2535 through 2537' Processing helix chain 'E' and resid 2545 through 2559 Processing helix chain 'E' and resid 2560 through 2562 No H-bonds generated for 'chain 'E' and resid 2560 through 2562' Processing helix chain 'E' and resid 2568 through 2586 Processing helix chain 'E' and resid 2592 through 2609 Processing helix chain 'E' and resid 2616 through 2634 removed outlier: 3.760A pdb=" N UNK E2634 " --> pdb=" O UNK E2630 " (cutoff:3.500A) Processing helix chain 'E' and resid 2639 through 2659 Processing helix chain 'E' and resid 2668 through 2686 removed outlier: 3.500A pdb=" N UNK E2686 " --> pdb=" O UNK E2682 " (cutoff:3.500A) Processing helix chain 'E' and resid 2692 through 2712 Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 3.728A pdb=" N ASP E2752 " --> pdb=" O PRO E2748 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS E2757 " --> pdb=" O SER E2753 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E2770 " --> pdb=" O TRP E2766 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN E2773 " --> pdb=" O ASP E2769 " (cutoff:3.500A) Processing helix chain 'E' and resid 2782 through 2786 Processing helix chain 'E' and resid 2793 through 2797 Processing helix chain 'E' and resid 2798 through 2819 removed outlier: 3.640A pdb=" N ILE E2804 " --> pdb=" O LYS E2800 " (cutoff:3.500A) removed outlier: 4.231A 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 2912 through 2934 removed outlier: 3.895A pdb=" N ARG E2918 " --> pdb=" O LYS E2914 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E2922 " --> pdb=" O ARG E2918 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E2929 " --> pdb=" O AGLU E2925 " (cutoff:3.500A) Processing helix chain 'E' and resid 3017 through 3038 Processing helix chain 'E' and resid 3044 through 3061 Processing helix chain 'E' and resid 3069 through 3089 removed outlier: 3.697A pdb=" N UNK E3088 " --> pdb=" O UNK E3084 " (cutoff:3.500A) Processing helix chain 'E' and resid 3096 through 3115 Processing helix chain 'E' and resid 3133 through 3152 removed outlier: 3.799A pdb=" N UNK E3137 " --> pdb=" O UNK E3133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK E3144 " --> pdb=" O UNK E3140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK E3151 " --> pdb=" O UNK E3147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNK E3152 " --> pdb=" O UNK E3148 " (cutoff:3.500A) Processing helix chain 'E' and resid 3159 through 3178 Processing helix chain 'E' and resid 3184 through 3199 Processing helix chain 'E' and resid 3205 through 3217 removed outlier: 3.938A pdb=" N UNK E3217 " --> pdb=" O UNK E3213 " (cutoff:3.500A) Processing helix chain 'E' and resid 3274 through 3289 Processing helix chain 'E' and resid 3295 through 3312 removed outlier: 3.912A pdb=" N UNK E3303 " --> pdb=" O UNK E3299 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N UNK E3304 " --> pdb=" O UNK E3300 " (cutoff:3.500A) Processing helix chain 'E' and resid 3318 through 3338 Processing helix chain 'E' and resid 3347 through 3362 Processing helix chain 'E' and resid 3369 through 3397 removed outlier: 3.504A pdb=" N UNK E3397 " --> pdb=" O UNK E3393 " (cutoff:3.500A) Processing helix chain 'E' and resid 3403 through 3424 removed outlier: 4.184A pdb=" N UNK E3408 " --> pdb=" O UNK E3404 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N UNK E3409 " --> pdb=" O UNK E3405 " (cutoff:3.500A) Processing helix chain 'E' and resid 3428 through 3435 removed outlier: 3.629A pdb=" N UNK E3435 " --> pdb=" O UNK E3431 " (cutoff:3.500A) Processing helix chain 'E' and resid 3437 through 3454 Processing helix chain 'E' and resid 3458 through 3469 Processing helix chain 'E' and resid 3479 through 3490 removed outlier: 3.788A pdb=" N UNK E3490 " --> pdb=" O UNK E3486 " (cutoff:3.500A) Processing helix chain 'E' and resid 3495 through 3504 Processing helix chain 'E' and resid 3514 through 3526 Processing helix chain 'E' and resid 3538 through 3544 Processing helix chain 'E' and resid 3550 through 3570 Processing helix chain 'E' and resid 3646 through 3661 removed outlier: 3.889A pdb=" N ALA E3659 " --> pdb=" O GLU E3655 " (cutoff:3.500A) Processing helix chain 'E' and resid 3665 through 3667 No H-bonds generated for 'chain 'E' and resid 3665 through 3667' Processing helix chain 'E' and resid 3668 through 3679 removed outlier: 3.969A pdb=" N ARG E3672 " --> pdb=" O SER E3668 " (cutoff:3.500A) Processing helix chain 'E' and resid 3696 through 3711 Processing helix chain 'E' and resid 3719 through 3733 removed outlier: 3.907A pdb=" N CYS E3733 " --> pdb=" O MET E3729 " (cutoff:3.500A) Processing helix chain 'E' and resid 3751 through 3773 removed outlier: 3.868A pdb=" N ARG E3773 " --> pdb=" O ARG E3769 " (cutoff:3.500A) Processing helix chain 'E' and resid 3774 through 3787 removed outlier: 3.961A pdb=" N LEU E3780 " --> pdb=" O ALA E3776 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E3783 " --> pdb=" O VAL E3779 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3806 removed outlier: 3.513A pdb=" N SER E3795 " --> pdb=" O GLY E3791 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E3800 " --> pdb=" O SER E3796 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3823 Processing helix chain 'E' and resid 3826 through 3838 removed outlier: 3.582A pdb=" N THR E3838 " --> pdb=" O ALA E3834 " (cutoff:3.500A) Processing helix chain 'E' and resid 3843 through 3852 removed outlier: 3.829A pdb=" N LYS E3852 " --> pdb=" O GLU E3848 " (cutoff:3.500A) Processing helix chain 'E' and resid 3878 through 3893 Processing helix chain 'E' and resid 3896 through 3906 Processing helix chain 'E' and resid 3914 through 3939 removed outlier: 4.306A pdb=" N GLY E3939 " --> pdb=" O TRP E3935 " (cutoff:3.500A) Processing helix chain 'E' and resid 3944 through 3971 removed outlier: 3.969A pdb=" N ILE E3969 " --> pdb=" O LEU E3965 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY E3971 " --> pdb=" O GLU E3967 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3982 removed outlier: 3.533A pdb=" N HIS E3982 " --> pdb=" O GLN E3978 " (cutoff:3.500A) Processing helix chain 'E' and resid 3984 through 4003 removed outlier: 4.030A pdb=" N ALA E3988 " --> pdb=" O ARG E3984 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E3993 " --> pdb=" O VAL E3989 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) Processing helix chain 'E' and resid 4006 through 4032 removed outlier: 3.794A pdb=" N GLU E4011 " --> pdb=" O SER E4007 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU E4012 " --> pdb=" O SER E4008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E4013 " --> pdb=" O GLN E4009 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E4032 " --> pdb=" O LEU E4028 " (cutoff:3.500A) Processing helix chain 'E' and resid 4038 through 4051 Processing helix chain 'E' and resid 4051 through 4063 removed outlier: 3.576A pdb=" N ASP E4063 " --> pdb=" O LEU E4059 " (cutoff:3.500A) Processing helix chain 'E' and resid 4072 through 4080 removed outlier: 3.783A pdb=" N TYR E4080 " --> pdb=" O ALA E4076 " (cutoff:3.500A) Processing helix chain 'E' and resid 4089 through 4099 removed outlier: 3.625A pdb=" N LYS E4095 " --> pdb=" O LYS E4091 " (cutoff:3.500A) Processing helix chain 'E' and resid 4104 through 4116 removed outlier: 3.567A pdb=" N GLU E4116 " --> pdb=" O LEU E4112 " (cutoff:3.500A) Processing helix chain 'E' and resid 4124 through 4130 removed outlier: 3.820A pdb=" N PHE E4128 " --> pdb=" O ASN E4124 " (cutoff:3.500A) Processing helix chain 'E' and resid 4136 through 4154 removed outlier: 3.747A pdb=" N GLY E4140 " --> pdb=" O ALA E4136 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4175 removed outlier: 5.348A pdb=" N SER E4169 " --> pdb=" O GLU E4165 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE E4170 " --> pdb=" O LEU E4166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR E4173 " --> pdb=" O SER E4169 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E4174 " --> pdb=" O ILE E4170 " (cutoff:3.500A) Processing helix chain 'E' and resid 4198 through 4205 Processing helix chain 'E' and resid 4208 through 4223 removed outlier: 4.492A pdb=" N GLU E4212 " --> pdb=" O PRO E4208 " (cutoff:3.500A) Processing helix chain 'E' and resid 4227 through 4250 removed outlier: 4.038A pdb=" N MET E4231 " --> pdb=" O GLU E4227 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) Processing helix chain 'E' and resid 4546 through 4558 Processing helix chain 'E' and resid 4558 through 4578 Processing helix chain 'E' and resid 4638 through 4663 removed outlier: 3.511A pdb=" N CYS E4663 " --> pdb=" O ILE E4659 " (cutoff:3.500A) Processing helix chain 'E' and resid 4664 through 4683 removed outlier: 3.894A pdb=" N LEU E4668 " --> pdb=" O LEU E4664 " (cutoff:3.500A) Processing helix chain 'E' and resid 4696 through 4702 Processing helix chain 'E' and resid 4702 through 4707 removed outlier: 3.868A pdb=" N LEU E4706 " --> pdb=" O ASP E4702 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN E4707 " --> pdb=" O ARG E4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4702 through 4707' Processing helix chain 'E' and resid 4719 through 4729 removed outlier: 3.699A pdb=" N LEU E4725 " --> pdb=" O LYS E4721 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E4726 " --> pdb=" O ARG E4722 " (cutoff:3.500A) Processing helix chain 'E' and resid 4733 through 4741 Processing helix chain 'E' and resid 4766 through 4771 removed outlier: 3.742A 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 Processing helix chain 'E' and resid 4808 through 4819 removed outlier: 3.641A pdb=" N LEU E4813 " --> pdb=" O ALA E4810 " (cutoff:3.500A) Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.617A pdb=" N ARG E4824 " --> pdb=" O VAL E4820 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E4825 " --> pdb=" O LYS E4821 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN E4833 " --> pdb=" O SER E4829 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 removed outlier: 3.671A pdb=" N LEU E4837 " --> pdb=" O ASN E4833 " (cutoff:3.500A) Processing helix chain 'E' and resid 4859 through 4863 removed outlier: 3.565A 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: 3.740A pdb=" N ASP E4899 " --> pdb=" O GLY E4896 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE E4901 " --> pdb=" O GLY E4898 " (cutoff:3.500A) Processing helix chain 'E' and resid 4907 through 4924 removed outlier: 3.604A pdb=" N VAL E4915 " --> pdb=" O LEU E4911 " (cutoff:3.500A) Processing helix chain 'E' and resid 4927 through 4956 removed outlier: 3.625A pdb=" N ILE E4937 " --> pdb=" O GLN E4933 " (cutoff:3.500A) Processing helix chain 'E' and resid 4964 through 4969 removed outlier: 4.077A pdb=" N PHE E4968 " --> pdb=" O GLY E4964 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4981 removed outlier: 4.052A pdb=" N THR E4977 " --> pdb=" O HIS E4973 " (cutoff:3.500A) Processing helix chain 'E' and resid 4985 through 4998 removed outlier: 3.675A pdb=" N MET E4989 " --> pdb=" O LEU E4985 " (cutoff:3.500A) Processing helix chain 'E' and resid 4999 through 5003 removed outlier: 3.723A pdb=" N HIS E5003 " --> pdb=" O GLU E5000 " (cutoff:3.500A) Processing helix chain 'E' and resid 5004 through 5016 Processing helix chain 'E' and resid 5027 through 5033 Processing helix chain 'F' and resid 40 through 43 Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.567A pdb=" N VAL F 63 " --> pdb=" O TRP F 59 " (cutoff:3.500A) 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: 4.151A 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 75 through 84 removed outlier: 3.606A pdb=" N ASN G 84 " --> pdb=" O GLU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 145 No H-bonds generated for 'chain 'G' and resid 143 through 145' Processing helix chain 'G' and resid 249 through 254 removed outlier: 4.103A pdb=" N VAL G 252 " --> pdb=" O GLY G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 257 No H-bonds generated for 'chain 'G' and resid 255 through 257' Processing helix chain 'G' and resid 308 through 313 Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.808A pdb=" N ALA G 387 " --> pdb=" O MET G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 421 removed outlier: 3.888A pdb=" N PHE G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 452 Processing helix chain 'G' and resid 460 through 480 removed outlier: 3.642A pdb=" N GLU G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 495 Processing helix chain 'G' and resid 508 through 513 Processing helix chain 'G' and resid 514 through 531 Processing helix chain 'G' and resid 533 through 540 removed outlier: 3.878A pdb=" N CYS G 537 " --> pdb=" O ASN G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 552 removed outlier: 3.956A pdb=" N ASP G 552 " --> pdb=" O VAL G 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 570 removed outlier: 4.130A pdb=" N ILE G 560 " --> pdb=" O ALA G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 578 Processing helix chain 'G' and resid 579 through 594 removed outlier: 3.627A pdb=" N ILE G 583 " --> pdb=" O GLN G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 608 removed outlier: 3.521A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 625 Processing helix chain 'G' and resid 626 through 629 Processing helix chain 'G' and resid 812 through 816 removed outlier: 4.119A pdb=" N LEU G 816 " --> pdb=" O GLU G 813 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 888 removed outlier: 3.852A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 935 removed outlier: 4.561A pdb=" N TYR G 920 " --> pdb=" O PRO G 916 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN G 921 " --> pdb=" O GLU G 917 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET G 924 " --> pdb=" O TYR G 920 " (cutoff:3.500A) Processing helix chain 'G' and resid 978 through 1002 Processing helix chain 'G' and resid 1028 through 1049 removed outlier: 4.379A pdb=" N SER G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) removed outlier: 4.608A 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 1217 through 1222 removed outlier: 3.952A pdb=" N GLU G1221 " --> pdb=" O CYS G1217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY G1222 " --> pdb=" O GLY G1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1217 through 1222' Processing helix chain 'G' and resid 1225 through 1229 Processing helix chain 'G' and resid 1531 through 1534 Processing helix chain 'G' and resid 1579 through 1585 Processing helix chain 'G' and resid 1641 through 1645 removed outlier: 3.946A pdb=" N ASN G1645 " --> pdb=" O PRO G1642 " (cutoff:3.500A) Processing helix chain 'G' and resid 1649 through 1654 Processing helix chain 'G' and resid 1656 through 1674 removed outlier: 3.933A pdb=" N GLN G1660 " --> pdb=" O ARG G1656 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS G1674 " --> pdb=" O TYR G1670 " (cutoff:3.500A) Processing helix chain 'G' and resid 1681 through 1690 removed outlier: 3.720A pdb=" N LEU G1685 " --> pdb=" O VAL G1681 " (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 1734 removed outlier: 4.638A pdb=" N ALA G1723 " --> pdb=" O HIS G1719 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER G1729 " --> pdb=" O ARG G1725 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR G1734 " --> pdb=" O MET G1730 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1745 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 1855 through 1867 Processing helix chain 'G' and resid 1932 through 1974 removed outlier: 3.774A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP G1967 " --> pdb=" O GLU G1963 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) Processing helix chain 'G' and resid 2034 through 2044 Processing helix chain 'G' and resid 2045 through 2047 No H-bonds generated for 'chain 'G' and resid 2045 through 2047' Processing helix chain 'G' and resid 2057 through 2057 No H-bonds generated for 'chain 'G' and resid 2057 through 2057' Processing helix chain 'G' and resid 2058 through 2071 Processing helix chain 'G' and resid 2094 through 2109 removed outlier: 3.582A pdb=" N ASP G2109 " --> pdb=" O TRP G2105 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2129 removed outlier: 4.046A pdb=" N VAL G2117 " --> pdb=" O SER G2113 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2138 Processing helix chain 'G' and resid 2139 through 2141 No H-bonds generated for 'chain 'G' and resid 2139 through 2141' Processing helix chain 'G' and resid 2145 through 2147 No H-bonds generated for 'chain 'G' and resid 2145 through 2147' Processing helix chain 'G' and resid 2148 through 2167 removed outlier: 4.503A pdb=" N SER G2164 " --> pdb=" O GLY G2160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G2167 " --> pdb=" O ARG G2163 " (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: 3.527A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G2202 " --> pdb=" O MET G2198 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.516A pdb=" N GLY G2216 " --> pdb=" O VAL G2212 " (cutoff:3.500A) Processing helix chain 'G' and resid 2227 through 2242 Processing helix chain 'G' and resid 2243 through 2252 removed outlier: 3.618A pdb=" N SER G2249 " --> pdb=" O GLN G2245 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N GLU G2259 " --> pdb=" O SER G2255 " (cutoff:3.500A) Processing helix chain 'G' and resid 2262 through 2263 No H-bonds generated for 'chain 'G' and resid 2262 through 2263' Processing helix chain 'G' and resid 2271 through 2271 No H-bonds generated for 'chain 'G' and resid 2271 through 2271' Processing helix chain 'G' and resid 2272 through 2282 removed outlier: 4.673A pdb=" N ASP G2282 " --> pdb=" O ALA G2278 " (cutoff:3.500A) Processing helix chain 'G' and resid 2283 through 2290 Processing helix chain 'G' and resid 2291 through 2305 removed outlier: 3.785A pdb=" N LEU G2295 " --> pdb=" O GLN G2291 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2340 removed outlier: 3.746A pdb=" N PHE G2340 " --> pdb=" O ARG G2336 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2360 removed outlier: 4.361A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) Processing helix chain 'G' and resid 2376 through 2385 Processing helix chain 'G' and resid 2420 through 2436 Processing helix chain 'G' and resid 2450 through 2459 Processing helix chain 'G' and resid 2466 through 2475 removed outlier: 3.603A pdb=" N UNK G2470 " --> pdb=" O UNK G2466 " (cutoff:3.500A) Processing helix chain 'G' and resid 2495 through 2510 removed outlier: 3.718A pdb=" N LYS G2499 " --> pdb=" O VAL G2495 " (cutoff:3.500A) Processing helix chain 'G' and resid 2515 through 2522 Processing helix chain 'G' and resid 2526 through 2534 removed outlier: 3.911A pdb=" N ALA G2534 " --> pdb=" O ASP G2530 " (cutoff:3.500A) Processing helix chain 'G' and resid 2535 through 2537 No H-bonds generated for 'chain 'G' and resid 2535 through 2537' Processing helix chain 'G' and resid 2545 through 2559 Processing helix chain 'G' and resid 2560 through 2562 No H-bonds generated for 'chain 'G' and resid 2560 through 2562' Processing helix chain 'G' and resid 2568 through 2586 Processing helix chain 'G' and resid 2592 through 2609 Processing helix chain 'G' and resid 2616 through 2634 removed outlier: 3.760A pdb=" N UNK G2634 " --> pdb=" O UNK G2630 " (cutoff:3.500A) Processing helix chain 'G' and resid 2639 through 2659 Processing helix chain 'G' and resid 2668 through 2686 removed outlier: 3.500A pdb=" N UNK G2686 " --> pdb=" O UNK G2682 " (cutoff:3.500A) Processing helix chain 'G' and resid 2692 through 2712 Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 3.728A pdb=" N ASP G2752 " --> pdb=" O PRO G2748 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS G2757 " --> pdb=" O SER G2753 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS G2770 " --> pdb=" O TRP G2766 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN G2773 " --> pdb=" O ASP G2769 " (cutoff:3.500A) Processing helix chain 'G' and resid 2782 through 2786 Processing helix chain 'G' and resid 2793 through 2797 Processing helix chain 'G' and resid 2798 through 2819 removed outlier: 3.640A pdb=" N ILE G2804 " --> pdb=" O LYS G2800 " (cutoff:3.500A) removed outlier: 4.231A 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 Processing helix chain 'G' and resid 2868 through 2898 Processing helix chain 'G' and resid 2912 through 2934 removed outlier: 3.895A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G2922 " --> pdb=" O ARG G2918 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G2929 " --> pdb=" O AGLU G2925 " (cutoff:3.500A) Processing helix chain 'G' and resid 3017 through 3038 Processing helix chain 'G' and resid 3044 through 3061 Processing helix chain 'G' and resid 3069 through 3089 removed outlier: 3.697A pdb=" N UNK G3088 " --> pdb=" O UNK G3084 " (cutoff:3.500A) Processing helix chain 'G' and resid 3096 through 3115 Processing helix chain 'G' and resid 3133 through 3152 removed outlier: 3.799A pdb=" N UNK G3137 " --> pdb=" O UNK G3133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK G3144 " --> pdb=" O UNK G3140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK G3151 " --> pdb=" O UNK G3147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNK G3152 " --> pdb=" O UNK G3148 " (cutoff:3.500A) Processing helix chain 'G' and resid 3159 through 3178 Processing helix chain 'G' and resid 3184 through 3199 Processing helix chain 'G' and resid 3205 through 3217 removed outlier: 3.938A pdb=" N UNK G3217 " --> pdb=" O UNK G3213 " (cutoff:3.500A) Processing helix chain 'G' and resid 3274 through 3289 Processing helix chain 'G' and resid 3295 through 3312 removed outlier: 3.912A pdb=" N UNK G3303 " --> pdb=" O UNK G3299 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N UNK G3304 " --> pdb=" O UNK G3300 " (cutoff:3.500A) Processing helix chain 'G' and resid 3318 through 3338 Processing helix chain 'G' and resid 3347 through 3362 Processing helix chain 'G' and resid 3369 through 3397 removed outlier: 3.504A pdb=" N UNK G3397 " --> pdb=" O UNK G3393 " (cutoff:3.500A) Processing helix chain 'G' and resid 3403 through 3424 removed outlier: 4.184A pdb=" N UNK G3408 " --> pdb=" O UNK G3404 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N UNK G3409 " --> pdb=" O UNK G3405 " (cutoff:3.500A) Processing helix chain 'G' and resid 3428 through 3435 removed outlier: 3.629A pdb=" N UNK G3435 " --> pdb=" O UNK G3431 " (cutoff:3.500A) Processing helix chain 'G' and resid 3437 through 3454 Processing helix chain 'G' and resid 3458 through 3469 Processing helix chain 'G' and resid 3479 through 3490 removed outlier: 3.788A pdb=" N UNK G3490 " --> pdb=" O UNK G3486 " (cutoff:3.500A) Processing helix chain 'G' and resid 3495 through 3504 Processing helix chain 'G' and resid 3514 through 3526 Processing helix chain 'G' and resid 3538 through 3544 Processing helix chain 'G' and resid 3550 through 3570 Processing helix chain 'G' and resid 3646 through 3661 removed outlier: 3.889A pdb=" N ALA G3659 " --> pdb=" O GLU G3655 " (cutoff:3.500A) Processing helix chain 'G' and resid 3665 through 3667 No H-bonds generated for 'chain 'G' and resid 3665 through 3667' Processing helix chain 'G' and resid 3668 through 3679 removed outlier: 3.969A pdb=" N ARG G3672 " --> pdb=" O SER G3668 " (cutoff:3.500A) Processing helix chain 'G' and resid 3696 through 3711 Processing helix chain 'G' and resid 3719 through 3733 removed outlier: 3.907A pdb=" N CYS G3733 " --> pdb=" O MET G3729 " (cutoff:3.500A) Processing helix chain 'G' and resid 3751 through 3773 removed outlier: 3.868A pdb=" N ARG G3773 " --> pdb=" O ARG G3769 " (cutoff:3.500A) Processing helix chain 'G' and resid 3774 through 3787 removed outlier: 3.961A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE G3783 " --> pdb=" O VAL G3779 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3806 removed outlier: 3.513A pdb=" N SER G3795 " --> pdb=" O GLY G3791 " (cutoff:3.500A) removed outlier: 3.509A 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 3838 removed outlier: 3.582A pdb=" N THR G3838 " --> pdb=" O ALA G3834 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3852 removed outlier: 3.829A pdb=" N LYS G3852 " --> pdb=" O GLU G3848 " (cutoff:3.500A) Processing helix chain 'G' and resid 3878 through 3893 Processing helix chain 'G' and resid 3896 through 3906 Processing helix chain 'G' and resid 3914 through 3939 removed outlier: 4.306A pdb=" N GLY G3939 " --> pdb=" O TRP G3935 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3971 removed outlier: 3.969A pdb=" N ILE G3969 " --> pdb=" O LEU G3965 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY G3971 " --> pdb=" O GLU G3967 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3982 removed outlier: 3.533A pdb=" N HIS G3982 " --> pdb=" O GLN G3978 " (cutoff:3.500A) Processing helix chain 'G' and resid 3984 through 4003 removed outlier: 4.030A pdb=" N ALA G3988 " --> pdb=" O ARG G3984 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G3993 " --> pdb=" O VAL G3989 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS G3998 " --> pdb=" O HIS G3994 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) Processing helix chain 'G' and resid 4006 through 4032 removed outlier: 3.794A pdb=" N GLU G4011 " --> pdb=" O SER G4007 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU G4012 " --> pdb=" O SER G4008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G4013 " --> pdb=" O GLN G4009 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU G4032 " --> pdb=" O LEU G4028 " (cutoff:3.500A) Processing helix chain 'G' and resid 4038 through 4051 Processing helix chain 'G' and resid 4051 through 4063 removed outlier: 3.576A pdb=" N ASP G4063 " --> pdb=" O LEU G4059 " (cutoff:3.500A) Processing helix chain 'G' and resid 4072 through 4080 removed outlier: 3.783A pdb=" N TYR G4080 " --> pdb=" O ALA G4076 " (cutoff:3.500A) Processing helix chain 'G' and resid 4089 through 4099 removed outlier: 3.625A pdb=" N LYS G4095 " --> pdb=" O LYS G4091 " (cutoff:3.500A) Processing helix chain 'G' and resid 4104 through 4116 removed outlier: 3.567A pdb=" N GLU G4116 " --> pdb=" O LEU G4112 " (cutoff:3.500A) Processing helix chain 'G' and resid 4124 through 4130 removed outlier: 3.820A pdb=" N PHE G4128 " --> pdb=" O ASN G4124 " (cutoff:3.500A) Processing helix chain 'G' and resid 4136 through 4154 removed outlier: 3.747A pdb=" N GLY G4140 " --> pdb=" O ALA G4136 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4175 removed outlier: 5.348A pdb=" N SER G4169 " --> pdb=" O GLU G4165 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE G4170 " --> pdb=" O LEU G4166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR G4173 " --> pdb=" O SER G4169 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G4174 " --> pdb=" O ILE G4170 " (cutoff:3.500A) Processing helix chain 'G' and resid 4198 through 4205 Processing helix chain 'G' and resid 4208 through 4223 removed outlier: 4.492A pdb=" N GLU G4212 " --> pdb=" O PRO G4208 " (cutoff:3.500A) Processing helix chain 'G' and resid 4227 through 4250 removed outlier: 4.038A pdb=" N MET G4231 " --> pdb=" O GLU G4227 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE G4234 " --> pdb=" O LYS G4230 " (cutoff:3.500A) Processing helix chain 'G' and resid 4546 through 4558 Processing helix chain 'G' and resid 4558 through 4578 Processing helix chain 'G' and resid 4638 through 4663 removed outlier: 3.511A pdb=" N CYS G4663 " --> pdb=" O ILE G4659 " (cutoff:3.500A) Processing helix chain 'G' and resid 4664 through 4683 removed outlier: 3.894A pdb=" N LEU G4668 " --> pdb=" O LEU G4664 " (cutoff:3.500A) Processing helix chain 'G' and resid 4696 through 4702 Processing helix chain 'G' and resid 4702 through 4707 removed outlier: 3.868A pdb=" N LEU G4706 " --> pdb=" O ASP G4702 " (cutoff:3.500A) removed outlier: 4.085A 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 4719 through 4729 removed outlier: 3.699A pdb=" N LEU G4725 " --> pdb=" O LYS G4721 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP G4726 " --> pdb=" O ARG G4722 " (cutoff:3.500A) Processing helix chain 'G' and resid 4733 through 4741 Processing helix chain 'G' and resid 4766 through 4771 removed outlier: 3.742A pdb=" N ILE G4771 " --> pdb=" O TRP G4767 " (cutoff:3.500A) Processing helix chain 'G' and resid 4773 through 4786 Processing helix chain 'G' and resid 4786 through 4805 Processing helix chain 'G' and resid 4808 through 4819 removed outlier: 3.641A pdb=" N LEU G4813 " --> pdb=" O ALA G4810 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.617A pdb=" N ARG G4824 " --> pdb=" O VAL G4820 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G4825 " --> pdb=" O LYS G4821 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 3.671A pdb=" N LEU G4837 " --> pdb=" O ASN G4833 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4863 removed outlier: 3.565A pdb=" N TYR G4863 " --> pdb=" O ARG G4860 " (cutoff:3.500A) Processing helix chain 'G' and resid 4878 through 4889 Processing helix chain 'G' and resid 4896 through 4901 removed outlier: 3.740A pdb=" N ASP G4899 " --> pdb=" O GLY G4896 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE G4901 " --> pdb=" O GLY G4898 " (cutoff:3.500A) Processing helix chain 'G' and resid 4907 through 4924 removed outlier: 3.604A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) Processing helix chain 'G' and resid 4927 through 4956 removed outlier: 3.625A pdb=" N ILE G4937 " --> pdb=" O GLN G4933 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4969 removed outlier: 4.077A pdb=" N PHE G4968 " --> pdb=" O GLY G4964 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4981 removed outlier: 4.052A pdb=" N THR G4977 " --> pdb=" O HIS G4973 " (cutoff:3.500A) Processing helix chain 'G' and resid 4985 through 4998 removed outlier: 3.675A pdb=" N MET G4989 " --> pdb=" O LEU G4985 " (cutoff:3.500A) Processing helix chain 'G' and resid 4999 through 5003 removed outlier: 3.723A pdb=" N HIS G5003 " --> pdb=" O GLU G5000 " (cutoff:3.500A) Processing helix chain 'G' and resid 5004 through 5016 Processing helix chain 'G' and resid 5027 through 5033 Processing helix chain 'H' and resid 40 through 43 Processing helix chain 'H' and resid 56 through 63 removed outlier: 3.567A pdb=" N VAL H 63 " --> pdb=" O TRP H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 77 through 81 Processing sheet with id= A, first strand: chain 'A' and resid 73 through 74 removed outlier: 4.712A pdb=" N HIS A 105 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.790A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.573A pdb=" N GLU A 40 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU A 46 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 124 removed outlier: 3.735A pdb=" N ASP A 134 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 133 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 135 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL A 191 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 298 through 302 removed outlier: 4.680A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LEU A 293 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N LEU A 280 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 230 through 233 Processing sheet with id= G, first strand: chain 'A' and resid 356 through 359 Processing sheet with id= H, first strand: chain 'A' and resid 634 through 635 removed outlier: 3.733A pdb=" N GLN A 634 " --> pdb=" O HIS A1640 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 638 through 639 Processing sheet with id= J, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= K, first strand: chain 'A' and resid 762 through 763 Processing sheet with id= L, first strand: chain 'A' and resid 762 through 763 removed outlier: 6.530A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 768 through 769 Processing sheet with id= N, first strand: chain 'A' and resid 831 through 833 Processing sheet with id= O, first strand: chain 'A' and resid 892 through 893 removed outlier: 5.875A pdb=" N THR A 892 " --> pdb=" O HIS A 904 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'A' and resid 1136 through 1137 removed outlier: 3.597A pdb=" N VAL A1102 " --> pdb=" O PHE A1124 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A1239 " --> pdb=" O ILE A1074 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 1148 through 1153 removed outlier: 3.604A pdb=" N ASN A1203 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1159 through 1160 removed outlier: 3.907A pdb=" N PHE A1179 " --> pdb=" O ILE A1160 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id= T, first strand: chain 'A' and resid 1275 through 1277 Processing sheet with id= U, first strand: chain 'A' and resid 1287 through 1290 Processing sheet with id= V, first strand: chain 'A' and resid 1438 through 1439 Processing sheet with id= W, first strand: chain 'A' and resid 1516 through 1519 Processing sheet with id= X, first strand: chain 'A' and resid 1735 through 1737 removed outlier: 6.661A pdb=" N VAL A1736 " --> pdb=" O ILE A2144 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 2822 through 2824 Processing sheet with id= Z, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id= AA, first strand: chain 'A' and resid 4580 through 4581 Processing sheet with id= AB, first strand: chain 'B' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG B 71 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 27 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU B 30 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS B 35 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG B 71 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 103 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS B 25 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 73 through 74 removed outlier: 4.712A pdb=" N HIS C 105 " --> pdb=" O MET C 150 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.790A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 23 through 24 removed outlier: 4.573A pdb=" N GLU C 40 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU C 46 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 117 through 124 removed outlier: 3.735A pdb=" N ASP C 134 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 133 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 135 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL C 191 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 298 through 302 removed outlier: 4.680A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LEU C 293 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N LEU C 280 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 230 through 233 Processing sheet with id= AJ, first strand: chain 'C' and resid 356 through 359 Processing sheet with id= AK, first strand: chain 'C' and resid 634 through 635 removed outlier: 3.733A pdb=" N GLN C 634 " --> pdb=" O HIS C1640 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 638 through 639 Processing sheet with id= AM, first strand: chain 'C' and resid 642 through 644 Processing sheet with id= AN, first strand: chain 'C' and resid 762 through 763 Processing sheet with id= AO, first strand: chain 'C' and resid 762 through 763 removed outlier: 6.530A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 768 through 769 Processing sheet with id= AQ, first strand: chain 'C' and resid 831 through 833 Processing sheet with id= AR, first strand: chain 'C' and resid 892 through 893 removed outlier: 5.875A pdb=" N THR C 892 " --> pdb=" O HIS C 904 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'C' and resid 1136 through 1137 removed outlier: 3.597A pdb=" N VAL C1102 " --> pdb=" O PHE C1124 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C1239 " --> pdb=" O ILE C1074 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 1148 through 1153 removed outlier: 3.604A pdb=" N ASN C1203 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 1159 through 1160 removed outlier: 3.907A pdb=" N PHE C1179 " --> pdb=" O ILE C1160 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id= AW, first strand: chain 'C' and resid 1275 through 1277 Processing sheet with id= AX, first strand: chain 'C' and resid 1287 through 1290 Processing sheet with id= AY, first strand: chain 'C' and resid 1438 through 1439 Processing sheet with id= AZ, first strand: chain 'C' and resid 1516 through 1519 Processing sheet with id= BA, first strand: chain 'C' and resid 1735 through 1737 removed outlier: 6.661A pdb=" N VAL C1736 " --> pdb=" O ILE C2144 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'C' and resid 2822 through 2824 Processing sheet with id= BC, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id= BD, first strand: chain 'C' and resid 4580 through 4581 Processing sheet with id= BE, first strand: chain 'D' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG D 71 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR D 27 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU D 30 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS D 35 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'D' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG D 71 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU D 103 " --> pdb=" O HIS D 25 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS D 25 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'E' and resid 73 through 74 removed outlier: 4.712A pdb=" N HIS E 105 " --> pdb=" O MET E 150 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'E' and resid 73 through 74 removed outlier: 6.790A pdb=" N GLU E 19 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'E' and resid 23 through 24 removed outlier: 4.573A pdb=" N GLU E 40 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU E 46 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'E' and resid 117 through 124 removed outlier: 3.735A pdb=" N ASP E 134 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE E 133 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL E 135 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL E 191 " --> pdb=" O VAL E 135 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'E' and resid 298 through 302 removed outlier: 4.680A pdb=" N ILE E 282 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LEU E 293 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N LEU E 280 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'E' and resid 230 through 233 Processing sheet with id= BM, first strand: chain 'E' and resid 356 through 359 Processing sheet with id= BN, first strand: chain 'E' and resid 634 through 635 removed outlier: 3.733A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'E' and resid 638 through 639 Processing sheet with id= BP, first strand: chain 'E' and resid 642 through 644 Processing sheet with id= BQ, first strand: chain 'E' and resid 762 through 763 Processing sheet with id= BR, first strand: chain 'E' and resid 762 through 763 removed outlier: 6.530A pdb=" N LYS E 788 " --> pdb=" O ASP E 669 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'E' and resid 768 through 769 Processing sheet with id= BT, first strand: chain 'E' and resid 831 through 833 Processing sheet with id= BU, first strand: chain 'E' and resid 892 through 893 removed outlier: 5.875A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'E' and resid 1136 through 1137 removed outlier: 3.597A pdb=" N VAL E1102 " --> pdb=" O PHE E1124 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER E1239 " --> pdb=" O ILE E1074 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'E' and resid 1148 through 1153 removed outlier: 3.604A pdb=" N ASN E1203 " --> pdb=" O GLU E1091 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'E' and resid 1159 through 1160 removed outlier: 3.907A pdb=" N PHE E1179 " --> pdb=" O ILE E1160 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'E' and resid 1244 through 1246 Processing sheet with id= BZ, first strand: chain 'E' and resid 1275 through 1277 Processing sheet with id= CA, first strand: chain 'E' and resid 1287 through 1290 Processing sheet with id= CB, first strand: chain 'E' and resid 1438 through 1439 Processing sheet with id= CC, first strand: chain 'E' and resid 1516 through 1519 Processing sheet with id= CD, first strand: chain 'E' and resid 1735 through 1737 removed outlier: 6.661A pdb=" N VAL E1736 " --> pdb=" O ILE E2144 " (cutoff:3.500A) No H-bonds generated for sheet with id= CD Processing sheet with id= CE, first strand: chain 'E' and resid 2822 through 2824 Processing sheet with id= CF, first strand: chain 'E' and resid 4178 through 4184 Processing sheet with id= CG, first strand: chain 'E' and resid 4580 through 4581 Processing sheet with id= CH, first strand: chain 'F' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU F 30 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS F 35 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'F' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU F 103 " --> pdb=" O HIS F 25 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS F 25 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'G' and resid 73 through 74 removed outlier: 4.712A pdb=" N HIS G 105 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'G' and resid 73 through 74 removed outlier: 6.790A pdb=" N GLU G 19 " --> pdb=" O ILE G 205 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'G' and resid 23 through 24 removed outlier: 4.573A pdb=" N GLU G 40 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU G 46 " --> pdb=" O GLU G 40 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'G' and resid 117 through 124 removed outlier: 3.735A pdb=" N ASP G 134 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE G 133 " --> pdb=" O ALA G 193 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL G 135 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL G 191 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'G' and resid 298 through 302 removed outlier: 4.680A pdb=" N ILE G 282 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LEU G 293 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N LEU G 280 " --> pdb=" O LEU G 293 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'G' and resid 230 through 233 Processing sheet with id= CP, first strand: chain 'G' and resid 356 through 359 Processing sheet with id= CQ, first strand: chain 'G' and resid 634 through 635 removed outlier: 3.733A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'G' and resid 638 through 639 Processing sheet with id= CS, first strand: chain 'G' and resid 642 through 644 Processing sheet with id= CT, first strand: chain 'G' and resid 762 through 763 Processing sheet with id= CU, first strand: chain 'G' and resid 762 through 763 removed outlier: 6.530A pdb=" N LYS G 788 " --> pdb=" O ASP G 669 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'G' and resid 768 through 769 Processing sheet with id= CW, first strand: chain 'G' and resid 831 through 833 Processing sheet with id= CX, first strand: chain 'G' and resid 892 through 893 removed outlier: 5.875A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id= CX Processing sheet with id= CY, first strand: chain 'G' and resid 1136 through 1137 removed outlier: 3.597A pdb=" N VAL G1102 " --> pdb=" O PHE G1124 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER G1239 " --> pdb=" O ILE G1074 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'G' and resid 1148 through 1153 removed outlier: 3.604A pdb=" N ASN G1203 " --> pdb=" O GLU G1091 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'G' and resid 1159 through 1160 removed outlier: 3.907A pdb=" N PHE G1179 " --> pdb=" O ILE G1160 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'G' and resid 1244 through 1246 Processing sheet with id= DC, first strand: chain 'G' and resid 1275 through 1277 Processing sheet with id= DD, first strand: chain 'G' and resid 1287 through 1290 Processing sheet with id= DE, first strand: chain 'G' and resid 1438 through 1439 Processing sheet with id= DF, first strand: chain 'G' and resid 1516 through 1519 Processing sheet with id= DG, first strand: chain 'G' and resid 1735 through 1737 removed outlier: 6.661A pdb=" N VAL G1736 " --> pdb=" O ILE G2144 " (cutoff:3.500A) No H-bonds generated for sheet with id= DG Processing sheet with id= DH, first strand: chain 'G' and resid 2822 through 2824 Processing sheet with id= DI, first strand: chain 'G' and resid 4178 through 4184 Processing sheet with id= DJ, first strand: chain 'G' and resid 4580 through 4581 Processing sheet with id= DK, first strand: chain 'H' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR H 27 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU H 30 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS H 35 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'H' and resid 5 through 8 removed outlier: 6.543A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU H 103 " --> pdb=" O HIS H 25 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS H 25 " --> pdb=" O LEU H 103 " (cutoff:3.500A) 6860 hydrogen bonds defined for protein. 19636 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: 82.41 Time building geometry restraints manager: 33.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 18824 1.31 - 1.44: 29236 1.44 - 1.56: 64040 1.56 - 1.69: 8 1.69 - 1.81: 1000 Bond restraints: 113108 Sorted by residual: bond pdb=" C ALA G 679 " pdb=" O ALA G 679 " ideal model delta sigma weight residual 1.234 1.314 -0.080 1.22e-02 6.72e+03 4.28e+01 bond pdb=" C ALA E 679 " pdb=" O ALA E 679 " ideal model delta sigma weight residual 1.234 1.314 -0.080 1.22e-02 6.72e+03 4.28e+01 bond pdb=" C ALA A 679 " pdb=" O ALA A 679 " ideal model delta sigma weight residual 1.234 1.314 -0.080 1.22e-02 6.72e+03 4.28e+01 bond pdb=" C ALA C 679 " pdb=" O ALA C 679 " ideal model delta sigma weight residual 1.234 1.314 -0.080 1.22e-02 6.72e+03 4.28e+01 bond pdb=" C ASP A4903 " pdb=" N PRO A4904 " ideal model delta sigma weight residual 1.331 1.404 -0.073 1.20e-02 6.94e+03 3.72e+01 ... (remaining 113103 not shown) Histogram of bond angle deviations from ideal: 89.69 - 101.56: 348 101.56 - 113.43: 63760 113.43 - 125.30: 87604 125.30 - 137.18: 1580 137.18 - 149.05: 24 Bond angle restraints: 153316 Sorted by residual: angle pdb=" N THR G 680 " pdb=" CA THR G 680 " pdb=" C THR G 680 " ideal model delta sigma weight residual 110.35 89.69 20.66 1.36e+00 5.41e-01 2.31e+02 angle pdb=" N THR A 680 " pdb=" CA THR A 680 " pdb=" C THR A 680 " ideal model delta sigma weight residual 110.35 89.69 20.66 1.36e+00 5.41e-01 2.31e+02 angle pdb=" N THR E 680 " pdb=" CA THR E 680 " pdb=" C THR E 680 " ideal model delta sigma weight residual 110.35 89.69 20.66 1.36e+00 5.41e-01 2.31e+02 angle pdb=" N THR C 680 " pdb=" CA THR C 680 " pdb=" C THR C 680 " ideal model delta sigma weight residual 110.35 89.69 20.66 1.36e+00 5.41e-01 2.31e+02 angle pdb=" N GLY C1764 " pdb=" CA GLY C1764 " pdb=" C GLY C1764 " ideal model delta sigma weight residual 113.18 149.05 -35.87 2.37e+00 1.78e-01 2.29e+02 ... (remaining 153311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.27: 65212 20.27 - 40.53: 1892 40.53 - 60.80: 352 60.80 - 81.06: 68 81.06 - 101.33: 16 Dihedral angle restraints: 67540 sinusoidal: 23828 harmonic: 43712 Sorted by residual: dihedral pdb=" CA PRO G1253 " pdb=" C PRO G1253 " pdb=" N HIS G1254 " pdb=" CA HIS G1254 " ideal model delta harmonic sigma weight residual 180.00 136.39 43.61 0 5.00e+00 4.00e-02 7.61e+01 dihedral pdb=" CA PRO E1253 " pdb=" C PRO E1253 " pdb=" N HIS E1254 " pdb=" CA HIS E1254 " ideal model delta harmonic sigma weight residual 180.00 136.39 43.61 0 5.00e+00 4.00e-02 7.61e+01 dihedral pdb=" CA PRO A1253 " pdb=" C PRO A1253 " pdb=" N HIS A1254 " pdb=" CA HIS A1254 " ideal model delta harmonic sigma weight residual 180.00 136.39 43.61 0 5.00e+00 4.00e-02 7.61e+01 ... (remaining 67537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 15196 0.076 - 0.152: 2200 0.152 - 0.228: 200 0.228 - 0.305: 36 0.305 - 0.381: 4 Chirality restraints: 17636 Sorted by residual: chirality pdb=" CA ARG C1964 " pdb=" N ARG C1964 " pdb=" C ARG C1964 " pdb=" CB ARG C1964 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ARG E1964 " pdb=" N ARG E1964 " pdb=" C ARG E1964 " pdb=" CB ARG E1964 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ARG A1964 " pdb=" N ARG A1964 " pdb=" C ARG A1964 " pdb=" CB ARG A1964 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 17633 not shown) Planarity restraints: 19828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 804 " 0.144 5.00e-02 4.00e+02 2.03e-01 6.60e+01 pdb=" N PRO C 805 " -0.350 5.00e-02 4.00e+02 pdb=" CA PRO C 805 " 0.119 5.00e-02 4.00e+02 pdb=" CD PRO C 805 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 804 " 0.144 5.00e-02 4.00e+02 2.03e-01 6.60e+01 pdb=" N PRO A 805 " -0.350 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " 0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 804 " -0.144 5.00e-02 4.00e+02 2.03e-01 6.60e+01 pdb=" N PRO E 805 " 0.350 5.00e-02 4.00e+02 pdb=" CA PRO E 805 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO E 805 " -0.087 5.00e-02 4.00e+02 ... (remaining 19825 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 156 2.17 - 2.85: 40344 2.85 - 3.54: 172324 3.54 - 4.22: 266648 4.22 - 4.90: 437252 Nonbonded interactions: 916724 Sorted by model distance: nonbonded pdb=" O VAL C1767 " pdb=" N THR C1769 " model vdw 1.488 2.520 nonbonded pdb=" O VAL A1767 " pdb=" N THR A1769 " model vdw 1.488 2.520 nonbonded pdb=" O VAL E1767 " pdb=" N THR E1769 " model vdw 1.488 2.520 nonbonded pdb=" O VAL G1767 " pdb=" N THR G1769 " model vdw 1.488 2.520 nonbonded pdb=" N TYR D 26 " pdb=" OG SER D 39 " model vdw 1.619 2.520 ... (remaining 916719 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: 1.690 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: 13.970 Check model and map are aligned: 1.230 Set scattering table: 0.740 Process input model: 325.490 Find NCS groups from input model: 6.020 Set up NCS constraints: 0.650 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:2.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 351.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 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 : 0.006 0.080 113108 Z= 0.409 Angle : 1.308 35.869 153316 Z= 0.877 Chirality : 0.055 0.381 17636 Planarity : 0.007 0.203 19828 Dihedral : 10.885 101.328 38996 Min Nonbonded Distance : 1.488 Molprobity Statistics. All-atom Clashscore : 33.49 Ramachandran Plot: Outliers : 1.94 % Allowed : 5.27 % Favored : 92.79 % Rotamer: Outliers : 2.47 % Allowed : 1.70 % Favored : 95.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.03 % Twisted Proline : 0.73 % Twisted General : 0.07 % 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: -2.06 (0.07), residues: 12392 helix: -2.37 (0.04), residues: 6208 sheet: -3.02 (0.13), residues: 1204 loop : 0.94 (0.10), residues: 4980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A5019 HIS 0.012 0.002 HIS A4650 PHE 0.042 0.003 PHE E 478 TYR 0.035 0.002 TYR C4194 ARG 0.009 0.001 ARG G 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24784 Ramachandran restraints generated. 12392 Oldfield, 0 Emsley, 12392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24784 Ramachandran restraints generated. 12392 Oldfield, 0 Emsley, 12392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2824 residues out of total 11200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 2544 time to evaluate : 8.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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