Starting phenix.real_space_refine on Mon Mar 11 17:58:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gl0_9520/03_2024/5gl0_9520.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gl0_9520/03_2024/5gl0_9520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gl0_9520/03_2024/5gl0_9520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gl0_9520/03_2024/5gl0_9520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gl0_9520/03_2024/5gl0_9520.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gl0_9520/03_2024/5gl0_9520.pdb" } resolution = 4.2 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 70536 2.51 5 N 19312 2.21 5 O 20504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1584": "NH1" <-> "NH2" Residue "A ARG 1594": "NH1" <-> "NH2" Residue "A ARG 1618": "NH1" <-> "NH2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 2104": "NH1" <-> "NH2" Residue "A TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2359": "NH1" <-> "NH2" Residue "A ARG 3648": "NH1" <-> "NH2" Residue "A ARG 3672": "NH1" <-> "NH2" Residue "A ARG 3886": "NH1" <-> "NH2" Residue "A ARG 3984": "NH1" <-> "NH2" Residue "A ARG 4161": "NH1" <-> "NH2" Residue "A TYR 4177": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4892": "NH1" <-> "NH2" Residue "A PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4944": "NH1" <-> "NH2" Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 820": "NH1" <-> "NH2" Residue "C TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 844": "NH1" <-> "NH2" Residue "C ARG 1087": "NH1" <-> "NH2" Residue "C PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1584": "NH1" <-> "NH2" Residue "C ARG 1594": "NH1" <-> "NH2" Residue "C ARG 1618": "NH1" <-> "NH2" Residue "C ARG 1725": "NH1" <-> "NH2" Residue "C ARG 2104": "NH1" <-> "NH2" Residue "C TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2359": "NH1" <-> "NH2" Residue "C ARG 3648": "NH1" <-> "NH2" Residue "C ARG 3672": "NH1" <-> "NH2" Residue "C ARG 3886": "NH1" <-> "NH2" Residue "C ARG 3984": "NH1" <-> "NH2" Residue "C ARG 4161": "NH1" <-> "NH2" Residue "C TYR 4177": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4892": "NH1" <-> "NH2" Residue "C PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4944": "NH1" <-> "NH2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 820": "NH1" <-> "NH2" Residue "E TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 844": "NH1" <-> "NH2" Residue "E ARG 1087": "NH1" <-> "NH2" Residue "E PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1584": "NH1" <-> "NH2" Residue "E ARG 1594": "NH1" <-> "NH2" Residue "E ARG 1618": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 2104": "NH1" <-> "NH2" Residue "E TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2359": "NH1" <-> "NH2" Residue "E GLU 2925": "OE1" <-> "OE2" Residue "E ARG 3648": "NH1" <-> "NH2" Residue "E ARG 3672": "NH1" <-> "NH2" Residue "E ARG 3886": "NH1" <-> "NH2" Residue "E ARG 3984": "NH1" <-> "NH2" Residue "E ARG 4161": "NH1" <-> "NH2" Residue "E TYR 4177": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4944": "NH1" <-> "NH2" Residue "E PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 281": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 820": "NH1" <-> "NH2" Residue "G TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 844": "NH1" <-> "NH2" Residue "G ARG 1087": "NH1" <-> "NH2" Residue "G PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1584": "NH1" <-> "NH2" Residue "G ARG 1594": "NH1" <-> "NH2" Residue "G ARG 1618": "NH1" <-> "NH2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 2104": "NH1" <-> "NH2" Residue "G TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2359": "NH1" <-> "NH2" Residue "G GLU 2925": "OE1" <-> "OE2" Residue "G ARG 3648": "NH1" <-> "NH2" Residue "G ARG 3672": "NH1" <-> "NH2" Residue "G ARG 3886": "NH1" <-> "NH2" Residue "G ARG 3984": "NH1" <-> "NH2" Residue "G ARG 4161": "NH1" <-> "NH2" Residue "G TYR 4177": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4944": "NH1" <-> "NH2" Residue "G PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 13": "NH1" <-> "NH2" Time to flip residues: 0.81s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 111000 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 26917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 81 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2521 Unresolved non-hydrogen angles: 3239 Unresolved non-hydrogen dihedrals: 2075 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 38, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1406 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: 26917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 81 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2521 Unresolved non-hydrogen angles: 3239 Unresolved non-hydrogen dihedrals: 2074 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 38, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1406 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: 26917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 81 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2521 Unresolved non-hydrogen angles: 3239 Unresolved non-hydrogen dihedrals: 2073 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 38, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1406 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: 26917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3660, 26917 Classifications: {'peptide': 3660} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 163, 'TRANS': 3494} Chain breaks: 81 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2521 Unresolved non-hydrogen angles: 3239 Unresolved non-hydrogen dihedrals: 2074 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 38, 'ASP:plan': 41, 'TYR:plan': 20, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 28, 'GLU:plan': 68, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1406 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 26278 SG CYS A4958 192.063 167.660 83.735 1.00 44.12 S ATOM 26303 SG CYS A4961 190.876 166.224 87.429 1.00 45.17 S ATOM 54027 SG CYS C4958 194.143 192.058 83.743 1.00 44.64 S ATOM 54052 SG CYS C4961 195.585 190.870 87.435 1.00 45.23 S ATOM 81776 SG CYS E4958 169.754 194.123 83.731 1.00 43.71 S ATOM 81801 SG CYS E4961 170.922 195.558 87.442 1.00 44.68 S ATOM A07CL SG CYS G4958 167.708 169.788 83.615 1.00 45.48 S ATOM A07DA SG CYS G4961 166.273 170.694 87.559 1.00 45.69 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N HIS B 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS B 87 " occ=0.99 residue: pdb=" N HIS D 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS D 87 " occ=0.99 residue: pdb=" N HIS F 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS F 87 " occ=0.99 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: 41.65, per 1000 atoms: 0.38 Number of scatterers: 111000 At special positions: 0 Unit cell: (363.14, 363.14, 198.32, 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 20504 8.00 N 19312 7.00 C 70536 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: 32.48 Conformation dependent library (CDL) restraints added in 14.4 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 A4978 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4958 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4961 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4983 " 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 E4978 " pdb="ZN ZN E6000 " - pdb=" NE2 HIS E4983 " 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 G4978 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4983 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4958 " Number of angles added : 8 28808 Ramachandran restraints generated. 14404 Oldfield, 0 Emsley, 14404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28288 Finding SS restraints... Secondary structure from input PDB file: 699 helices and 132 sheets defined 58.6% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.93 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.847A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.613A pdb=" N ALA A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 removed outlier: 3.526A pdb=" N CYS A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.659A pdb=" N ARG A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.840A 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 Processing helix chain 'A' and resid 482 through 495 removed outlier: 3.519A pdb=" N ASN A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 531 removed outlier: 3.952A pdb=" N ASN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 removed outlier: 4.216A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 571 through 578 removed outlier: 3.881A pdb=" N LEU A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'A' and resid 596 through 608 removed outlier: 4.243A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.606A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 812 through 815 removed outlier: 3.744A pdb=" N VAL A 815 " --> pdb=" O HIS A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'A' and resid 864 through 884 removed outlier: 3.514A pdb=" N LEU A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 901 Processing helix chain 'A' and resid 917 through 920 Processing helix chain 'A' and resid 921 through 935 removed outlier: 3.671A pdb=" N SER A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1001 removed outlier: 3.921A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1048 removed outlier: 3.885A pdb=" N ARG A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN A1035 " --> pdb=" O THR A1031 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1082 Processing helix chain 'A' and resid 1211 through 1216 removed outlier: 3.740A pdb=" N ILE A1216 " --> pdb=" O ARG A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1222 removed outlier: 3.668A pdb=" N GLU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1584 Processing helix chain 'A' and resid 1641 through 1645 removed outlier: 3.913A pdb=" N ASN A1645 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1655 Processing helix chain 'A' and resid 1656 through 1675 removed outlier: 3.616A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 3.807A pdb=" N ALA A1682 " --> pdb=" O ASN A1678 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1685 " --> pdb=" O VAL A1681 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1700 removed outlier: 3.503A pdb=" N LEU A1694 " --> pdb=" O ASP A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 removed outlier: 3.916A pdb=" N HIS A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1719 through 1734 removed outlier: 4.077A pdb=" N ALA A1723 " --> pdb=" O HIS A1719 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A1729 " --> pdb=" O ARG A1725 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR A1734 " --> pdb=" O MET A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1744 Processing helix chain 'A' and resid 1803 through 1824 removed outlier: 4.269A pdb=" N ASP A1821 " --> pdb=" O GLU A1817 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A1822 " --> pdb=" O ALA A1818 " (cutoff:3.500A) 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: 4.736A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A1968 " --> pdb=" O ARG A1964 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN A1972 " --> pdb=" O LYS A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2043 Processing helix chain 'A' and resid 2044 through 2047 Processing helix chain 'A' and resid 2058 through 2071 Processing helix chain 'A' and resid 2094 through 2109 removed outlier: 4.267A pdb=" N ARG A2104 " --> pdb=" O HIS A2100 " (cutoff:3.500A) Processing helix chain 'A' and resid 2115 through 2128 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 2166 removed outlier: 3.842A pdb=" N SER A2164 " --> pdb=" O GLY A2160 " (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 2201 removed outlier: 3.563A pdb=" N MET A2198 " --> pdb=" O HIS A2194 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2215 Processing helix chain 'A' and resid 2227 through 2242 removed outlier: 4.361A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2250 Processing helix chain 'A' and resid 2253 through 2261 Processing helix chain 'A' and resid 2272 through 2281 removed outlier: 3.723A pdb=" N ALA A2276 " --> pdb=" O PRO A2272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 removed outlier: 3.568A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2304 removed outlier: 3.879A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2305 through 2307 No H-bonds generated for 'chain 'A' and resid 2305 through 2307' Processing helix chain 'A' and resid 2327 through 2341 removed outlier: 4.123A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2360 removed outlier: 4.636A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A2359 " --> pdb=" O ARG A2355 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2386 removed outlier: 3.753A pdb=" N GLU A2381 " --> pdb=" O LEU A2377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A2386 " --> pdb=" O GLU A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2420 through 2434 Processing helix chain 'A' and resid 2450 through 2459 Processing helix chain 'A' and resid 2467 through 2475 Proline residue: A2473 - end of helix Processing helix chain 'A' and resid 2495 through 2510 removed outlier: 3.654A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2516 No H-bonds generated for 'chain 'A' and resid 2514 through 2516' Processing helix chain 'A' and resid 2517 through 2522 removed outlier: 3.806A pdb=" N LEU A2522 " --> pdb=" O LEU A2518 " (cutoff:3.500A) Processing helix chain 'A' and resid 2525 through 2534 removed outlier: 3.729A pdb=" N MET A2530 " --> pdb=" O PHE A2526 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A2531 " --> pdb=" O LEU A2527 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A2534 " --> pdb=" O MET A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2559 removed outlier: 4.862A pdb=" N ASN A2551 " --> pdb=" O ALA A2547 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ARG A2552 " --> pdb=" O LEU A2548 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A2558 " --> pdb=" O LEU A2554 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A2559 " --> pdb=" O CYS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2586 removed outlier: 3.690A pdb=" N VAL A2586 " --> pdb=" O MET A2582 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2608 Processing helix chain 'A' and resid 2616 through 2634 Proline residue: A2631 - end of helix Processing helix chain 'A' and resid 2639 through 2660 Proline residue: A2658 - end of helix Processing helix chain 'A' and resid 2668 through 2686 removed outlier: 3.878A pdb=" N LEU A2686 " --> pdb=" O ILE A2682 " (cutoff:3.500A) Processing helix chain 'A' and resid 2692 through 2710 Proline residue: A2701 - end of helix Processing helix chain 'A' and resid 2749 through 2773 removed outlier: 3.907A pdb=" N SER A2753 " --> pdb=" O GLU A2749 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.662A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.183A 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 2897 Processing helix chain 'A' and resid 2907 through 2911 removed outlier: 3.511A pdb=" N LEU A2911 " --> pdb=" O TYR A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2934 removed outlier: 4.358A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A2930 " --> pdb=" O LEU A2926 " (cutoff:3.500A) Processing helix chain 'A' and resid 3018 through 3038 Processing helix chain 'A' and resid 3044 through 3061 Processing helix chain 'A' and resid 3069 through 3090 Proline residue: A3085 - end of helix removed outlier: 4.009A pdb=" N VAL A3088 " --> pdb=" O GLY A3084 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A3090 " --> pdb=" O GLU A3086 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3115 Processing helix chain 'A' and resid 3132 through 3134 No H-bonds generated for 'chain 'A' and resid 3132 through 3134' Processing helix chain 'A' and resid 3135 through 3151 removed outlier: 3.912A pdb=" N VAL A3139 " --> pdb=" O ALA A3135 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A3144 " --> pdb=" O LEU A3140 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A3151 " --> pdb=" O ILE A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3159 through 3177 Processing helix chain 'A' and resid 3185 through 3199 Processing helix chain 'A' and resid 3205 through 3216 Processing helix chain 'A' and resid 3274 through 3288 Proline residue: A3282 - end of helix Processing helix chain 'A' and resid 3295 through 3300 Processing helix chain 'A' and resid 3301 through 3312 Processing helix chain 'A' and resid 3318 through 3337 Processing helix chain 'A' and resid 3348 through 3363 Proline residue: A3360 - end of helix Processing helix chain 'A' and resid 3368 through 3397 removed outlier: 3.626A pdb=" N GLU A3397 " --> pdb=" O LEU A3393 " (cutoff:3.500A) Processing helix chain 'A' and resid 3403 through 3424 removed outlier: 3.780A pdb=" N TYR A3409 " --> pdb=" O LEU A3405 " (cutoff:3.500A) Proline residue: A3410 - end of helix Processing helix chain 'A' and resid 3428 through 3435 Processing helix chain 'A' and resid 3438 through 3455 Processing helix chain 'A' and resid 3458 through 3469 Processing helix chain 'A' and resid 3478 through 3481 removed outlier: 3.744A pdb=" N ALA A3481 " --> pdb=" O MET A3478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3478 through 3481' Processing helix chain 'A' and resid 3482 through 3491 removed outlier: 3.922A pdb=" N SER A3486 " --> pdb=" O GLY A3482 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A3487 " --> pdb=" O ASP A3483 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A3489 " --> pdb=" O GLN A3485 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A3490 " --> pdb=" O SER A3486 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3482 through 3491' Processing helix chain 'A' and resid 3495 through 3504 removed outlier: 3.878A pdb=" N SER A3504 " --> pdb=" O GLY A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3513 through 3515 No H-bonds generated for 'chain 'A' and resid 3513 through 3515' Processing helix chain 'A' and resid 3516 through 3525 Processing helix chain 'A' and resid 3538 through 3544 removed outlier: 3.618A pdb=" N ASP A3544 " --> pdb=" O TYR A3540 " (cutoff:3.500A) Processing helix chain 'A' and resid 3550 through 3570 Proline residue: A3567 - end of helix Processing helix chain 'A' and resid 3646 through 3660 Processing helix chain 'A' and resid 3664 through 3668 removed outlier: 3.950A pdb=" N HIS A3667 " --> pdb=" O THR A3664 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3678 removed outlier: 3.563A pdb=" N MET A3673 " --> pdb=" O PHE A3669 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3710 Processing helix chain 'A' and resid 3721 through 3731 Processing helix chain 'A' and resid 3751 through 3772 Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.648A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3792 through 3805 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3839 Processing helix chain 'A' and resid 3843 through 3851 removed outlier: 3.540A pdb=" N PHE A3847 " --> pdb=" O ASP A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3878 through 3892 Processing helix chain 'A' and resid 3896 through 3905 Processing helix chain 'A' and resid 3914 through 3938 Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.779A pdb=" N SER A3952 " --> pdb=" O LYS A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3982 removed outlier: 3.623A pdb=" N GLN A3977 " --> pdb=" O CYS A3973 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3984 through 4004 removed outlier: 3.670A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4006 through 4008 No H-bonds generated for 'chain 'A' and resid 4006 through 4008' Processing helix chain 'A' and resid 4009 through 4030 Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 3.665A pdb=" N MET A4044 " --> pdb=" O ILE A4040 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A4052 " --> pdb=" O LEU A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4052 through 4062 Processing helix chain 'A' and resid 4063 through 4064 No H-bonds generated for 'chain 'A' and resid 4063 through 4064' Processing helix chain 'A' and resid 4071 through 4074 Processing helix chain 'A' and resid 4076 through 4080 Processing helix chain 'A' and resid 4089 through 4097 Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 4.355A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4136 through 4154 removed outlier: 3.907A pdb=" N GLY A4140 " --> pdb=" O ALA A4136 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4167 Processing helix chain 'A' and resid 4167 through 4175 removed outlier: 3.545A pdb=" N LEU A4171 " --> pdb=" O ALA A4167 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A4173 " --> pdb=" O SER A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4205 Processing helix chain 'A' and resid 4208 through 4223 removed outlier: 4.393A pdb=" N GLU A4212 " --> pdb=" O PRO A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4228 through 4251 removed outlier: 4.367A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4547 through 4558 removed outlier: 6.061A pdb=" N ASN A4553 " --> pdb=" O VAL A4549 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4663 removed outlier: 3.795A pdb=" N ALA A4642 " --> pdb=" O TYR A4638 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) Processing helix chain 'A' and resid 4664 through 4683 removed outlier: 3.977A pdb=" N LEU A4668 " --> pdb=" O LEU A4664 " (cutoff:3.500A) Processing helix chain 'A' and resid 4701 through 4706 Processing helix chain 'A' and resid 4719 through 4727 Processing helix chain 'A' and resid 4737 through 4742 Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 3.875A 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 4788 through 4805 removed outlier: 3.723A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4807 through 4818 removed outlier: 3.571A pdb=" N ALA A4811 " --> pdb=" O PHE A4808 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4832 removed outlier: 3.535A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4857 Processing helix chain 'A' and resid 4858 through 4862 removed outlier: 4.391A pdb=" N LYS A4861 " --> pdb=" O PHE A4858 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4888 Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 3.625A pdb=" N ILE A4901 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4927 through 4955 removed outlier: 4.005A pdb=" N LYS A4951 " --> pdb=" O GLN A4947 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A4954 " --> pdb=" O VAL A4950 " (cutoff:3.500A) Processing helix chain 'A' and resid 4966 through 4971 removed outlier: 3.733A pdb=" N THR A4970 " --> pdb=" O TYR A4967 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A4971 " --> pdb=" O PHE A4968 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4985 through 4998 removed outlier: 3.740A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) Processing helix chain 'A' and resid 4999 through 5003 removed outlier: 3.722A pdb=" N HIS A5003 " --> pdb=" O GLU A5000 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 56 through 65 removed outlier: 3.858A pdb=" N ALA B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.836A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.549A pdb=" N ALA C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.526A pdb=" N CYS C 146 " --> pdb=" O GLY C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 398 through 421 removed outlier: 3.661A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) removed outlier: 3.837A 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 Processing helix chain 'C' and resid 482 through 495 removed outlier: 3.522A pdb=" N ASN C 495 " --> pdb=" O ILE C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 531 removed outlier: 3.956A pdb=" N ASN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 removed outlier: 4.215A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP C 546 " --> pdb=" O THR C 542 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP C 552 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.883A pdb=" N LEU C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 Processing helix chain 'C' and resid 596 through 608 removed outlier: 4.238A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 removed outlier: 3.608A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 690 through 692 No H-bonds generated for 'chain 'C' and resid 690 through 692' Processing helix chain 'C' and resid 812 through 815 removed outlier: 3.747A pdb=" N VAL C 815 " --> pdb=" O HIS C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 812 through 815' Processing helix chain 'C' and resid 864 through 884 removed outlier: 3.515A pdb=" N LEU C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 898 through 901 Processing helix chain 'C' and resid 917 through 920 Processing helix chain 'C' and resid 921 through 935 removed outlier: 3.693A pdb=" N SER C 925 " --> pdb=" O ASN C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1001 removed outlier: 3.922A pdb=" N THR C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP C 999 " --> pdb=" O VAL C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1048 removed outlier: 3.895A pdb=" N ARG C1033 " --> pdb=" O GLU C1029 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER C1034 " --> pdb=" O ALA C1030 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN C1035 " --> pdb=" O THR C1031 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1082 Processing helix chain 'C' and resid 1211 through 1216 removed outlier: 3.733A pdb=" N ILE C1216 " --> pdb=" O ARG C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1222 removed outlier: 3.697A pdb=" N GLU C1221 " --> pdb=" O CYS C1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1225 through 1230 removed outlier: 4.111A pdb=" N ASN C1229 " --> pdb=" O PRO C1225 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET C1230 " --> pdb=" O PHE C1226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1225 through 1230' Processing helix chain 'C' and resid 1580 through 1584 Processing helix chain 'C' and resid 1641 through 1645 removed outlier: 3.874A pdb=" N ASN C1645 " --> pdb=" O PRO C1642 " (cutoff:3.500A) Processing helix chain 'C' and resid 1651 through 1655 Processing helix chain 'C' and resid 1656 through 1675 removed outlier: 3.610A pdb=" N ALA C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1690 removed outlier: 3.808A pdb=" N ALA C1682 " --> pdb=" O ASN C1678 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS C1683 " --> pdb=" O ASN C1679 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C1685 " --> pdb=" O VAL C1681 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C1690 " --> pdb=" O CYS C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1700 removed outlier: 3.507A pdb=" N LEU C1694 " --> pdb=" O ASP C1690 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 removed outlier: 3.915A pdb=" N HIS C1719 " --> pdb=" O LEU C1715 " (cutoff:3.500A) Processing helix chain 'C' and resid 1719 through 1734 removed outlier: 4.072A pdb=" N ALA C1723 " --> pdb=" O HIS C1719 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER C1729 " --> pdb=" O ARG C1725 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR C1734 " --> pdb=" O MET C1730 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1744 Processing helix chain 'C' and resid 1803 through 1824 removed outlier: 4.282A pdb=" N ASP C1821 " --> pdb=" O GLU C1817 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C1822 " --> pdb=" O ALA C1818 " (cutoff:3.500A) 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: 4.734A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS C1968 " --> pdb=" O ARG C1964 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN C1972 " --> pdb=" O LYS C1968 " (cutoff:3.500A) Processing helix chain 'C' and resid 2034 through 2043 Processing helix chain 'C' and resid 2044 through 2047 Processing helix chain 'C' and resid 2058 through 2071 Processing helix chain 'C' and resid 2094 through 2109 removed outlier: 4.260A pdb=" N ARG C2104 " --> pdb=" O HIS C2100 " (cutoff:3.500A) Processing helix chain 'C' and resid 2115 through 2128 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 2166 removed outlier: 3.842A pdb=" N SER C2164 " --> pdb=" O GLY C2160 " (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 2201 removed outlier: 3.564A pdb=" N MET C2198 " --> pdb=" O HIS C2194 " (cutoff:3.500A) Processing helix chain 'C' and resid 2203 through 2215 Processing helix chain 'C' and resid 2227 through 2242 removed outlier: 4.369A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) Processing helix chain 'C' and resid 2243 through 2250 Processing helix chain 'C' and resid 2253 through 2261 Processing helix chain 'C' and resid 2272 through 2281 removed outlier: 3.725A pdb=" N ALA C2276 " --> pdb=" O PRO C2272 " (cutoff:3.500A) Processing helix chain 'C' and resid 2283 through 2290 removed outlier: 3.569A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) Processing helix chain 'C' and resid 2291 through 2304 removed outlier: 3.878A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2305 through 2307 No H-bonds generated for 'chain 'C' and resid 2305 through 2307' Processing helix chain 'C' and resid 2327 through 2341 removed outlier: 4.123A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2360 removed outlier: 4.640A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2386 removed outlier: 3.753A pdb=" N GLU C2381 " --> pdb=" O LEU C2377 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C2386 " --> pdb=" O GLU C2382 " (cutoff:3.500A) Processing helix chain 'C' and resid 2420 through 2434 Processing helix chain 'C' and resid 2450 through 2459 Processing helix chain 'C' and resid 2467 through 2475 Proline residue: C2473 - end of helix Processing helix chain 'C' and resid 2495 through 2510 removed outlier: 3.656A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2516 No H-bonds generated for 'chain 'C' and resid 2514 through 2516' Processing helix chain 'C' and resid 2517 through 2522 removed outlier: 3.804A pdb=" N LEU C2522 " --> pdb=" O LEU C2518 " (cutoff:3.500A) Processing helix chain 'C' and resid 2525 through 2534 removed outlier: 3.727A pdb=" N MET C2530 " --> pdb=" O PHE C2526 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C2531 " --> pdb=" O LEU C2527 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C2534 " --> pdb=" O MET C2530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2559 removed outlier: 4.858A pdb=" N ASN C2551 " --> pdb=" O ALA C2547 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG C2552 " --> pdb=" O LEU C2548 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C2558 " --> pdb=" O LEU C2554 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C2559 " --> pdb=" O CYS C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2568 through 2586 removed outlier: 3.688A pdb=" N VAL C2586 " --> pdb=" O MET C2582 " (cutoff:3.500A) Processing helix chain 'C' and resid 2592 through 2608 Processing helix chain 'C' and resid 2616 through 2634 Proline residue: C2631 - end of helix Processing helix chain 'C' and resid 2639 through 2660 Proline residue: C2658 - end of helix Processing helix chain 'C' and resid 2668 through 2686 removed outlier: 3.877A pdb=" N LEU C2686 " --> pdb=" O ILE C2682 " (cutoff:3.500A) Processing helix chain 'C' and resid 2692 through 2710 Proline residue: C2701 - end of helix Processing helix chain 'C' and resid 2749 through 2773 removed outlier: 3.906A pdb=" N SER C2753 " --> pdb=" O GLU C2749 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE C2754 " --> pdb=" O LYS C2750 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.663A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.187A 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 2897 Processing helix chain 'C' and resid 2907 through 2911 removed outlier: 3.503A pdb=" N LEU C2911 " --> pdb=" O TYR C2908 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2934 removed outlier: 4.359A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) Processing helix chain 'C' and resid 3018 through 3038 Processing helix chain 'C' and resid 3044 through 3061 Processing helix chain 'C' and resid 3069 through 3090 Proline residue: C3085 - end of helix removed outlier: 4.010A pdb=" N VAL C3088 " --> pdb=" O GLY C3084 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C3090 " --> pdb=" O GLU C3086 " (cutoff:3.500A) Processing helix chain 'C' and resid 3096 through 3115 Processing helix chain 'C' and resid 3132 through 3134 No H-bonds generated for 'chain 'C' and resid 3132 through 3134' Processing helix chain 'C' and resid 3135 through 3151 removed outlier: 3.914A pdb=" N VAL C3139 " --> pdb=" O ALA C3135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C3144 " --> pdb=" O LEU C3140 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C3151 " --> pdb=" O ILE C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3159 through 3177 Processing helix chain 'C' and resid 3185 through 3199 Processing helix chain 'C' and resid 3205 through 3216 Processing helix chain 'C' and resid 3274 through 3288 Proline residue: C3282 - end of helix Processing helix chain 'C' and resid 3295 through 3300 Processing helix chain 'C' and resid 3301 through 3312 Processing helix chain 'C' and resid 3318 through 3337 Processing helix chain 'C' and resid 3348 through 3363 Proline residue: C3360 - end of helix Processing helix chain 'C' and resid 3368 through 3397 removed outlier: 3.627A pdb=" N GLU C3397 " --> pdb=" O LEU C3393 " (cutoff:3.500A) Processing helix chain 'C' and resid 3403 through 3424 removed outlier: 3.790A pdb=" N TYR C3409 " --> pdb=" O LEU C3405 " (cutoff:3.500A) Proline residue: C3410 - end of helix Processing helix chain 'C' and resid 3428 through 3435 Processing helix chain 'C' and resid 3438 through 3455 Processing helix chain 'C' and resid 3458 through 3469 Processing helix chain 'C' and resid 3478 through 3481 removed outlier: 3.745A pdb=" N ALA C3481 " --> pdb=" O MET C3478 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3478 through 3481' Processing helix chain 'C' and resid 3482 through 3491 removed outlier: 3.921A pdb=" N SER C3486 " --> pdb=" O GLY C3482 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C3487 " --> pdb=" O ASP C3483 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C3488 " --> pdb=" O ALA C3484 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C3489 " --> pdb=" O GLN C3485 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C3490 " --> pdb=" O SER C3486 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C3491 " --> pdb=" O GLY C3487 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3482 through 3491' Processing helix chain 'C' and resid 3495 through 3504 removed outlier: 3.882A pdb=" N SER C3504 " --> pdb=" O GLY C3500 " (cutoff:3.500A) Processing helix chain 'C' and resid 3513 through 3515 No H-bonds generated for 'chain 'C' and resid 3513 through 3515' Processing helix chain 'C' and resid 3516 through 3525 Processing helix chain 'C' and resid 3538 through 3544 removed outlier: 3.618A pdb=" N ASP C3544 " --> pdb=" O TYR C3540 " (cutoff:3.500A) Processing helix chain 'C' and resid 3550 through 3570 Proline residue: C3567 - end of helix Processing helix chain 'C' and resid 3646 through 3660 Processing helix chain 'C' and resid 3664 through 3668 removed outlier: 3.933A pdb=" N HIS C3667 " --> pdb=" O THR C3664 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3678 removed outlier: 3.559A pdb=" N MET C3673 " --> pdb=" O PHE C3669 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3710 Processing helix chain 'C' and resid 3721 through 3731 Processing helix chain 'C' and resid 3751 through 3772 Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 3.644A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3792 through 3805 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3839 Processing helix chain 'C' and resid 3843 through 3851 removed outlier: 3.542A pdb=" N PHE C3847 " --> pdb=" O ASP C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3878 through 3892 Processing helix chain 'C' and resid 3896 through 3905 Processing helix chain 'C' and resid 3914 through 3938 Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.781A pdb=" N SER C3952 " --> pdb=" O LYS C3948 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3982 removed outlier: 3.622A pdb=" N GLN C3977 " --> pdb=" O CYS C3973 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3984 through 4004 removed outlier: 3.671A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4006 through 4008 No H-bonds generated for 'chain 'C' and resid 4006 through 4008' Processing helix chain 'C' and resid 4009 through 4030 Processing helix chain 'C' and resid 4038 through 4052 removed outlier: 3.666A pdb=" N MET C4044 " --> pdb=" O ILE C4040 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C4052 " --> pdb=" O LEU C4048 " (cutoff:3.500A) Processing helix chain 'C' and resid 4052 through 4062 Processing helix chain 'C' and resid 4063 through 4064 No H-bonds generated for 'chain 'C' and resid 4063 through 4064' Processing helix chain 'C' and resid 4071 through 4074 Processing helix chain 'C' and resid 4076 through 4080 Processing helix chain 'C' and resid 4089 through 4097 Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 4.359A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4136 through 4154 removed outlier: 3.906A pdb=" N GLY C4140 " --> pdb=" O ALA C4136 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4167 Processing helix chain 'C' and resid 4167 through 4175 removed outlier: 3.546A pdb=" N LEU C4171 " --> pdb=" O ALA C4167 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR C4173 " --> pdb=" O SER C4169 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4205 Processing helix chain 'C' and resid 4208 through 4223 removed outlier: 4.389A pdb=" N GLU C4212 " --> pdb=" O PRO C4208 " (cutoff:3.500A) Processing helix chain 'C' and resid 4228 through 4251 removed outlier: 4.368A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4547 through 4558 removed outlier: 6.063A pdb=" N ASN C4553 " --> pdb=" O VAL C4549 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C4558 " --> pdb=" O TYR C4554 " (cutoff:3.500A) Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4663 removed outlier: 3.799A pdb=" N ALA C4642 " --> pdb=" O TYR C4638 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP C4644 " --> pdb=" O GLU C4640 " (cutoff:3.500A) Processing helix chain 'C' and resid 4664 through 4683 removed outlier: 3.978A pdb=" N LEU C4668 " --> pdb=" O LEU C4664 " (cutoff:3.500A) Processing helix chain 'C' and resid 4701 through 4706 Processing helix chain 'C' and resid 4719 through 4727 Processing helix chain 'C' and resid 4737 through 4742 Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 3.874A 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 4788 through 4805 removed outlier: 3.716A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4807 through 4818 removed outlier: 3.599A pdb=" N ALA C4811 " --> pdb=" O PHE C4808 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4832 removed outlier: 3.542A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4857 Processing helix chain 'C' and resid 4858 through 4862 removed outlier: 4.380A pdb=" N LYS C4861 " --> pdb=" O PHE C4858 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4888 Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 3.618A pdb=" N ILE C4901 " --> pdb=" O GLY C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4927 through 4955 removed outlier: 3.617A pdb=" N LEU C4935 " --> pdb=" O ILE C4931 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS C4951 " --> pdb=" O GLN C4947 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET C4954 " --> pdb=" O VAL C4950 " (cutoff:3.500A) Processing helix chain 'C' and resid 4966 through 4971 removed outlier: 3.732A pdb=" N THR C4970 " --> pdb=" O TYR C4967 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C4971 " --> pdb=" O PHE C4968 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4985 through 4998 removed outlier: 3.742A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) Processing helix chain 'C' and resid 4999 through 5003 removed outlier: 3.719A pdb=" N HIS C5003 " --> pdb=" O GLU C5000 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 56 through 65 removed outlier: 3.861A pdb=" N ALA D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.830A pdb=" N CYS E 65 " --> pdb=" O ASP E 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 66' Processing helix chain 'E' and resid 74 through 83 removed outlier: 3.548A pdb=" N ALA E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.529A pdb=" N CYS E 146 " --> pdb=" O GLY E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 255 through 258 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 398 through 421 removed outlier: 3.662A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE E 404 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 407 " --> pdb=" O MET E 403 " (cutoff:3.500A) removed outlier: 3.841A 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 Processing helix chain 'E' and resid 482 through 495 removed outlier: 3.523A pdb=" N ASN E 495 " --> pdb=" O ILE E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 531 removed outlier: 3.954A pdb=" N ASN E 520 " --> pdb=" O LYS E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 552 removed outlier: 4.212A pdb=" N CYS E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN E 543 " --> pdb=" O LEU E 539 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASP E 545 " --> pdb=" O SER E 541 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP E 546 " --> pdb=" O THR E 542 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP E 552 " --> pdb=" O VAL E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 569 Processing helix chain 'E' and resid 571 through 578 removed outlier: 3.881A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 578 " --> pdb=" O VAL E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 593 Processing helix chain 'E' and resid 596 through 608 removed outlier: 4.241A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 626 removed outlier: 3.604A pdb=" N GLN E 618 " --> pdb=" O VAL E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 629 No H-bonds generated for 'chain 'E' and resid 627 through 629' Processing helix chain 'E' and resid 690 through 692 No H-bonds generated for 'chain 'E' and resid 690 through 692' Processing helix chain 'E' and resid 812 through 815 removed outlier: 3.731A pdb=" N VAL E 815 " --> pdb=" O HIS E 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 812 through 815' Processing helix chain 'E' and resid 864 through 884 removed outlier: 3.515A pdb=" N LEU E 881 " --> pdb=" O ASN E 877 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP E 882 " --> pdb=" O ILE E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 898 through 901 Processing helix chain 'E' and resid 917 through 920 Processing helix chain 'E' and resid 921 through 935 removed outlier: 3.686A pdb=" N SER E 925 " --> pdb=" O ASN E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 1001 removed outlier: 3.913A pdb=" N THR E 982 " --> pdb=" O THR E 978 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP E 999 " --> pdb=" O VAL E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1048 removed outlier: 3.884A pdb=" N ARG E1033 " --> pdb=" O GLU E1029 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER E1034 " --> pdb=" O ALA E1030 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN E1035 " --> pdb=" O THR E1031 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER E1038 " --> pdb=" O SER E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1082 Processing helix chain 'E' and resid 1211 through 1216 removed outlier: 3.734A pdb=" N ILE E1216 " --> pdb=" O ARG E1212 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1222 removed outlier: 3.699A pdb=" N GLU E1221 " --> pdb=" O CYS E1217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1225 through 1230 removed outlier: 4.129A pdb=" N ASN E1229 " --> pdb=" O PRO E1225 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E1230 " --> pdb=" O PHE E1226 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1225 through 1230' Processing helix chain 'E' and resid 1580 through 1584 Processing helix chain 'E' and resid 1641 through 1645 removed outlier: 3.874A pdb=" N ASN E1645 " --> pdb=" O PRO E1642 " (cutoff:3.500A) Processing helix chain 'E' and resid 1651 through 1655 Processing helix chain 'E' and resid 1656 through 1675 removed outlier: 3.617A pdb=" N ALA E1675 " --> pdb=" O ARG E1671 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1690 removed outlier: 3.810A pdb=" N ALA E1682 " --> pdb=" O ASN E1678 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS E1683 " --> pdb=" O ASN E1679 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E1685 " --> pdb=" O VAL E1681 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP E1690 " --> pdb=" O CYS E1686 " (cutoff:3.500A) Processing helix chain 'E' and resid 1690 through 1700 removed outlier: 3.505A pdb=" N LEU E1694 " --> pdb=" O ASP E1690 " (cutoff:3.500A) Processing helix chain 'E' and resid 1704 through 1719 removed outlier: 3.912A pdb=" N HIS E1719 " --> pdb=" O LEU E1715 " (cutoff:3.500A) Processing helix chain 'E' and resid 1719 through 1734 removed outlier: 4.075A pdb=" N ALA E1723 " --> pdb=" O HIS E1719 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER E1729 " --> pdb=" O ARG E1725 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR E1734 " --> pdb=" O MET E1730 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 Processing helix chain 'E' and resid 1803 through 1824 removed outlier: 4.270A pdb=" N ASP E1821 " --> pdb=" O GLU E1817 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E1822 " --> pdb=" O ALA E1818 " (cutoff:3.500A) 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: 4.735A pdb=" N ASP E1967 " --> pdb=" O GLU E1963 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN E1972 " --> pdb=" O LYS E1968 " (cutoff:3.500A) Processing helix chain 'E' and resid 2034 through 2043 Processing helix chain 'E' and resid 2044 through 2047 Processing helix chain 'E' and resid 2058 through 2071 Processing helix chain 'E' and resid 2094 through 2109 removed outlier: 4.252A pdb=" N ARG E2104 " --> pdb=" O HIS E2100 " (cutoff:3.500A) Processing helix chain 'E' and resid 2115 through 2128 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 2166 removed outlier: 3.820A pdb=" N SER E2164 " --> pdb=" O GLY E2160 " (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 2201 removed outlier: 3.560A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) Processing helix chain 'E' and resid 2203 through 2215 Processing helix chain 'E' and resid 2227 through 2242 removed outlier: 4.353A pdb=" N SER E2231 " --> pdb=" O LYS E2227 " (cutoff:3.500A) Processing helix chain 'E' and resid 2243 through 2250 Processing helix chain 'E' and resid 2253 through 2261 Processing helix chain 'E' and resid 2272 through 2281 removed outlier: 3.726A pdb=" N ALA E2276 " --> pdb=" O PRO E2272 " (cutoff:3.500A) Processing helix chain 'E' and resid 2283 through 2290 removed outlier: 3.568A pdb=" N LEU E2290 " --> pdb=" O LEU E2286 " (cutoff:3.500A) Processing helix chain 'E' and resid 2291 through 2304 removed outlier: 3.881A pdb=" N LEU E2295 " --> pdb=" O GLN E2291 " (cutoff:3.500A) Processing helix chain 'E' and resid 2305 through 2307 No H-bonds generated for 'chain 'E' and resid 2305 through 2307' Processing helix chain 'E' and resid 2327 through 2341 removed outlier: 4.125A pdb=" N VAL E2341 " --> pdb=" O PHE E2337 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2360 removed outlier: 4.635A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E2359 " --> pdb=" O ARG E2355 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS E2360 " --> pdb=" O LEU E2356 " (cutoff:3.500A) Processing helix chain 'E' and resid 2377 through 2386 removed outlier: 3.755A pdb=" N GLU E2381 " --> pdb=" O LEU E2377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E2386 " --> pdb=" O GLU E2382 " (cutoff:3.500A) Processing helix chain 'E' and resid 2420 through 2435 Processing helix chain 'E' and resid 2450 through 2459 Processing helix chain 'E' and resid 2467 through 2475 Proline residue: E2473 - end of helix Processing helix chain 'E' and resid 2495 through 2510 removed outlier: 3.669A pdb=" N LYS E2499 " --> pdb=" O VAL E2495 " (cutoff:3.500A) Processing helix chain 'E' and resid 2514 through 2516 No H-bonds generated for 'chain 'E' and resid 2514 through 2516' Processing helix chain 'E' and resid 2517 through 2522 removed outlier: 3.807A pdb=" N LEU E2522 " --> pdb=" O LEU E2518 " (cutoff:3.500A) Processing helix chain 'E' and resid 2525 through 2534 removed outlier: 3.727A pdb=" N MET E2530 " --> pdb=" O PHE E2526 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG E2531 " --> pdb=" O LEU E2527 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E2534 " --> pdb=" O MET E2530 " (cutoff:3.500A) Processing helix chain 'E' and resid 2545 through 2559 removed outlier: 4.862A pdb=" N ASN E2551 " --> pdb=" O ALA E2547 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG E2552 " --> pdb=" O LEU E2548 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL E2558 " --> pdb=" O LEU E2554 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU E2559 " --> pdb=" O CYS E2555 " (cutoff:3.500A) Processing helix chain 'E' and resid 2568 through 2586 removed outlier: 3.694A pdb=" N VAL E2586 " --> pdb=" O MET E2582 " (cutoff:3.500A) Processing helix chain 'E' and resid 2592 through 2608 Processing helix chain 'E' and resid 2616 through 2634 Proline residue: E2631 - end of helix Processing helix chain 'E' and resid 2639 through 2660 Proline residue: E2658 - end of helix Processing helix chain 'E' and resid 2668 through 2686 removed outlier: 3.877A pdb=" N LEU E2686 " --> pdb=" O ILE E2682 " (cutoff:3.500A) Processing helix chain 'E' and resid 2692 through 2710 Proline residue: E2701 - end of helix Processing helix chain 'E' and resid 2749 through 2773 removed outlier: 3.898A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E2770 " --> pdb=" O TRP E2766 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.656A pdb=" N ILE E2804 " --> pdb=" O LYS E2800 " (cutoff:3.500A) removed outlier: 4.188A 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 removed outlier: 3.506A pdb=" N GLY E2864 " --> pdb=" O ASP E2861 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2897 Processing helix chain 'E' and resid 2907 through 2911 removed outlier: 3.503A pdb=" N LEU E2911 " --> pdb=" O TYR E2908 " (cutoff:3.500A) Processing helix chain 'E' and resid 2912 through 2934 removed outlier: 4.358A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS E2922 " --> pdb=" O ARG E2918 " (cutoff:3.500A) Processing helix chain 'E' and resid 3018 through 3038 Processing helix chain 'E' and resid 3044 through 3061 Processing helix chain 'E' and resid 3069 through 3090 Proline residue: E3085 - end of helix removed outlier: 4.012A pdb=" N VAL E3088 " --> pdb=" O GLY E3084 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA E3090 " --> pdb=" O GLU E3086 " (cutoff:3.500A) Processing helix chain 'E' and resid 3096 through 3115 Processing helix chain 'E' and resid 3132 through 3134 No H-bonds generated for 'chain 'E' and resid 3132 through 3134' Processing helix chain 'E' and resid 3135 through 3151 removed outlier: 3.912A pdb=" N VAL E3139 " --> pdb=" O ALA E3135 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE E3144 " --> pdb=" O LEU E3140 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E3151 " --> pdb=" O ILE E3147 " (cutoff:3.500A) Processing helix chain 'E' and resid 3159 through 3177 Processing helix chain 'E' and resid 3185 through 3199 Processing helix chain 'E' and resid 3205 through 3216 Processing helix chain 'E' and resid 3274 through 3288 Proline residue: E3282 - end of helix Processing helix chain 'E' and resid 3295 through 3300 Processing helix chain 'E' and resid 3301 through 3312 Processing helix chain 'E' and resid 3318 through 3337 Processing helix chain 'E' and resid 3348 through 3363 Proline residue: E3360 - end of helix Processing helix chain 'E' and resid 3368 through 3397 removed outlier: 3.626A pdb=" N GLU E3397 " --> pdb=" O LEU E3393 " (cutoff:3.500A) Processing helix chain 'E' and resid 3403 through 3424 removed outlier: 3.762A pdb=" N TYR E3409 " --> pdb=" O LEU E3405 " (cutoff:3.500A) Proline residue: E3410 - end of helix Processing helix chain 'E' and resid 3428 through 3435 Processing helix chain 'E' and resid 3438 through 3455 Processing helix chain 'E' and resid 3458 through 3469 Processing helix chain 'E' and resid 3478 through 3481 removed outlier: 3.745A pdb=" N ALA E3481 " --> pdb=" O MET E3478 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3478 through 3481' Processing helix chain 'E' and resid 3482 through 3491 removed outlier: 3.921A pdb=" N SER E3486 " --> pdb=" O GLY E3482 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY E3487 " --> pdb=" O ASP E3483 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E3488 " --> pdb=" O ALA E3484 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E3489 " --> pdb=" O GLN E3485 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP E3490 " --> pdb=" O SER E3486 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E3491 " --> pdb=" O GLY E3487 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3482 through 3491' Processing helix chain 'E' and resid 3495 through 3504 removed outlier: 3.877A pdb=" N SER E3504 " --> pdb=" O GLY E3500 " (cutoff:3.500A) Processing helix chain 'E' and resid 3513 through 3515 No H-bonds generated for 'chain 'E' and resid 3513 through 3515' Processing helix chain 'E' and resid 3516 through 3525 Processing helix chain 'E' and resid 3538 through 3544 removed outlier: 3.615A pdb=" N ASP E3544 " --> pdb=" O TYR E3540 " (cutoff:3.500A) Processing helix chain 'E' and resid 3550 through 3570 Proline residue: E3567 - end of helix Processing helix chain 'E' and resid 3646 through 3660 Processing helix chain 'E' and resid 3664 through 3668 removed outlier: 3.938A pdb=" N HIS E3667 " --> pdb=" O THR E3664 " (cutoff:3.500A) Processing helix chain 'E' and resid 3669 through 3678 removed outlier: 3.557A pdb=" N MET E3673 " --> pdb=" O PHE E3669 " (cutoff:3.500A) Processing helix chain 'E' and resid 3696 through 3710 Processing helix chain 'E' and resid 3721 through 3731 Processing helix chain 'E' and resid 3751 through 3772 Processing helix chain 'E' and resid 3774 through 3787 removed outlier: 3.648A pdb=" N LYS E3787 " --> pdb=" O ILE E3783 " (cutoff:3.500A) Processing helix chain 'E' and resid 3792 through 3805 Processing helix chain 'E' and resid 3809 through 3824 Processing helix chain 'E' and resid 3826 through 3839 Processing helix chain 'E' and resid 3843 through 3851 removed outlier: 3.541A pdb=" N PHE E3847 " --> pdb=" O ASP E3843 " (cutoff:3.500A) Processing helix chain 'E' and resid 3878 through 3892 Processing helix chain 'E' and resid 3896 through 3905 Processing helix chain 'E' and resid 3914 through 3938 Processing helix chain 'E' and resid 3944 through 3970 removed outlier: 3.777A pdb=" N SER E3952 " --> pdb=" O LYS E3948 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3982 removed outlier: 3.623A pdb=" N GLN E3977 " --> pdb=" O CYS E3973 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS E3982 " --> pdb=" O GLN E3978 " (cutoff:3.500A) Processing helix chain 'E' and resid 3984 through 4004 removed outlier: 3.671A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET E4001 " --> pdb=" O ALA E3997 " (cutoff:3.500A) Processing helix chain 'E' and resid 4006 through 4008 No H-bonds generated for 'chain 'E' and resid 4006 through 4008' Processing helix chain 'E' and resid 4009 through 4030 Processing helix chain 'E' and resid 4038 through 4052 removed outlier: 3.664A pdb=" N MET E4044 " --> pdb=" O ILE E4040 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E4052 " --> pdb=" O LEU E4048 " (cutoff:3.500A) Processing helix chain 'E' and resid 4052 through 4062 Processing helix chain 'E' and resid 4063 through 4064 No H-bonds generated for 'chain 'E' and resid 4063 through 4064' Processing helix chain 'E' and resid 4071 through 4074 Processing helix chain 'E' and resid 4076 through 4080 Processing helix chain 'E' and resid 4089 through 4097 Processing helix chain 'E' and resid 4104 through 4116 removed outlier: 4.359A pdb=" N GLU E4116 " --> pdb=" O LEU E4112 " (cutoff:3.500A) Processing helix chain 'E' and resid 4136 through 4154 removed outlier: 3.908A pdb=" N GLY E4140 " --> pdb=" O ALA E4136 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4167 Processing helix chain 'E' and resid 4167 through 4175 removed outlier: 3.550A pdb=" N LEU E4171 " --> pdb=" O ALA E4167 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR E4173 " --> pdb=" O SER E4169 " (cutoff:3.500A) Processing helix chain 'E' and resid 4198 through 4205 Processing helix chain 'E' and resid 4208 through 4223 removed outlier: 4.385A pdb=" N GLU E4212 " --> pdb=" O PRO E4208 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4251 removed outlier: 4.377A pdb=" N GLU E4232 " --> pdb=" O ALA E4228 " (cutoff:3.500A) Processing helix chain 'E' and resid 4547 through 4558 removed outlier: 6.065A pdb=" N ASN E4553 " --> pdb=" O VAL E4549 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN E4558 " --> pdb=" O TYR E4554 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4578 Processing helix chain 'E' and resid 4638 through 4663 removed outlier: 3.799A pdb=" N ALA E4642 " --> pdb=" O TYR E4638 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP E4644 " --> pdb=" O GLU E4640 " (cutoff:3.500A) Processing helix chain 'E' and resid 4664 through 4683 removed outlier: 3.974A pdb=" N LEU E4668 " --> pdb=" O LEU E4664 " (cutoff:3.500A) Processing helix chain 'E' and resid 4701 through 4706 Processing helix chain 'E' and resid 4719 through 4727 Processing helix chain 'E' and resid 4737 through 4742 Processing helix chain 'E' and resid 4766 through 4771 removed outlier: 3.875A 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 4788 through 4805 removed outlier: 3.734A pdb=" N HIS E4803 " --> pdb=" O SER E4799 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR E4804 " --> pdb=" O LEU E4800 " (cutoff:3.500A) Processing helix chain 'E' and resid 4807 through 4818 removed outlier: 3.589A pdb=" N ALA E4811 " --> pdb=" O PHE E4808 " (cutoff:3.500A) Processing helix chain 'E' and resid 4820 through 4832 removed outlier: 3.553A pdb=" N VAL E4830 " --> pdb=" O ILE E4826 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4857 Processing helix chain 'E' and resid 4858 through 4862 removed outlier: 4.383A pdb=" N LYS E4861 " --> pdb=" O PHE E4858 " (cutoff:3.500A) Processing helix chain 'E' and resid 4878 through 4888 Processing helix chain 'E' and resid 4896 through 4901 removed outlier: 3.618A pdb=" N ILE E4901 " --> pdb=" O GLY E4898 " (cutoff:3.500A) Processing helix chain 'E' and resid 4909 through 4924 Processing helix chain 'E' and resid 4927 through 4955 removed outlier: 4.013A pdb=" N LYS E4951 " --> pdb=" O GLN E4947 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E4954 " --> pdb=" O VAL E4950 " (cutoff:3.500A) Processing helix chain 'E' and resid 4966 through 4971 removed outlier: 3.724A pdb=" N THR E4970 " --> pdb=" O TYR E4967 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR E4971 " --> pdb=" O PHE E4968 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4981 Processing helix chain 'E' and resid 4985 through 4998 removed outlier: 3.743A pdb=" N MET E4989 " --> pdb=" O LEU E4985 " (cutoff:3.500A) Processing helix chain 'E' and resid 4999 through 5003 removed outlier: 3.721A pdb=" N HIS E5003 " --> pdb=" O GLU E5000 " (cutoff:3.500A) Processing helix chain 'E' and resid 5004 through 5017 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.855A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.850A pdb=" N CYS G 65 " --> pdb=" O ASP G 61 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 66' Processing helix chain 'G' and resid 74 through 83 removed outlier: 3.550A pdb=" N ALA G 83 " --> pdb=" O GLN G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 146 removed outlier: 3.530A pdb=" N CYS G 146 " --> pdb=" O GLY G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 143 through 146' Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 258 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 398 through 421 removed outlier: 3.662A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE G 404 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR G 407 " --> pdb=" O MET G 403 " (cutoff:3.500A) removed outlier: 3.838A 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 Processing helix chain 'G' and resid 482 through 495 removed outlier: 3.521A pdb=" N ASN G 495 " --> pdb=" O ILE G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 531 removed outlier: 3.948A pdb=" N ASN G 520 " --> pdb=" O LYS G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 552 removed outlier: 4.210A pdb=" N CYS G 537 " --> pdb=" O ASN G 533 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR G 542 " --> pdb=" O ALA G 538 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN G 543 " --> pdb=" O LEU G 539 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASP G 545 " --> pdb=" O SER G 541 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP G 546 " --> pdb=" O THR G 542 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP G 552 " --> pdb=" O VAL G 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 569 Processing helix chain 'G' and resid 571 through 578 removed outlier: 3.882A pdb=" N LEU G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 578 " --> pdb=" O VAL G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 593 Processing helix chain 'G' and resid 596 through 608 removed outlier: 4.239A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 626 removed outlier: 3.602A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 629 No H-bonds generated for 'chain 'G' and resid 627 through 629' Processing helix chain 'G' and resid 690 through 692 No H-bonds generated for 'chain 'G' and resid 690 through 692' Processing helix chain 'G' and resid 812 through 815 removed outlier: 3.748A pdb=" N VAL G 815 " --> pdb=" O HIS G 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 812 through 815' Processing helix chain 'G' and resid 864 through 884 removed outlier: 3.513A pdb=" N LEU G 881 " --> pdb=" O ASN G 877 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP G 882 " --> pdb=" O ILE G 878 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 890 Processing helix chain 'G' and resid 898 through 901 Processing helix chain 'G' and resid 917 through 920 Processing helix chain 'G' and resid 921 through 935 removed outlier: 3.671A pdb=" N SER G 925 " --> pdb=" O ASN G 921 " (cutoff:3.500A) Processing helix chain 'G' and resid 978 through 1001 removed outlier: 3.920A pdb=" N THR G 982 " --> pdb=" O THR G 978 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP G 999 " --> pdb=" O VAL G 995 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1048 removed outlier: 3.886A pdb=" N ARG G1033 " --> pdb=" O GLU G1029 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN G1035 " --> pdb=" O THR G1031 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER G1038 " --> pdb=" O SER G1034 " (cutoff:3.500A) Processing helix chain 'G' and resid 1078 through 1082 Processing helix chain 'G' and resid 1211 through 1216 removed outlier: 3.734A pdb=" N ILE G1216 " --> pdb=" O ARG G1212 " (cutoff:3.500A) Processing helix chain 'G' and resid 1217 through 1222 removed outlier: 3.702A pdb=" N GLU G1221 " --> pdb=" O CYS G1217 " (cutoff:3.500A) Processing helix chain 'G' and resid 1225 through 1230 removed outlier: 4.119A pdb=" N ASN G1229 " --> pdb=" O PRO G1225 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET G1230 " --> pdb=" O PHE G1226 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1225 through 1230' Processing helix chain 'G' and resid 1580 through 1584 Processing helix chain 'G' and resid 1641 through 1645 removed outlier: 3.878A pdb=" N ASN G1645 " --> pdb=" O PRO G1642 " (cutoff:3.500A) Processing helix chain 'G' and resid 1651 through 1655 Processing helix chain 'G' and resid 1656 through 1675 removed outlier: 3.613A pdb=" N ALA G1675 " --> pdb=" O ARG G1671 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1690 removed outlier: 3.811A pdb=" N ALA G1682 " --> pdb=" O ASN G1678 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS G1683 " --> pdb=" O ASN G1679 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA G1684 " --> pdb=" O ARG G1680 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G1685 " --> pdb=" O VAL G1681 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP G1690 " --> pdb=" O CYS G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1690 through 1700 removed outlier: 3.505A pdb=" N LEU G1694 " --> pdb=" O ASP G1690 " (cutoff:3.500A) Processing helix chain 'G' and resid 1704 through 1719 removed outlier: 3.912A pdb=" N HIS G1719 " --> pdb=" O LEU G1715 " (cutoff:3.500A) Processing helix chain 'G' and resid 1719 through 1734 removed outlier: 4.077A pdb=" N ALA G1723 " --> pdb=" O HIS G1719 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER G1729 " --> pdb=" O ARG G1725 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET G1730 " --> pdb=" O SER G1726 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR G1734 " --> pdb=" O MET G1730 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 Processing helix chain 'G' and resid 1803 through 1824 removed outlier: 4.289A pdb=" N ASP G1821 " --> pdb=" O GLU G1817 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY G1822 " --> pdb=" O ALA G1818 " (cutoff:3.500A) 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: 4.758A pdb=" N ASP G1967 " --> pdb=" O GLU G1963 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN G1972 " --> pdb=" O LYS G1968 " (cutoff:3.500A) Processing helix chain 'G' and resid 2034 through 2043 Processing helix chain 'G' and resid 2044 through 2047 Processing helix chain 'G' and resid 2058 through 2071 Processing helix chain 'G' and resid 2094 through 2109 removed outlier: 4.267A pdb=" N ARG G2104 " --> pdb=" O HIS G2100 " (cutoff:3.500A) Processing helix chain 'G' and resid 2115 through 2128 removed outlier: 3.542A pdb=" N TYR G2128 " --> pdb=" O LEU G2124 " (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 2166 removed outlier: 4.506A pdb=" N GLU G2150 " --> pdb=" O PRO G2146 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASP G2151 " --> pdb=" O SER G2147 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER G2164 " --> pdb=" O GLY G2160 " (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 2201 removed outlier: 3.557A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2203 through 2215 Processing helix chain 'G' and resid 2227 through 2242 removed outlier: 4.357A pdb=" N SER G2231 " --> pdb=" O LYS G2227 " (cutoff:3.500A) Processing helix chain 'G' and resid 2243 through 2250 Processing helix chain 'G' and resid 2253 through 2261 Processing helix chain 'G' and resid 2272 through 2281 removed outlier: 3.725A pdb=" N ALA G2276 " --> pdb=" O PRO G2272 " (cutoff:3.500A) Processing helix chain 'G' and resid 2283 through 2290 removed outlier: 3.551A pdb=" N LEU G2290 " --> pdb=" O LEU G2286 " (cutoff:3.500A) Processing helix chain 'G' and resid 2291 through 2304 removed outlier: 3.870A pdb=" N LEU G2295 " --> pdb=" O GLN G2291 " (cutoff:3.500A) Processing helix chain 'G' and resid 2305 through 2307 No H-bonds generated for 'chain 'G' and resid 2305 through 2307' Processing helix chain 'G' and resid 2327 through 2341 removed outlier: 4.124A pdb=" N VAL G2341 " --> pdb=" O PHE G2337 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2360 removed outlier: 4.649A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG G2359 " --> pdb=" O ARG G2355 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS G2360 " --> pdb=" O LEU G2356 " (cutoff:3.500A) Processing helix chain 'G' and resid 2377 through 2386 removed outlier: 3.754A pdb=" N GLU G2381 " --> pdb=" O LEU G2377 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G2386 " --> pdb=" O GLU G2382 " (cutoff:3.500A) Processing helix chain 'G' and resid 2420 through 2435 Processing helix chain 'G' and resid 2450 through 2459 Processing helix chain 'G' and resid 2467 through 2475 Proline residue: G2473 - end of helix Processing helix chain 'G' and resid 2495 through 2510 removed outlier: 3.657A pdb=" N LYS G2499 " --> pdb=" O VAL G2495 " (cutoff:3.500A) Processing helix chain 'G' and resid 2514 through 2516 No H-bonds generated for 'chain 'G' and resid 2514 through 2516' Processing helix chain 'G' and resid 2517 through 2522 removed outlier: 3.806A pdb=" N LEU G2522 " --> pdb=" O LEU G2518 " (cutoff:3.500A) Processing helix chain 'G' and resid 2525 through 2534 removed outlier: 3.729A pdb=" N MET G2530 " --> pdb=" O PHE G2526 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG G2531 " --> pdb=" O LEU G2527 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA G2534 " --> pdb=" O MET G2530 " (cutoff:3.500A) Processing helix chain 'G' and resid 2545 through 2559 removed outlier: 4.858A pdb=" N ASN G2551 " --> pdb=" O ALA G2547 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG G2552 " --> pdb=" O LEU G2548 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL G2558 " --> pdb=" O LEU G2554 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU G2559 " --> pdb=" O CYS G2555 " (cutoff:3.500A) Processing helix chain 'G' and resid 2568 through 2586 removed outlier: 3.694A pdb=" N VAL G2586 " --> pdb=" O MET G2582 " (cutoff:3.500A) Processing helix chain 'G' and resid 2592 through 2608 Processing helix chain 'G' and resid 2616 through 2634 Proline residue: G2631 - end of helix Processing helix chain 'G' and resid 2639 through 2660 Proline residue: G2658 - end of helix Processing helix chain 'G' and resid 2668 through 2686 removed outlier: 3.874A pdb=" N LEU G2686 " --> pdb=" O ILE G2682 " (cutoff:3.500A) Processing helix chain 'G' and resid 2692 through 2710 Proline residue: G2701 - end of helix Processing helix chain 'G' and resid 2749 through 2773 removed outlier: 3.961A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS G2770 " --> pdb=" O TRP G2766 " (cutoff:3.500A) removed outlier: 3.507A 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: 3.646A pdb=" N ILE G2804 " --> pdb=" O LYS G2800 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR G2805 " --> pdb=" O ASP G2801 " (cutoff:3.500A) Proline residue: G2808 - end of helix Processing helix chain 'G' and resid 2861 through 2865 removed outlier: 3.545A pdb=" N GLY G2864 " --> pdb=" O ASP G2861 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2897 removed outlier: 3.594A pdb=" N TRP G2886 " --> pdb=" O TYR G2882 " (cutoff:3.500A) Processing helix chain 'G' and resid 2907 through 2911 removed outlier: 3.648A pdb=" N LEU G2911 " --> pdb=" O TYR G2908 " (cutoff:3.500A) Processing helix chain 'G' and resid 2912 through 2934 removed outlier: 3.970A pdb=" N ALA G2917 " --> pdb=" O ALA G2913 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS G2922 " --> pdb=" O ARG G2918 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G2923 " --> pdb=" O ASP G2919 " (cutoff:3.500A) Processing helix chain 'G' and resid 3018 through 3038 removed outlier: 3.517A pdb=" N LEU G3025 " --> pdb=" O PRO G3021 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER G3032 " --> pdb=" O GLY G3028 " (cutoff:3.500A) Processing helix chain 'G' and resid 3044 through 3061 removed outlier: 3.764A pdb=" N ALA G3048 " --> pdb=" O CYS G3044 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL G3050 " --> pdb=" O LEU G3046 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG G3053 " --> pdb=" O LEU G3049 " (cutoff:3.500A) Processing helix chain 'G' and resid 3069 through 3090 removed outlier: 3.522A pdb=" N ARG G3078 " --> pdb=" O SER G3074 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR G3079 " --> pdb=" O LEU G3075 " (cutoff:3.500A) Proline residue: G3085 - end of helix removed outlier: 4.529A pdb=" N VAL G3088 " --> pdb=" O GLY G3084 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA G3090 " --> pdb=" O GLU G3086 " (cutoff:3.500A) Processing helix chain 'G' and resid 3096 through 3115 removed outlier: 3.918A pdb=" N GLY G3113 " --> pdb=" O ASN G3109 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS G3114 " --> pdb=" O LEU G3110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL G3115 " --> pdb=" O ARG G3111 " (cutoff:3.500A) Processing helix chain 'G' and resid 3116 through 3116 No H-bonds generated for 'chain 'G' and resid 3116 through 3116' Processing helix chain 'G' and resid 3132 through 3135 removed outlier: 3.855A pdb=" N ALA G3135 " --> pdb=" O THR G3132 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3132 through 3135' Processing helix chain 'G' and resid 3136 through 3150 removed outlier: 3.641A pdb=" N LEU G3140 " --> pdb=" O LEU G3136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS G3150 " --> pdb=" O HIS G3146 " (cutoff:3.500A) Processing helix chain 'G' and resid 3151 through 3152 No H-bonds generated for 'chain 'G' and resid 3151 through 3152' Processing helix chain 'G' and resid 3158 through 3158 No H-bonds generated for 'chain 'G' and resid 3158 through 3158' Processing helix chain 'G' and resid 3159 through 3177 removed outlier: 3.954A pdb=" N VAL G3163 " --> pdb=" O ASP G3159 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER G3164 " --> pdb=" O ASP G3160 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G3176 " --> pdb=" O ILE G3172 " (cutoff:3.500A) Processing helix chain 'G' and resid 3185 through 3199 removed outlier: 3.816A pdb=" N ARG G3196 " --> pdb=" O GLU G3192 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU G3197 " --> pdb=" O CYS G3193 " (cutoff:3.500A) Processing helix chain 'G' and resid 3205 through 3216 removed outlier: 3.834A pdb=" N ASN G3211 " --> pdb=" O GLU G3207 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G3216 " --> pdb=" O GLU G3212 " (cutoff:3.500A) Processing helix chain 'G' and resid 3274 through 3279 Processing helix chain 'G' and resid 3279 through 3287 removed outlier: 3.984A pdb=" N TRP G3285 " --> pdb=" O LEU G3281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU G3286 " --> pdb=" O PRO G3282 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG G3287 " --> pdb=" O ARG G3283 " (cutoff:3.500A) Processing helix chain 'G' and resid 3295 through 3300 Processing helix chain 'G' and resid 3301 through 3313 removed outlier: 3.806A pdb=" N ASN G3313 " --> pdb=" O SER G3309 " (cutoff:3.500A) Processing helix chain 'G' and resid 3318 through 3337 Processing helix chain 'G' and resid 3348 through 3363 removed outlier: 3.821A pdb=" N PHE G3358 " --> pdb=" O LEU G3354 " (cutoff:3.500A) Proline residue: G3360 - end of helix Processing helix chain 'G' and resid 3368 through 3397 Processing helix chain 'G' and resid 3403 through 3424 Proline residue: G3410 - end of helix removed outlier: 3.751A pdb=" N ASN G3419 " --> pdb=" O TYR G3415 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS G3422 " --> pdb=" O ASN G3418 " (cutoff:3.500A) Processing helix chain 'G' and resid 3428 through 3435 removed outlier: 3.778A pdb=" N GLU G3433 " --> pdb=" O ALA G3429 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU G3434 " --> pdb=" O ASN G3430 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE G3435 " --> pdb=" O ALA G3431 " (cutoff:3.500A) Processing helix chain 'G' and resid 3438 through 3455 removed outlier: 3.641A pdb=" N SER G3446 " --> pdb=" O PHE G3442 " (cutoff:3.500A) Processing helix chain 'G' and resid 3458 through 3469 removed outlier: 3.944A pdb=" N ILE G3464 " --> pdb=" O VAL G3460 " (cutoff:3.500A) Processing helix chain 'G' and resid 3478 through 3482 Processing helix chain 'G' and resid 3483 through 3489 removed outlier: 3.625A pdb=" N GLY G3487 " --> pdb=" O ASP G3483 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER G3489 " --> pdb=" O GLN G3485 " (cutoff:3.500A) Processing helix chain 'G' and resid 3490 through 3491 No H-bonds generated for 'chain 'G' and resid 3490 through 3491' Processing helix chain 'G' and resid 3494 through 3494 No H-bonds generated for 'chain 'G' and resid 3494 through 3494' Processing helix chain 'G' and resid 3495 through 3499 Processing helix chain 'G' and resid 3499 through 3504 removed outlier: 3.794A pdb=" N SER G3504 " --> pdb=" O GLY G3500 " (cutoff:3.500A) Processing helix chain 'G' and resid 3513 through 3515 No H-bonds generated for 'chain 'G' and resid 3513 through 3515' Processing helix chain 'G' and resid 3516 through 3526 removed outlier: 3.597A pdb=" N ILE G3520 " --> pdb=" O LYS G3516 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY G3521 " --> pdb=" O MET G3517 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN G3523 " --> pdb=" O PRO G3519 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET G3524 " --> pdb=" O ILE G3520 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA G3526 " --> pdb=" O LEU G3522 " (cutoff:3.500A) Processing helix chain 'G' and resid 3537 through 3544 Processing helix chain 'G' and resid 3550 through 3570 Proline residue: G3567 - end of helix Processing helix chain 'G' and resid 3646 through 3660 removed outlier: 3.759A pdb=" N LYS G3658 " --> pdb=" O LEU G3654 " (cutoff:3.500A) Processing helix chain 'G' and resid 3664 through 3668 removed outlier: 3.865A pdb=" N HIS G3667 " --> pdb=" O THR G3664 " (cutoff:3.500A) Processing helix chain 'G' and resid 3669 through 3678 Processing helix chain 'G' and resid 3696 through 3711 removed outlier: 3.515A pdb=" N LEU G3710 " --> pdb=" O SER G3706 " (cutoff:3.500A) Processing helix chain 'G' and resid 3721 through 3731 removed outlier: 3.600A pdb=" N ASP G3727 " --> pdb=" O MET G3723 " (cutoff:3.500A) Processing helix chain 'G' and resid 3751 through 3768 Processing helix chain 'G' and resid 3774 through 3787 removed outlier: 4.102A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) Processing helix chain 'G' and resid 3792 through 3804 Processing helix chain 'G' and resid 3809 through 3824 removed outlier: 3.785A pdb=" N LEU G3820 " --> pdb=" O MET G3816 " (cutoff:3.500A) Processing helix chain 'G' and resid 3826 through 3839 removed outlier: 3.768A pdb=" N ALA G3834 " --> pdb=" O GLN G3830 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3852 removed outlier: 3.875A pdb=" N PHE G3847 " --> pdb=" O ASP G3843 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU G3848 " --> pdb=" O LEU G3844 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG G3849 " --> pdb=" O ASN G3845 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS G3852 " --> pdb=" O GLU G3848 " (cutoff:3.500A) Processing helix chain 'G' and resid 3878 through 3893 removed outlier: 3.553A pdb=" N ARG G3886 " --> pdb=" O GLN G3882 " (cutoff:3.500A) Processing helix chain 'G' and resid 3896 through 3905 removed outlier: 3.602A pdb=" N TYR G3902 " --> pdb=" O ASP G3898 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG G3904 " --> pdb=" O GLN G3900 " (cutoff:3.500A) Processing helix chain 'G' and resid 3914 through 3939 removed outlier: 3.638A pdb=" N LEU G3923 " --> pdb=" O THR G3919 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER G3929 " --> pdb=" O ARG G3925 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP G3935 " --> pdb=" O SER G3931 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY G3939 " --> pdb=" O TRP G3935 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3968 removed outlier: 3.672A pdb=" N SER G3952 " --> pdb=" O LYS G3948 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN G3963 " --> pdb=" O LYS G3959 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3982 removed outlier: 3.649A pdb=" N GLN G3977 " --> pdb=" O CYS G3973 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS G3982 " --> pdb=" O GLN G3978 " (cutoff:3.500A) Processing helix chain 'G' and resid 3984 through 4004 removed outlier: 3.588A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET G4001 " --> pdb=" O ALA G3997 " (cutoff:3.500A) Processing helix chain 'G' and resid 4009 through 4030 Processing helix chain 'G' and resid 4038 through 4051 removed outlier: 3.717A pdb=" N MET G4044 " --> pdb=" O ILE G4040 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G4048 " --> pdb=" O MET G4044 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G4049 " --> pdb=" O VAL G4045 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4062 removed outlier: 3.689A pdb=" N LEU G4059 " --> pdb=" O VAL G4055 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G4061 " --> pdb=" O MET G4057 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE G4062 " --> pdb=" O ILE G4058 " (cutoff:3.500A) Processing helix chain 'G' and resid 4063 through 4064 No H-bonds generated for 'chain 'G' and resid 4063 through 4064' Processing helix chain 'G' and resid 4071 through 4074 Processing helix chain 'G' and resid 4076 through 4080 Processing helix chain 'G' and resid 4089 through 4097 Processing helix chain 'G' and resid 4104 through 4116 removed outlier: 3.621A pdb=" N GLN G4109 " --> pdb=" O GLY G4105 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G4110 " --> pdb=" O PRO G4106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G4112 " --> pdb=" O ILE G4108 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU G4116 " --> pdb=" O LEU G4112 " (cutoff:3.500A) Processing helix chain 'G' and resid 4136 through 4154 removed outlier: 3.892A pdb=" N GLY G4140 " --> pdb=" O ALA G4136 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4167 removed outlier: 3.526A pdb=" N ALA G4167 " --> pdb=" O PHE G4163 " (cutoff:3.500A) Processing helix chain 'G' and resid 4167 through 4175 removed outlier: 3.905A pdb=" N TYR G4173 " --> pdb=" O SER G4169 " (cutoff:3.500A) Processing helix chain 'G' and resid 4198 through 4205 removed outlier: 3.748A pdb=" N ARG G4202 " --> pdb=" O SER G4198 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA G4203 " --> pdb=" O GLU G4199 " (cutoff:3.500A) Processing helix chain 'G' and resid 4208 through 4223 removed outlier: 4.146A pdb=" N GLU G4212 " --> pdb=" O PRO G4208 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG G4215 " --> pdb=" O LYS G4211 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4250 removed outlier: 3.665A pdb=" N GLU G4232 " --> pdb=" O ALA G4228 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER G4236 " --> pdb=" O GLU G4232 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE G4243 " --> pdb=" O GLU G4239 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN G4250 " --> pdb=" O GLN G4246 " (cutoff:3.500A) Processing helix chain 'G' and resid 4251 through 4251 No H-bonds generated for 'chain 'G' and resid 4251 through 4251' Processing helix chain 'G' and resid 4545 through 4546 No H-bonds generated for 'chain 'G' and resid 4545 through 4546' Processing helix chain 'G' and resid 4547 through 4558 removed outlier: 6.016A pdb=" N ASN G4553 " --> pdb=" O VAL G4549 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN G4558 " --> pdb=" O TYR G4554 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4578 removed outlier: 3.594A pdb=" N ASN G4574 " --> pdb=" O ALA G4570 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE G4576 " --> pdb=" O ALA G4572 " (cutoff:3.500A) Processing helix chain 'G' and resid 4638 through 4663 removed outlier: 3.562A pdb=" N CYS G4645 " --> pdb=" O PRO G4641 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G4646 " --> pdb=" O ALA G4642 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR G4651 " --> pdb=" O SER G4647 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE G4658 " --> pdb=" O ALA G4654 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY G4660 " --> pdb=" O LEU G4656 " (cutoff:3.500A) Processing helix chain 'G' and resid 4664 through 4679 removed outlier: 3.724A pdb=" N LEU G4668 " --> pdb=" O LEU G4664 " (cutoff:3.500A) Processing helix chain 'G' and resid 4701 through 4706 removed outlier: 3.602A pdb=" N VAL G4705 " --> pdb=" O TRP G4701 " (cutoff:3.500A) Processing helix chain 'G' and resid 4719 through 4727 removed outlier: 3.750A pdb=" N LEU G4725 " --> pdb=" O LYS G4721 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP G4726 " --> pdb=" O ARG G4722 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS G4727 " --> pdb=" O LYS G4723 " (cutoff:3.500A) Processing helix chain 'G' and resid 4737 through 4742 Processing helix chain 'G' and resid 4766 through 4771 removed outlier: 3.855A 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 4788 through 4805 removed outlier: 3.798A pdb=" N MET G4798 " --> pdb=" O TRP G4794 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS G4803 " --> pdb=" O SER G4799 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR G4804 " --> pdb=" O LEU G4800 " (cutoff:3.500A) Processing helix chain 'G' and resid 4807 through 4814 Processing helix chain 'G' and resid 4815 through 4820 removed outlier: 3.739A pdb=" N VAL G4820 " --> pdb=" O ILE G4816 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4832 removed outlier: 3.525A pdb=" N ARG G4824 " --> pdb=" O VAL G4820 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS G4832 " --> pdb=" O SER G4828 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 4.036A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR G4840 " --> pdb=" O GLN G4836 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G4841 " --> pdb=" O LEU G4837 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4862 Processing helix chain 'G' and resid 4878 through 4888 Processing helix chain 'G' and resid 4896 through 4901 removed outlier: 3.621A pdb=" N ILE G4901 " --> pdb=" O GLY G4898 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4924 removed outlier: 3.962A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE G4916 " --> pdb=" O TYR G4912 " (cutoff:3.500A) Processing helix chain 'G' and resid 4927 through 4955 removed outlier: 3.588A pdb=" N LEU G4935 " --> pdb=" O ILE G4931 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG G4944 " --> pdb=" O PHE G4940 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP G4945 " --> pdb=" O GLY G4941 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS G4951 " --> pdb=" O GLN G4947 " (cutoff:3.500A) Processing helix chain 'G' and resid 4966 through 4971 removed outlier: 3.739A pdb=" N THR G4970 " --> pdb=" O TYR G4967 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR G4971 " --> pdb=" O PHE G4968 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4981 Processing helix chain 'G' and resid 4986 through 4998 Processing helix chain 'G' and resid 4999 through 5003 removed outlier: 3.708A pdb=" N HIS G5003 " --> pdb=" O GLU G5000 " (cutoff:3.500A) Processing helix chain 'G' and resid 5004 through 5017 Processing helix chain 'H' and resid 39 through 43 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.671A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 21 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 203 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 151 Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 284 Processing sheet with id=AA7, first strand: chain 'A' and resid 230 through 233 Processing sheet with id=AA8, first strand: chain 'A' and resid 290 through 292 Processing sheet with id=AA9, first strand: chain 'A' and resid 314 through 317 Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 359 Processing sheet with id=AB2, first strand: chain 'A' and resid 635 through 639 Processing sheet with id=AB3, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB4, first strand: chain 'A' and resid 743 through 748 removed outlier: 3.558A pdb=" N TYR A 663 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 743 through 748 removed outlier: 6.383A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 683 through 684 Processing sheet with id=AB7, first strand: chain 'A' and resid 687 through 688 Processing sheet with id=AB8, first strand: chain 'A' and resid 721 through 723 Processing sheet with id=AB9, first strand: chain 'A' and resid 758 through 759 Processing sheet with id=AC1, first strand: chain 'A' and resid 768 through 769 removed outlier: 4.107A pdb=" N MET A1476 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER A1486 " --> pdb=" O MET A1476 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 830 through 833 removed outlier: 5.066A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A1203 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A1091 " --> pdb=" O ASN A1203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 892 through 893 removed outlier: 6.657A pdb=" N THR A 892 " --> pdb=" O HIS A 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1136 through 1137 removed outlier: 3.536A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1163 through 1164 Processing sheet with id=AC6, first strand: chain 'A' and resid 1245 through 1246 removed outlier: 3.503A pdb=" N GLU A1246 " --> pdb=" O VAL A1603 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1603 " --> pdb=" O GLU A1246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 1287 through 1289 removed outlier: 3.679A pdb=" N PHE A1553 " --> pdb=" O TRP A1449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1433 through 1434 Processing sheet with id=AC9, first strand: chain 'A' and resid 1513 through 1514 Processing sheet with id=AD1, first strand: chain 'A' and resid 1530 through 1531 Processing sheet with id=AD2, first strand: chain 'A' and resid 1736 through 1737 removed outlier: 6.670A pdb=" N VAL A1736 " --> pdb=" O ILE A2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 2822 through 2824 Processing sheet with id=AD4, first strand: chain 'A' and resid 4178 through 4183 removed outlier: 3.737A pdb=" N ILE A4181 " --> pdb=" O ILE A4193 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A4193 " --> pdb=" O ILE A4181 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 5 through 8 removed outlier: 4.801A pdb=" N THR B 6 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS B 73 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 27 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 28 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 5 through 8 removed outlier: 4.801A pdb=" N THR B 6 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS B 73 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 23 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.667A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 21 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 203 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 35 through 38 Processing sheet with id=AD9, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AE1, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AE2, first strand: chain 'C' and resid 179 through 183 Processing sheet with id=AE3, first strand: chain 'C' and resid 280 through 284 Processing sheet with id=AE4, first strand: chain 'C' and resid 230 through 233 Processing sheet with id=AE5, first strand: chain 'C' and resid 290 through 292 Processing sheet with id=AE6, first strand: chain 'C' and resid 314 through 317 Processing sheet with id=AE7, first strand: chain 'C' and resid 356 through 359 Processing sheet with id=AE8, first strand: chain 'C' and resid 635 through 639 Processing sheet with id=AE9, first strand: chain 'C' and resid 781 through 783 Processing sheet with id=AF1, first strand: chain 'C' and resid 743 through 748 removed outlier: 3.554A pdb=" N TYR C 663 " --> pdb=" O ALA C 809 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 743 through 748 removed outlier: 6.381A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 683 through 684 Processing sheet with id=AF4, first strand: chain 'C' and resid 687 through 688 Processing sheet with id=AF5, first strand: chain 'C' and resid 721 through 723 Processing sheet with id=AF6, first strand: chain 'C' and resid 758 through 759 Processing sheet with id=AF7, first strand: chain 'C' and resid 768 through 769 removed outlier: 4.110A pdb=" N MET C1476 " --> pdb=" O SER C1486 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER C1486 " --> pdb=" O MET C1476 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 830 through 833 removed outlier: 5.061A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C1203 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C1091 " --> pdb=" O ASN C1203 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 892 through 893 removed outlier: 6.662A pdb=" N THR C 892 " --> pdb=" O HIS C 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 1136 through 1137 removed outlier: 3.537A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1163 through 1164 Processing sheet with id=AG3, first strand: chain 'C' and resid 1245 through 1246 removed outlier: 3.692A pdb=" N VAL C1603 " --> pdb=" O GLU C1246 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1287 through 1289 removed outlier: 3.681A pdb=" N PHE C1553 " --> pdb=" O TRP C1449 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1433 through 1434 Processing sheet with id=AG6, first strand: chain 'C' and resid 1513 through 1515 Processing sheet with id=AG7, first strand: chain 'C' and resid 1530 through 1531 Processing sheet with id=AG8, first strand: chain 'C' and resid 1736 through 1737 removed outlier: 6.669A pdb=" N VAL C1736 " --> pdb=" O ILE C2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'C' and resid 2822 through 2824 Processing sheet with id=AH1, first strand: chain 'C' and resid 4178 through 4183 removed outlier: 3.735A pdb=" N ILE C4181 " --> pdb=" O ILE C4193 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C4193 " --> pdb=" O ILE C4181 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 5 through 8 removed outlier: 4.800A pdb=" N THR D 6 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS D 73 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 27 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY D 28 " --> pdb=" O PHE D 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 5 through 8 removed outlier: 4.800A pdb=" N THR D 6 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS D 73 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL D 23 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 109 through 111 removed outlier: 6.665A pdb=" N GLU E 19 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AH6, first strand: chain 'E' and resid 118 through 120 Processing sheet with id=AH7, first strand: chain 'E' and resid 148 through 151 Processing sheet with id=AH8, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AH9, first strand: chain 'E' and resid 280 through 284 Processing sheet with id=AI1, first strand: chain 'E' and resid 230 through 233 Processing sheet with id=AI2, first strand: chain 'E' and resid 290 through 292 Processing sheet with id=AI3, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AI4, first strand: chain 'E' and resid 356 through 359 Processing sheet with id=AI5, first strand: chain 'E' and resid 635 through 639 Processing sheet with id=AI6, first strand: chain 'E' and resid 781 through 783 Processing sheet with id=AI7, first strand: chain 'E' and resid 743 through 748 removed outlier: 3.553A pdb=" N TYR E 663 " --> pdb=" O ALA E 809 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 743 through 748 removed outlier: 6.388A pdb=" N LYS E 788 " --> pdb=" O ASP E 669 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 683 through 684 Processing sheet with id=AJ1, first strand: chain 'E' and resid 687 through 688 Processing sheet with id=AJ2, first strand: chain 'E' and resid 721 through 723 Processing sheet with id=AJ3, first strand: chain 'E' and resid 758 through 759 Processing sheet with id=AJ4, first strand: chain 'E' and resid 768 through 769 removed outlier: 4.108A pdb=" N MET E1476 " --> pdb=" O SER E1486 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER E1486 " --> pdb=" O MET E1476 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 830 through 833 removed outlier: 5.060A pdb=" N LEU E1202 " --> pdb=" O PRO E 837 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E1203 " --> pdb=" O GLU E1091 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU E1091 " --> pdb=" O ASN E1203 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.660A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'E' and resid 1136 through 1137 removed outlier: 3.537A pdb=" N VAL E1123 " --> pdb=" O TRP E1132 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 1163 through 1164 Processing sheet with id=AJ9, first strand: chain 'E' and resid 1245 through 1246 removed outlier: 3.500A pdb=" N GLU E1246 " --> pdb=" O VAL E1603 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E1603 " --> pdb=" O GLU E1246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'E' and resid 1287 through 1289 removed outlier: 3.675A pdb=" N PHE E1553 " --> pdb=" O TRP E1449 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 1433 through 1434 Processing sheet with id=AK3, first strand: chain 'E' and resid 1513 through 1514 Processing sheet with id=AK4, first strand: chain 'E' and resid 1530 through 1531 Processing sheet with id=AK5, first strand: chain 'E' and resid 1736 through 1737 removed outlier: 6.668A pdb=" N VAL E1736 " --> pdb=" O ILE E2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'E' and resid 2822 through 2824 Processing sheet with id=AK7, first strand: chain 'E' and resid 4178 through 4183 removed outlier: 3.737A pdb=" N ILE E4181 " --> pdb=" O ILE E4193 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E4193 " --> pdb=" O ILE E4181 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 5 through 8 removed outlier: 4.799A pdb=" N THR F 6 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS F 73 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY F 28 " --> pdb=" O PHE F 36 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 5 through 8 removed outlier: 4.799A pdb=" N THR F 6 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS F 73 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 23 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 109 through 111 removed outlier: 6.671A pdb=" N GLU G 19 " --> pdb=" O ILE G 205 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL G 21 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN G 203 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 35 through 38 Processing sheet with id=AL3, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AL4, first strand: chain 'G' and resid 148 through 151 Processing sheet with id=AL5, first strand: chain 'G' and resid 179 through 183 Processing sheet with id=AL6, first strand: chain 'G' and resid 280 through 284 Processing sheet with id=AL7, first strand: chain 'G' and resid 230 through 233 Processing sheet with id=AL8, first strand: chain 'G' and resid 290 through 292 Processing sheet with id=AL9, first strand: chain 'G' and resid 314 through 317 Processing sheet with id=AM1, first strand: chain 'G' and resid 356 through 359 Processing sheet with id=AM2, first strand: chain 'G' and resid 635 through 639 Processing sheet with id=AM3, first strand: chain 'G' and resid 781 through 783 Processing sheet with id=AM4, first strand: chain 'G' and resid 743 through 748 removed outlier: 3.553A pdb=" N TYR G 663 " --> pdb=" O ALA G 809 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'G' and resid 743 through 748 removed outlier: 6.368A pdb=" N LYS G 788 " --> pdb=" O ASP G 669 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 683 through 684 Processing sheet with id=AM7, first strand: chain 'G' and resid 687 through 688 Processing sheet with id=AM8, first strand: chain 'G' and resid 721 through 723 Processing sheet with id=AM9, first strand: chain 'G' and resid 758 through 759 Processing sheet with id=AN1, first strand: chain 'G' and resid 768 through 769 removed outlier: 4.109A pdb=" N MET G1476 " --> pdb=" O SER G1486 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER G1486 " --> pdb=" O MET G1476 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'G' and resid 830 through 833 removed outlier: 5.062A pdb=" N LEU G1202 " --> pdb=" O PRO G 837 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN G1203 " --> pdb=" O GLU G1091 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU G1091 " --> pdb=" O ASN G1203 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.660A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN3 Processing sheet with id=AN4, first strand: chain 'G' and resid 1136 through 1137 removed outlier: 3.537A pdb=" N VAL G1123 " --> pdb=" O TRP G1132 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'G' and resid 1163 through 1164 Processing sheet with id=AN6, first strand: chain 'G' and resid 1245 through 1246 removed outlier: 3.698A pdb=" N VAL G1603 " --> pdb=" O GLU G1246 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'G' and resid 1287 through 1289 removed outlier: 3.678A pdb=" N PHE G1553 " --> pdb=" O TRP G1449 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'G' and resid 1433 through 1434 Processing sheet with id=AN9, first strand: chain 'G' and resid 1513 through 1514 removed outlier: 3.590A pdb=" N VAL G1439 " --> pdb=" O ASP G1513 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'G' and resid 1530 through 1531 Processing sheet with id=AO2, first strand: chain 'G' and resid 1736 through 1737 removed outlier: 6.671A pdb=" N VAL G1736 " --> pdb=" O ILE G2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'G' and resid 4178 through 4180 Processing sheet with id=AO4, first strand: chain 'G' and resid 4580 through 4581 Processing sheet with id=AO5, first strand: chain 'H' and resid 5 through 8 removed outlier: 6.498A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL H 23 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'H' and resid 35 through 38 removed outlier: 6.839A pdb=" N LYS H 35 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU H 30 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP H 37 " --> pdb=" O GLY H 28 " (cutoff:3.500A) 6099 hydrogen bonds defined for protein. 17301 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: 80.01 Time building geometry restraints manager: 35.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 18755 1.27 - 1.43: 30133 1.43 - 1.58: 62978 1.58 - 1.74: 87 1.74 - 1.89: 991 Bond restraints: 112944 Sorted by residual: bond pdb=" N ASN C4987 " pdb=" CA ASN C4987 " ideal model delta sigma weight residual 1.459 1.305 0.154 1.21e-02 6.83e+03 1.62e+02 bond pdb=" N ASN A4987 " pdb=" CA ASN A4987 " ideal model delta sigma weight residual 1.459 1.306 0.153 1.21e-02 6.83e+03 1.60e+02 bond pdb=" N ASN E4987 " pdb=" CA ASN E4987 " ideal model delta sigma weight residual 1.459 1.307 0.152 1.21e-02 6.83e+03 1.58e+02 bond pdb=" CA ILE G4181 " pdb=" CB ILE G4181 " ideal model delta sigma weight residual 1.540 1.391 0.149 1.36e-02 5.41e+03 1.20e+02 bond pdb=" CA ILE E4181 " pdb=" CB ILE E4181 " ideal model delta sigma weight residual 1.540 1.395 0.145 1.36e-02 5.41e+03 1.14e+02 ... (remaining 112939 not shown) Histogram of bond angle deviations from ideal: 90.89 - 101.47: 329 101.47 - 112.06: 52647 112.06 - 122.64: 83522 122.64 - 133.22: 16303 133.22 - 143.81: 207 Bond angle restraints: 153008 Sorted by residual: angle pdb=" C GLU A 915 " pdb=" N PRO A 916 " pdb=" CA PRO A 916 " ideal model delta sigma weight residual 119.84 143.81 -23.97 1.25e+00 6.40e-01 3.68e+02 angle pdb=" C GLU G 915 " pdb=" N PRO G 916 " pdb=" CA PRO G 916 " ideal model delta sigma weight residual 119.84 143.77 -23.93 1.25e+00 6.40e-01 3.67e+02 angle pdb=" C GLU C 915 " pdb=" N PRO C 916 " pdb=" CA PRO C 916 " ideal model delta sigma weight residual 119.84 143.69 -23.85 1.25e+00 6.40e-01 3.64e+02 angle pdb=" C GLU E 915 " pdb=" N PRO E 916 " pdb=" CA PRO E 916 " ideal model delta sigma weight residual 119.84 143.65 -23.81 1.25e+00 6.40e-01 3.63e+02 angle pdb=" N VAL G1284 " pdb=" CA VAL G1284 " pdb=" C VAL G1284 " ideal model delta sigma weight residual 110.62 125.10 -14.48 1.02e+00 9.61e-01 2.02e+02 ... (remaining 153003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.85: 66058 26.85 - 53.71: 1053 53.71 - 80.56: 66 80.56 - 107.42: 31 107.42 - 134.27: 36 Dihedral angle restraints: 67244 sinusoidal: 23796 harmonic: 43448 Sorted by residual: dihedral pdb=" CA GLU G 332 " pdb=" C GLU G 332 " pdb=" N GLY G 333 " pdb=" CA GLY G 333 " ideal model delta harmonic sigma weight residual -180.00 -45.73 -134.27 0 5.00e+00 4.00e-02 7.21e+02 dihedral pdb=" CA GLU E 332 " pdb=" C GLU E 332 " pdb=" N GLY E 333 " pdb=" CA GLY E 333 " ideal model delta harmonic sigma weight residual -180.00 -45.76 -134.24 0 5.00e+00 4.00e-02 7.21e+02 dihedral pdb=" CA GLU C 332 " pdb=" C GLU C 332 " pdb=" N GLY C 333 " pdb=" CA GLY C 333 " ideal model delta harmonic sigma weight residual -180.00 -45.80 -134.20 0 5.00e+00 4.00e-02 7.20e+02 ... (remaining 67241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 14478 0.127 - 0.254: 2504 0.254 - 0.381: 448 0.381 - 0.508: 65 0.508 - 0.635: 13 Chirality restraints: 17508 Sorted by residual: chirality pdb=" CA ASP C4868 " pdb=" N ASP C4868 " pdb=" C ASP C4868 " pdb=" CB ASP C4868 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA ASP G4868 " pdb=" N ASP G4868 " pdb=" C ASP G4868 " pdb=" CB ASP G4868 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.81e+00 chirality pdb=" CA ASP A4868 " pdb=" N ASP A4868 " pdb=" C ASP A4868 " pdb=" CB ASP A4868 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 17505 not shown) Planarity restraints: 19816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E4849 " 0.155 2.00e-02 2.50e+03 8.79e-02 1.54e+02 pdb=" CG TYR E4849 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR E4849 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR E4849 " -0.143 2.00e-02 2.50e+03 pdb=" CE1 TYR E4849 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR E4849 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR E4849 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR E4849 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C4849 " 0.154 2.00e-02 2.50e+03 8.75e-02 1.53e+02 pdb=" CG TYR C4849 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR C4849 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C4849 " -0.142 2.00e-02 2.50e+03 pdb=" CE1 TYR C4849 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TYR C4849 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR C4849 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR C4849 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A4849 " 0.150 2.00e-02 2.50e+03 8.53e-02 1.46e+02 pdb=" CG TYR A4849 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A4849 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A4849 " -0.136 2.00e-02 2.50e+03 pdb=" CE1 TYR A4849 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TYR A4849 " 0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A4849 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR A4849 " 0.064 2.00e-02 2.50e+03 ... (remaining 19813 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 1107 2.55 - 3.13: 99861 3.13 - 3.72: 179999 3.72 - 4.31: 253024 4.31 - 4.90: 377093 Nonbonded interactions: 911084 Sorted by model distance: nonbonded pdb=" O TYR G3936 " pdb=" NZ LYS G3940 " model vdw 1.957 2.520 nonbonded pdb=" NZ LYS A1585 " pdb=" OE1 GLU A1596 " model vdw 2.001 2.520 nonbonded pdb=" NZ LYS E1585 " pdb=" OE1 GLU E1596 " model vdw 2.001 2.520 nonbonded pdb=" NZ LYS G1585 " pdb=" OE1 GLU G1596 " model vdw 2.001 2.520 nonbonded pdb=" NZ LYS C1585 " pdb=" OE1 GLU C1596 " model vdw 2.001 2.520 ... (remaining 911079 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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=0.99 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 13.830 Check model and map are aligned: 1.170 Set scattering table: 0.710 Process input model: 273.660 Find NCS groups from input model: 5.680 Set up NCS constraints: 0.640 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 299.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.018 0.180 112944 Z= 1.199 Angle : 1.723 23.966 153008 Z= 1.106 Chirality : 0.103 0.635 17508 Planarity : 0.008 0.131 19816 Dihedral : 11.341 134.270 38956 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 2.89 % Allowed : 6.55 % Favored : 90.57 % Rotamer: Outliers : 0.51 % Allowed : 1.71 % Favored : 97.77 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.18 % 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: -2.58 (0.06), residues: 14404 helix: -2.48 (0.04), residues: 7704 sheet: -3.40 (0.13), residues: 1004 loop : 0.20 (0.10), residues: 5696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.009 TRP C5019 HIS 0.034 0.004 HIS E4886 PHE 0.098 0.010 PHE G4808 TYR 0.155 0.010 TYR E4849 ARG 0.033 0.003 ARG G3984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28808 Ramachandran restraints generated. 14404 Oldfield, 0 Emsley, 14404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28808 Ramachandran restraints generated. 14404 Oldfield, 0 Emsley, 14404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2723 residues out of total 13160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 2646 time to evaluate : 9.111 Fit side-chains revert: symmetry clash revert: symmetry clash 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-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable