Starting phenix.real_space_refine on Mon Mar 11 17:37:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gkz_9519/03_2024/5gkz_9519.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gkz_9519/03_2024/5gkz_9519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gkz_9519/03_2024/5gkz_9519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gkz_9519/03_2024/5gkz_9519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gkz_9519/03_2024/5gkz_9519.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gkz_9519/03_2024/5gkz_9519.pdb" } resolution = 4.0 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= 0.018 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 115": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ARG 1212": "NH1" <-> "NH2" Residue "A PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1584": "NH1" <-> "NH2" Residue "A ARG 1618": "NH1" <-> "NH2" Residue "A ARG 1656": "NH1" <-> "NH2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1813": "NH1" <-> "NH2" Residue "A ARG 1820": "NH1" <-> "NH2" Residue "A ARG 2355": "NH1" <-> "NH2" Residue "A ARG 2552": "NH1" <-> "NH2" Residue "A ARG 3648": "NH1" <-> "NH2" Residue "A ARG 3672": "NH1" <-> "NH2" Residue "A ARG 4161": "NH1" <-> "NH2" Residue "A ARG 4192": "NH1" <-> "NH2" Residue "A ARG 4202": "NH1" <-> "NH2" Residue "A ARG 4548": "NH1" <-> "NH2" Residue "A ARG 4557": "NH1" <-> "NH2" Residue "A PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4563": "NH1" <-> "NH2" Residue "A TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4860": "NH1" <-> "NH2" Residue "A ARG 4892": "NH1" <-> "NH2" Residue "A PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 835": "NH1" <-> "NH2" Residue "C ARG 844": "NH1" <-> "NH2" Residue "C PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1110": "NH1" <-> "NH2" Residue "C ARG 1212": "NH1" <-> "NH2" Residue "C TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1584": "NH1" <-> "NH2" Residue "C ARG 1618": "NH1" <-> "NH2" Residue "C ARG 1656": "NH1" <-> "NH2" Residue "C ARG 1725": "NH1" <-> "NH2" Residue "C ARG 1813": "NH1" <-> "NH2" Residue "C ARG 1820": "NH1" <-> "NH2" Residue "C ARG 2355": "NH1" <-> "NH2" Residue "C ARG 2552": "NH1" <-> "NH2" Residue "C ARG 3648": "NH1" <-> "NH2" Residue "C ARG 3672": "NH1" <-> "NH2" Residue "C ARG 4161": "NH1" <-> "NH2" Residue "C ARG 4192": "NH1" <-> "NH2" Residue "C ARG 4202": "NH1" <-> "NH2" Residue "C ARG 4548": "NH1" <-> "NH2" Residue "C ARG 4557": "NH1" <-> "NH2" Residue "C PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4563": "NH1" <-> "NH2" Residue "C TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4860": "NH1" <-> "NH2" Residue "C ARG 4892": "NH1" <-> "NH2" Residue "C PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 835": "NH1" <-> "NH2" Residue "E ARG 844": "NH1" <-> "NH2" Residue "E PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1110": "NH1" <-> "NH2" Residue "E ARG 1212": "NH1" <-> "NH2" Residue "E TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1584": "NH1" <-> "NH2" Residue "E ARG 1618": "NH1" <-> "NH2" Residue "E ARG 1656": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1813": "NH1" <-> "NH2" Residue "E ARG 1820": "NH1" <-> "NH2" Residue "E ARG 2355": "NH1" <-> "NH2" Residue "E ARG 2552": "NH1" <-> "NH2" Residue "E ARG 3648": "NH1" <-> "NH2" Residue "E ARG 3672": "NH1" <-> "NH2" Residue "E ARG 4161": "NH1" <-> "NH2" Residue "E ARG 4192": "NH1" <-> "NH2" Residue "E ARG 4202": "NH1" <-> "NH2" Residue "E ARG 4548": "NH1" <-> "NH2" Residue "E ARG 4557": "NH1" <-> "NH2" Residue "E PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4563": "NH1" <-> "NH2" Residue "E TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "F PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 835": "NH1" <-> "NH2" Residue "G ARG 844": "NH1" <-> "NH2" Residue "G PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1110": "NH1" <-> "NH2" Residue "G ARG 1212": "NH1" <-> "NH2" Residue "G TYR 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1584": "NH1" <-> "NH2" Residue "G ARG 1618": "NH1" <-> "NH2" Residue "G ARG 1656": "NH1" <-> "NH2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 1813": "NH1" <-> "NH2" Residue "G ARG 1820": "NH1" <-> "NH2" Residue "G ARG 2355": "NH1" <-> "NH2" Residue "G ARG 2552": "NH1" <-> "NH2" Residue "G ARG 3648": "NH1" <-> "NH2" Residue "G ARG 3672": "NH1" <-> "NH2" Residue "G ARG 4161": "NH1" <-> "NH2" Residue "G TYR 4177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4202": "NH1" <-> "NH2" Residue "G ARG 4548": "NH1" <-> "NH2" Residue "G ARG 4557": "NH1" <-> "NH2" Residue "G PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G PHE 4916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 4988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.33s 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: {'PCIS': 2, 'PTRANS': 162, 'TRANS': 3495} Chain breaks: 81 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2521 Unresolved non-hydrogen angles: 3239 Unresolved non-hydrogen dihedrals: 2072 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: {'PCIS': 2, 'PTRANS': 162, 'TRANS': 3495} 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: "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: {'PCIS': 2, 'PTRANS': 162, 'TRANS': 3495} 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: "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: {'PCIS': 2, 'PTRANS': 162, 'TRANS': 3495} 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 190.499 166.219 87.429 1.00 34.35 S ATOM 26303 SG CYS A4961 189.056 164.776 91.110 1.00 38.61 S ATOM 54027 SG CYS C4958 166.233 168.616 87.428 1.00 33.78 S ATOM 54052 SG CYS C4961 164.779 170.057 91.111 1.00 38.41 S ATOM 81776 SG CYS E4958 168.632 192.897 87.434 1.00 33.70 S ATOM 81801 SG CYS E4961 170.068 194.347 91.119 1.00 39.58 S ATOM A07CL SG CYS G4958 192.903 190.422 87.519 1.00 27.38 S ATOM A07DA SG CYS G4961 194.295 189.164 91.124 1.00 27.72 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: 41.67, per 1000 atoms: 0.38 Number of scatterers: 111000 At special positions: 0 Unit cell: (360.46, 360.46, 209.04, 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: 33.83 Conformation dependent library (CDL) restraints added in 14.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4961 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4958 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4983 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4961 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4958 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4983 " pdb=" ZN E6000 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4961 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4958 " pdb="ZN ZN E6000 " - pdb=" NE2 HIS E4978 " pdb="ZN ZN E6000 " - pdb=" NE2 HIS E4983 " pdb=" ZN G6000 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4961 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4958 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4978 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4983 " 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: 674 helices and 120 sheets defined 57.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.11 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.687A pdb=" N ILE A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.503A pdb=" N GLN A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 removed outlier: 3.923A 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 255 through 258 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 394 through 421 Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 460 through 481 Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 514 through 531 removed outlier: 3.929A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 557 through 570 removed outlier: 4.071A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.577A pdb=" N ILE A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.581A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 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 810 through 816 Processing helix chain 'A' and resid 864 through 888 removed outlier: 4.172A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 908 Processing helix chain 'A' and resid 918 through 935 removed outlier: 4.385A pdb=" N MET A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.954A pdb=" N VAL A 975 " --> pdb=" O LEU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1000 Processing helix chain 'A' and resid 1001 through 1003 No H-bonds generated for 'chain 'A' and resid 1001 through 1003' Processing helix chain 'A' and resid 1028 through 1049 removed outlier: 5.143A pdb=" N SER A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN A1035 " --> pdb=" O THR A1031 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASP A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1082 Processing helix chain 'A' and resid 1211 through 1216 removed outlier: 3.971A pdb=" N ILE A1216 " --> pdb=" O ARG A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 4.322A pdb=" N GLN A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1216 through 1221' Processing helix chain 'A' and resid 1225 through 1229 Processing helix chain 'A' and resid 1580 through 1585 removed outlier: 3.952A pdb=" N LYS A1585 " --> pdb=" O LEU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1645 removed outlier: 3.824A pdb=" N ASN A1645 " --> pdb=" O PRO A1642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1642 through 1645' Processing helix chain 'A' and resid 1650 through 1654 removed outlier: 3.631A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1650 through 1654' Processing helix chain 'A' and resid 1656 through 1674 removed outlier: 3.819A pdb=" N CYS A1674 " --> pdb=" O TYR A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 4.446A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1698 Processing helix chain 'A' and resid 1704 through 1716 Processing helix chain 'A' and resid 1721 through 1727 Processing helix chain 'A' and resid 1728 through 1733 Processing helix chain 'A' and resid 1739 through 1744 removed outlier: 4.077A pdb=" N ALA A1744 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1824 removed outlier: 3.772A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1818 " --> pdb=" O MET A1814 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP A1821 " --> pdb=" O GLU A1817 " (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: 3.631A pdb=" N ARG A1974 " --> pdb=" O GLN A1970 " (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 2057 through 2057 No H-bonds generated for 'chain 'A' and resid 2057 through 2057' Processing helix chain 'A' and resid 2058 through 2071 removed outlier: 4.182A pdb=" N ARG A2062 " --> pdb=" O SER A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2108 Processing helix chain 'A' and resid 2113 through 2129 removed outlier: 3.983A pdb=" N TYR A2128 " --> pdb=" O LEU A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2138 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: 3.919A pdb=" N THR A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A2157 " --> pdb=" O MET A2153 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS A2158 " --> pdb=" O SER A2154 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A2165 " --> pdb=" O GLN A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2174 through 2188 Processing helix chain 'A' and resid 2194 through 2202 removed outlier: 3.725A pdb=" N GLY A2202 " --> pdb=" O MET A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2215 Processing helix chain 'A' and resid 2227 through 2242 Processing helix chain 'A' and resid 2246 through 2252 removed outlier: 3.768A pdb=" N MET A2250 " --> pdb=" O ASN A2246 " (cutoff:3.500A) Processing helix chain 'A' and resid 2253 through 2261 Processing helix chain 'A' and resid 2272 through 2281 Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2304 removed outlier: 4.100A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2327 through 2340 Processing helix chain 'A' and resid 2346 through 2358 removed outlier: 3.728A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2386 Processing helix chain 'A' and resid 2420 through 2435 Processing helix chain 'A' and resid 2451 through 2459 removed outlier: 3.568A pdb=" N ALA A2455 " --> pdb=" O LEU A2451 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2472 Processing helix chain 'A' and resid 2495 through 2510 Processing helix chain 'A' and resid 2515 through 2522 Processing helix chain 'A' and resid 2526 through 2533 Processing helix chain 'A' and resid 2534 through 2537 removed outlier: 4.076A pdb=" N LEU A2537 " --> pdb=" O ALA A2534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2534 through 2537' Processing helix chain 'A' and resid 2544 through 2544 No H-bonds generated for 'chain 'A' and resid 2544 through 2544' Processing helix chain 'A' and resid 2545 through 2556 removed outlier: 3.694A pdb=" N ASN A2551 " --> pdb=" O ALA A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2557 through 2562 removed outlier: 4.086A pdb=" N LEU A2561 " --> pdb=" O ALA A2557 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A2562 " --> pdb=" O VAL A2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2557 through 2562' Processing helix chain 'A' and resid 2568 through 2585 Processing helix chain 'A' and resid 2592 through 2609 removed outlier: 3.531A pdb=" N ALA A2609 " --> pdb=" O ASP A2605 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2634 Proline residue: A2631 - end of helix removed outlier: 3.944A pdb=" N ASN A2634 " --> pdb=" O VAL A2630 " (cutoff:3.500A) Processing helix chain 'A' and resid 2639 through 2660 Proline residue: A2658 - end of helix Processing helix chain 'A' and resid 2668 through 2685 Processing helix chain 'A' and resid 2692 through 2710 Proline residue: A2701 - end of helix Processing helix chain 'A' and resid 2748 through 2750 No H-bonds generated for 'chain 'A' and resid 2748 through 2750' Processing helix chain 'A' and resid 2751 through 2772 removed outlier: 3.720A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2819 removed outlier: 3.623A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) Proline residue: A2808 - end of helix Processing helix chain 'A' and resid 2861 through 2865 Processing helix chain 'A' and resid 2868 through 2898 Processing helix chain 'A' and resid 2907 through 2911 Processing helix chain 'A' and resid 2912 through 2933 removed outlier: 3.726A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) Processing helix chain 'A' and resid 3018 through 3038 Processing helix chain 'A' and resid 3044 through 3061 Processing helix chain 'A' and resid 3069 through 3090 Proline residue: A3085 - end of helix removed outlier: 3.627A pdb=" N VAL A3088 " --> pdb=" O GLY A3084 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3114 Processing helix chain 'A' and resid 3133 through 3152 Proline residue: A3138 - end of helix removed outlier: 3.620A pdb=" N HIS A3146 " --> pdb=" O THR A3142 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A3147 " --> pdb=" O LEU A3143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A3148 " --> pdb=" O PHE A3144 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A3150 " --> pdb=" O HIS A3146 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A3151 " --> pdb=" O ILE A3147 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A3152 " --> pdb=" O ALA A3148 " (cutoff:3.500A) Processing helix chain 'A' and resid 3159 through 3178 Processing helix chain 'A' and resid 3185 through 3199 removed outlier: 3.649A pdb=" N ALA A3199 " --> pdb=" O ALA A3195 " (cutoff:3.500A) 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 3300 through 3311 removed outlier: 3.520A pdb=" N CYS A3304 " --> pdb=" O ALA A3300 " (cutoff:3.500A) Processing helix chain 'A' and resid 3318 through 3338 removed outlier: 3.859A pdb=" N LEU A3338 " --> pdb=" O TRP A3334 " (cutoff:3.500A) Processing helix chain 'A' and resid 3339 through 3339 No H-bonds generated for 'chain 'A' and resid 3339 through 3339' Processing helix chain 'A' and resid 3346 through 3349 Processing helix chain 'A' and resid 3350 through 3362 Proline residue: A3360 - end of helix Processing helix chain 'A' and resid 3368 through 3396 removed outlier: 3.898A pdb=" N VAL A3373 " --> pdb=" O ALA A3369 " (cutoff:3.500A) Processing helix chain 'A' and resid 3403 through 3423 removed outlier: 3.811A pdb=" N LEU A3408 " --> pdb=" O ASP A3404 " (cutoff:3.500A) removed outlier: 3.982A 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 3433 Processing helix chain 'A' and resid 3438 through 3454 Processing helix chain 'A' and resid 3458 through 3469 removed outlier: 3.514A pdb=" N PHE A3469 " --> pdb=" O ASN A3465 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 removed outlier: 3.517A pdb=" N GLY A3487 " --> pdb=" O ASP A3483 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3489 through 3491 No H-bonds generated for 'chain 'A' and resid 3489 through 3491' Processing helix chain 'A' and resid 3495 through 3502 Processing helix chain 'A' and resid 3516 through 3525 Processing helix chain 'A' and resid 3538 through 3543 Processing helix chain 'A' and resid 3550 through 3570 Proline residue: A3567 - end of helix Processing helix chain 'A' and resid 3646 through 3659 removed outlier: 3.624A pdb=" N ALA A3659 " --> pdb=" O GLU A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3677 removed outlier: 4.627A pdb=" N ARG A3672 " --> pdb=" O SER A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3733 removed outlier: 3.951A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) Processing helix chain 'A' and resid 3751 through 3772 removed outlier: 3.790A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A3772 " --> pdb=" O SER A3768 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.891A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3805 removed outlier: 3.792A pdb=" N SER A3795 " --> pdb=" O GLY A3791 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3823 removed outlier: 3.870A pdb=" N GLN A3813 " --> pdb=" O ASN A3809 " (cutoff:3.500A) Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 3.808A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) Processing helix chain 'A' and resid 3844 through 3852 removed outlier: 3.514A pdb=" N LYS A3852 " --> pdb=" O GLU A3848 " (cutoff:3.500A) Processing helix chain 'A' and resid 3878 through 3893 Processing helix chain 'A' and resid 3896 through 3906 removed outlier: 3.530A pdb=" N THR A3905 " --> pdb=" O ASN A3901 " (cutoff:3.500A) Processing helix chain 'A' and resid 3915 through 3938 Processing helix chain 'A' and resid 3945 through 3969 removed outlier: 4.034A pdb=" N PHE A3951 " --> pdb=" O GLY A3947 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3982 Processing helix chain 'A' and resid 3984 through 4001 removed outlier: 4.168A pdb=" N PHE A3992 " --> pdb=" O ALA A3988 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 Processing helix chain 'A' and resid 4040 through 4052 Processing helix chain 'A' and resid 4052 through 4063 removed outlier: 3.582A pdb=" N ASP A4063 " --> pdb=" O LEU A4059 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4080 removed outlier: 3.966A pdb=" N GLN A4078 " --> pdb=" O SER A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4090 through 4094 Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4136 through 4154 Processing helix chain 'A' and resid 4157 through 4167 Processing helix chain 'A' and resid 4167 through 4175 removed outlier: 3.664A pdb=" N LEU A4171 " --> pdb=" O ALA A4167 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A4173 " --> pdb=" O SER A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4205 removed outlier: 3.662A pdb=" N TRP A4205 " --> pdb=" O ASN A4201 " (cutoff:3.500A) Processing helix chain 'A' and resid 4209 through 4225 removed outlier: 3.946A pdb=" N ARG A4215 " --> pdb=" O LYS A4211 " (cutoff:3.500A) Processing helix chain 'A' and resid 4228 through 4251 removed outlier: 4.579A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A4251 " --> pdb=" O ILE A4247 " (cutoff:3.500A) Processing helix chain 'A' and resid 4546 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4663 removed outlier: 3.740A pdb=" N ALA A4642 " --> pdb=" O TYR A4638 " (cutoff:3.500A) Processing helix chain 'A' and resid 4664 through 4683 removed outlier: 4.260A pdb=" N LEU A4668 " --> pdb=" O LEU A4664 " (cutoff:3.500A) Processing helix chain 'A' and resid 4697 through 4702 removed outlier: 3.557A pdb=" N ASP A4702 " --> pdb=" O LYS A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 4.116A pdb=" N LEU A4706 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4729 Processing helix chain 'A' and resid 4733 through 4741 Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 3.932A pdb=" N ILE A4771 " --> pdb=" O TRP A4767 " (cutoff:3.500A) Processing helix chain 'A' and resid 4772 through 4785 Processing helix chain 'A' and resid 4786 through 4805 Processing helix chain 'A' and resid 4807 through 4819 Processing helix chain 'A' and resid 4820 through 4832 removed outlier: 3.705A pdb=" N ARG A4824 " --> pdb=" O VAL A4820 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A4825 " --> pdb=" O LYS A4821 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4858 Processing helix chain 'A' and resid 4878 through 4889 Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 3.576A pdb=" N ASP A4899 " --> pdb=" O GLY A4896 " (cutoff:3.500A) removed outlier: 3.959A 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 4957 removed outlier: 3.518A pdb=" N GLU A4955 " --> pdb=" O LYS A4951 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A4957 " --> pdb=" O ASP A4953 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.991A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4974 through 4981 Processing helix chain 'A' and resid 4985 through 4998 removed outlier: 3.759A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) Processing helix chain 'A' and resid 4999 through 5003 removed outlier: 3.513A 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 56 through 66 removed outlier: 4.424A pdb=" N ALA B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.692A pdb=" N ILE C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.715A pdb=" N GLU C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.926A 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 255 through 258 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 394 through 421 Processing helix chain 'C' and resid 438 through 452 Processing helix chain 'C' and resid 460 through 481 Processing helix chain 'C' and resid 482 through 495 Processing helix chain 'C' and resid 514 through 531 removed outlier: 3.928A pdb=" N ILE C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 557 through 570 removed outlier: 4.068A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 575 Processing helix chain 'C' and resid 579 through 593 removed outlier: 3.577A pdb=" N ILE C 583 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 608 removed outlier: 3.582A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 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 810 through 816 Processing helix chain 'C' and resid 864 through 888 removed outlier: 4.170A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 908 Processing helix chain 'C' and resid 918 through 935 removed outlier: 4.381A pdb=" N MET C 924 " --> pdb=" O TYR C 920 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 925 " --> pdb=" O ASN C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 975 removed outlier: 3.932A pdb=" N VAL C 975 " --> pdb=" O LEU C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1000 Processing helix chain 'C' and resid 1001 through 1003 No H-bonds generated for 'chain 'C' and resid 1001 through 1003' Processing helix chain 'C' and resid 1028 through 1049 removed outlier: 5.141A pdb=" N SER C1034 " --> pdb=" O ALA C1030 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN C1035 " --> pdb=" O THR C1031 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1082 Processing helix chain 'C' and resid 1211 through 1216 removed outlier: 3.971A pdb=" N ILE C1216 " --> pdb=" O ARG C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1221 removed outlier: 4.329A pdb=" N GLN C1220 " --> pdb=" O ILE C1216 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C1221 " --> pdb=" O CYS C1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1216 through 1221' Processing helix chain 'C' and resid 1225 through 1229 Processing helix chain 'C' and resid 1580 through 1585 removed outlier: 3.952A pdb=" N LYS C1585 " --> pdb=" O LEU C1581 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1645 removed outlier: 3.800A pdb=" N ASN C1645 " --> pdb=" O PRO C1642 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1642 through 1645' Processing helix chain 'C' and resid 1650 through 1654 removed outlier: 3.630A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1650 through 1654' Processing helix chain 'C' and resid 1656 through 1674 removed outlier: 3.817A pdb=" N CYS C1674 " --> pdb=" O TYR C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1690 removed outlier: 4.447A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1698 Processing helix chain 'C' and resid 1704 through 1716 Processing helix chain 'C' and resid 1721 through 1727 Processing helix chain 'C' and resid 1728 through 1733 Processing helix chain 'C' and resid 1739 through 1744 removed outlier: 4.083A pdb=" N ALA C1744 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1824 removed outlier: 3.773A pdb=" N ASP C1809 " --> pdb=" O GLU C1805 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C1818 " --> pdb=" O MET C1814 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP C1821 " --> pdb=" O GLU C1817 " (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: 3.631A pdb=" N ARG C1974 " --> pdb=" O GLN C1970 " (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 2057 through 2057 No H-bonds generated for 'chain 'C' and resid 2057 through 2057' Processing helix chain 'C' and resid 2058 through 2071 removed outlier: 4.180A pdb=" N ARG C2062 " --> pdb=" O SER C2058 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2110 removed outlier: 4.123A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR C2110 " --> pdb=" O ALA C2106 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2129 removed outlier: 3.984A pdb=" N TYR C2128 " --> pdb=" O LEU C2124 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2138 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: 3.923A pdb=" N THR C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C2157 " --> pdb=" O MET C2153 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS C2158 " --> pdb=" O SER C2154 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C2165 " --> pdb=" O GLN C2161 " (cutoff:3.500A) Processing helix chain 'C' and resid 2174 through 2188 Processing helix chain 'C' and resid 2194 through 2202 removed outlier: 3.729A pdb=" N GLY C2202 " --> pdb=" O MET C2198 " (cutoff:3.500A) Processing helix chain 'C' and resid 2202 through 2215 Processing helix chain 'C' and resid 2227 through 2242 Processing helix chain 'C' and resid 2246 through 2252 removed outlier: 3.767A pdb=" N MET C2250 " --> pdb=" O ASN C2246 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2261 Processing helix chain 'C' and resid 2272 through 2281 Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2304 removed outlier: 4.101A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2327 through 2341 removed outlier: 3.745A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2358 removed outlier: 3.734A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) Processing helix chain 'C' and resid 2376 through 2386 Processing helix chain 'C' and resid 2420 through 2435 Processing helix chain 'C' and resid 2451 through 2459 removed outlier: 3.569A pdb=" N ALA C2455 " --> pdb=" O LEU C2451 " (cutoff:3.500A) Processing helix chain 'C' and resid 2466 through 2472 Processing helix chain 'C' and resid 2495 through 2510 Processing helix chain 'C' and resid 2515 through 2522 Processing helix chain 'C' and resid 2526 through 2533 Processing helix chain 'C' and resid 2534 through 2537 removed outlier: 4.074A pdb=" N LEU C2537 " --> pdb=" O ALA C2534 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2534 through 2537' Processing helix chain 'C' and resid 2544 through 2544 No H-bonds generated for 'chain 'C' and resid 2544 through 2544' Processing helix chain 'C' and resid 2545 through 2556 removed outlier: 3.688A pdb=" N ASN C2551 " --> pdb=" O ALA C2547 " (cutoff:3.500A) Processing helix chain 'C' and resid 2557 through 2562 removed outlier: 4.091A pdb=" N LEU C2561 " --> pdb=" O ALA C2557 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C2562 " --> pdb=" O VAL C2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2557 through 2562' Processing helix chain 'C' and resid 2568 through 2585 Processing helix chain 'C' and resid 2592 through 2609 Processing helix chain 'C' and resid 2616 through 2633 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 2685 Processing helix chain 'C' and resid 2692 through 2710 Proline residue: C2701 - end of helix Processing helix chain 'C' and resid 2748 through 2750 No H-bonds generated for 'chain 'C' and resid 2748 through 2750' Processing helix chain 'C' and resid 2751 through 2772 removed outlier: 3.721A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2819 removed outlier: 3.623A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR C2805 " --> pdb=" O ASP C2801 " (cutoff:3.500A) Proline residue: C2808 - end of helix Processing helix chain 'C' and resid 2868 through 2898 Processing helix chain 'C' and resid 2907 through 2911 Processing helix chain 'C' and resid 2912 through 2933 removed outlier: 3.725A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) Processing helix chain 'C' and resid 3018 through 3038 Processing helix chain 'C' and resid 3044 through 3061 Processing helix chain 'C' and resid 3069 through 3090 Proline residue: C3085 - end of helix removed outlier: 3.622A pdb=" N VAL C3088 " --> pdb=" O GLY C3084 " (cutoff:3.500A) Processing helix chain 'C' and resid 3096 through 3114 Processing helix chain 'C' and resid 3133 through 3152 Proline residue: C3138 - end of helix removed outlier: 3.621A pdb=" N HIS C3146 " --> pdb=" O THR C3142 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C3147 " --> pdb=" O LEU C3143 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C3148 " --> pdb=" O PHE C3144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS C3150 " --> pdb=" O HIS C3146 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C3151 " --> pdb=" O ILE C3147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C3152 " --> pdb=" O ALA C3148 " (cutoff:3.500A) Processing helix chain 'C' and resid 3159 through 3178 Processing helix chain 'C' and resid 3185 through 3199 removed outlier: 3.648A pdb=" N ALA C3199 " --> pdb=" O ALA C3195 " (cutoff:3.500A) 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 3300 through 3311 removed outlier: 3.525A pdb=" N CYS C3304 " --> pdb=" O ALA C3300 " (cutoff:3.500A) Processing helix chain 'C' and resid 3318 through 3337 Processing helix chain 'C' and resid 3338 through 3339 No H-bonds generated for 'chain 'C' and resid 3338 through 3339' Processing helix chain 'C' and resid 3346 through 3349 Processing helix chain 'C' and resid 3350 through 3362 Proline residue: C3360 - end of helix Processing helix chain 'C' and resid 3368 through 3396 removed outlier: 3.899A pdb=" N VAL C3373 " --> pdb=" O ALA C3369 " (cutoff:3.500A) Processing helix chain 'C' and resid 3403 through 3423 removed outlier: 3.806A pdb=" N LEU C3408 " --> pdb=" O ASP C3404 " (cutoff:3.500A) removed outlier: 3.966A 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 3433 Processing helix chain 'C' and resid 3438 through 3454 Processing helix chain 'C' and resid 3458 through 3469 removed outlier: 3.510A pdb=" N PHE C3469 " --> pdb=" O ASN C3465 " (cutoff:3.500A) Processing helix chain 'C' and resid 3479 through 3488 removed outlier: 3.517A pdb=" N GLY C3487 " --> pdb=" O ASP C3483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C3488 " --> pdb=" O ALA C3484 " (cutoff:3.500A) Processing helix chain 'C' and resid 3489 through 3491 No H-bonds generated for 'chain 'C' and resid 3489 through 3491' Processing helix chain 'C' and resid 3495 through 3502 Processing helix chain 'C' and resid 3516 through 3525 Processing helix chain 'C' and resid 3538 through 3543 Processing helix chain 'C' and resid 3550 through 3570 Proline residue: C3567 - end of helix Processing helix chain 'C' and resid 3646 through 3659 removed outlier: 3.627A pdb=" N ALA C3659 " --> pdb=" O GLU C3655 " (cutoff:3.500A) Processing helix chain 'C' and resid 3668 through 3677 removed outlier: 4.624A pdb=" N ARG C3672 " --> pdb=" O SER C3668 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3733 removed outlier: 3.953A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) Processing helix chain 'C' and resid 3751 through 3772 removed outlier: 3.789A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C3772 " --> pdb=" O SER C3768 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 3.888A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3805 removed outlier: 3.782A pdb=" N SER C3795 " --> pdb=" O GLY C3791 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3823 removed outlier: 3.874A pdb=" N GLN C3813 " --> pdb=" O ASN C3809 " (cutoff:3.500A) Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 3.809A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) Processing helix chain 'C' and resid 3844 through 3851 Processing helix chain 'C' and resid 3878 through 3893 Processing helix chain 'C' and resid 3896 through 3906 removed outlier: 3.532A pdb=" N THR C3905 " --> pdb=" O ASN C3901 " (cutoff:3.500A) Processing helix chain 'C' and resid 3915 through 3938 Processing helix chain 'C' and resid 3945 through 3969 removed outlier: 4.035A pdb=" N PHE C3951 " --> pdb=" O GLY C3947 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA C3954 " --> pdb=" O ASN C3950 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3982 Processing helix chain 'C' and resid 3984 through 4003 removed outlier: 4.169A pdb=" N PHE C3992 " --> pdb=" O ALA C3988 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 Processing helix chain 'C' and resid 4040 through 4052 Processing helix chain 'C' and resid 4052 through 4063 removed outlier: 3.586A pdb=" N ASP C4063 " --> pdb=" O LEU C4059 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4080 removed outlier: 3.958A pdb=" N GLN C4078 " --> pdb=" O SER C4074 " (cutoff:3.500A) Processing helix chain 'C' and resid 4090 through 4094 Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4136 through 4154 Processing helix chain 'C' and resid 4157 through 4167 Processing helix chain 'C' and resid 4167 through 4175 removed outlier: 3.666A pdb=" N LEU C4171 " --> pdb=" O ALA C4167 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR C4173 " --> pdb=" O SER C4169 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4205 removed outlier: 3.661A pdb=" N TRP C4205 " --> pdb=" O ASN C4201 " (cutoff:3.500A) Processing helix chain 'C' and resid 4209 through 4225 removed outlier: 3.951A pdb=" N ARG C4215 " --> pdb=" O LYS C4211 " (cutoff:3.500A) Processing helix chain 'C' and resid 4228 through 4251 removed outlier: 4.582A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C4251 " --> pdb=" O ILE C4247 " (cutoff:3.500A) Processing helix chain 'C' and resid 4546 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4663 removed outlier: 3.742A pdb=" N ALA C4642 " --> pdb=" O TYR C4638 " (cutoff:3.500A) Processing helix chain 'C' and resid 4664 through 4683 removed outlier: 4.264A pdb=" N LEU C4668 " --> pdb=" O LEU C4664 " (cutoff:3.500A) Processing helix chain 'C' and resid 4697 through 4702 removed outlier: 3.563A pdb=" N ASP C4702 " --> pdb=" O LYS C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4708 removed outlier: 4.115A pdb=" N LEU C4706 " --> pdb=" O ARG C4703 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4729 Processing helix chain 'C' and resid 4733 through 4741 Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 3.935A pdb=" N ILE C4771 " --> pdb=" O TRP C4767 " (cutoff:3.500A) Processing helix chain 'C' and resid 4772 through 4785 Processing helix chain 'C' and resid 4786 through 4805 Processing helix chain 'C' and resid 4807 through 4819 removed outlier: 3.515A pdb=" N LEU C4813 " --> pdb=" O ALA C4810 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4832 removed outlier: 3.694A pdb=" N ARG C4824 " --> pdb=" O VAL C4820 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C4825 " --> pdb=" O LYS C4821 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4858 Processing helix chain 'C' and resid 4878 through 4889 Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 3.573A pdb=" N ASP C4899 " --> pdb=" O GLY C4896 " (cutoff:3.500A) removed outlier: 3.957A 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 4957 removed outlier: 3.519A pdb=" N GLU C4955 " --> pdb=" O LYS C4951 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C4957 " --> pdb=" O ASP C4953 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.991A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4974 through 4981 Processing helix chain 'C' and resid 4985 through 4998 removed outlier: 3.760A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) Processing helix chain 'C' and resid 4999 through 5003 Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'D' and resid 56 through 66 removed outlier: 4.423A pdb=" N ALA D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.687A pdb=" N ILE E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 84 removed outlier: 3.695A pdb=" N GLN E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 80 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.915A 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 255 through 258 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 394 through 421 Processing helix chain 'E' and resid 438 through 452 Processing helix chain 'E' and resid 460 through 481 Processing helix chain 'E' and resid 482 through 495 Processing helix chain 'E' and resid 514 through 531 removed outlier: 3.930A pdb=" N ILE E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 540 through 542 No H-bonds generated for 'chain 'E' and resid 540 through 542' Processing helix chain 'E' and resid 543 through 550 Processing helix chain 'E' and resid 557 through 570 removed outlier: 4.070A pdb=" N GLU E 570 " --> pdb=" O CYS E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 575 Processing helix chain 'E' and resid 579 through 593 removed outlier: 3.578A pdb=" N ILE E 583 " --> pdb=" O GLN E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 608 removed outlier: 3.577A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 626 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 810 through 816 Processing helix chain 'E' and resid 864 through 888 removed outlier: 4.181A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 908 Processing helix chain 'E' and resid 918 through 935 removed outlier: 4.379A pdb=" N MET E 924 " --> pdb=" O TYR E 920 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER E 925 " --> pdb=" O ASN E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 971 through 975 removed outlier: 3.949A pdb=" N VAL E 975 " --> pdb=" O LEU E 972 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 1000 Processing helix chain 'E' and resid 1001 through 1003 No H-bonds generated for 'chain 'E' and resid 1001 through 1003' Processing helix chain 'E' and resid 1028 through 1049 removed outlier: 5.142A pdb=" N SER E1034 " --> pdb=" O ALA E1030 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN E1035 " --> pdb=" O THR E1031 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASP E1037 " --> pdb=" O ARG E1033 " (cutoff:3.500A) Processing helix chain 'E' and resid 1079 through 1082 Processing helix chain 'E' and resid 1211 through 1216 removed outlier: 3.977A pdb=" N ILE E1216 " --> pdb=" O ARG E1212 " (cutoff:3.500A) Processing helix chain 'E' and resid 1216 through 1221 removed outlier: 4.472A pdb=" N GLN E1220 " --> pdb=" O ILE E1216 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU E1221 " --> pdb=" O CYS E1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1216 through 1221' Processing helix chain 'E' and resid 1225 through 1230 removed outlier: 4.005A pdb=" N ASN E1229 " --> pdb=" O PRO E1225 " (cutoff:3.500A) Processing helix chain 'E' and resid 1579 through 1585 removed outlier: 3.758A pdb=" N GLU E1583 " --> pdb=" O MET E1579 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS E1585 " --> pdb=" O LEU E1581 " (cutoff:3.500A) Processing helix chain 'E' and resid 1642 through 1645 removed outlier: 3.794A pdb=" N ASN E1645 " --> pdb=" O PRO E1642 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1642 through 1645' Processing helix chain 'E' and resid 1650 through 1654 removed outlier: 3.633A pdb=" N SER E1654 " --> pdb=" O ILE E1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1650 through 1654' Processing helix chain 'E' and resid 1656 through 1674 removed outlier: 3.820A pdb=" N CYS E1674 " --> pdb=" O TYR E1670 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1690 removed outlier: 4.447A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E1687 " --> pdb=" O HIS E1683 " (cutoff:3.500A) Processing helix chain 'E' and resid 1690 through 1698 removed outlier: 3.781A pdb=" N LEU E1694 " --> pdb=" O ASP E1690 " (cutoff:3.500A) Processing helix chain 'E' and resid 1704 through 1716 Processing helix chain 'E' and resid 1721 through 1727 Processing helix chain 'E' and resid 1728 through 1733 Processing helix chain 'E' and resid 1739 through 1744 removed outlier: 4.079A pdb=" N ALA E1744 " --> pdb=" O GLU E1741 " (cutoff:3.500A) Processing helix chain 'E' and resid 1803 through 1824 removed outlier: 3.770A pdb=" N ASP E1809 " --> pdb=" O GLU E1805 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E1818 " --> pdb=" O MET E1814 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP E1821 " --> pdb=" O GLU E1817 " (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: 3.631A pdb=" N ARG E1974 " --> pdb=" O GLN E1970 " (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 2057 through 2057 No H-bonds generated for 'chain 'E' and resid 2057 through 2057' Processing helix chain 'E' and resid 2058 through 2071 removed outlier: 4.181A pdb=" N ARG E2062 " --> pdb=" O SER E2058 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2108 Processing helix chain 'E' and resid 2113 through 2129 removed outlier: 3.983A pdb=" N TYR E2128 " --> pdb=" O LEU E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2131 through 2138 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: 3.920A pdb=" N THR E2152 " --> pdb=" O SER E2148 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU E2157 " --> pdb=" O MET E2153 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS E2158 " --> pdb=" O SER E2154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E2165 " --> pdb=" O GLN E2161 " (cutoff:3.500A) Processing helix chain 'E' and resid 2174 through 2188 Processing helix chain 'E' and resid 2194 through 2202 removed outlier: 3.724A pdb=" N GLY E2202 " --> pdb=" O MET E2198 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2215 Processing helix chain 'E' and resid 2227 through 2242 Processing helix chain 'E' and resid 2246 through 2252 removed outlier: 3.767A pdb=" N MET E2250 " --> pdb=" O ASN E2246 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2261 Processing helix chain 'E' and resid 2272 through 2281 Processing helix chain 'E' and resid 2283 through 2290 Processing helix chain 'E' and resid 2291 through 2304 removed outlier: 4.099A pdb=" N LEU E2295 " --> pdb=" O GLN E2291 " (cutoff:3.500A) Processing helix chain 'E' and resid 2327 through 2340 Processing helix chain 'E' and resid 2346 through 2358 removed outlier: 3.740A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) Processing helix chain 'E' and resid 2376 through 2386 Processing helix chain 'E' and resid 2420 through 2435 Processing helix chain 'E' and resid 2451 through 2459 removed outlier: 3.569A pdb=" N ALA E2455 " --> pdb=" O LEU E2451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2466 through 2472 Processing helix chain 'E' and resid 2495 through 2510 Processing helix chain 'E' and resid 2515 through 2522 Processing helix chain 'E' and resid 2526 through 2533 Processing helix chain 'E' and resid 2534 through 2537 removed outlier: 4.072A pdb=" N LEU E2537 " --> pdb=" O ALA E2534 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2534 through 2537' Processing helix chain 'E' and resid 2544 through 2544 No H-bonds generated for 'chain 'E' and resid 2544 through 2544' Processing helix chain 'E' and resid 2545 through 2556 removed outlier: 3.686A pdb=" N ASN E2551 " --> pdb=" O ALA E2547 " (cutoff:3.500A) Processing helix chain 'E' and resid 2557 through 2562 removed outlier: 4.090A pdb=" N LEU E2561 " --> pdb=" O ALA E2557 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE E2562 " --> pdb=" O VAL E2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2557 through 2562' Processing helix chain 'E' and resid 2568 through 2585 Processing helix chain 'E' and resid 2592 through 2609 Processing helix chain 'E' and resid 2616 through 2634 Proline residue: E2631 - end of helix removed outlier: 3.949A pdb=" N ASN E2634 " --> pdb=" O VAL E2630 " (cutoff:3.500A) Processing helix chain 'E' and resid 2639 through 2660 Proline residue: E2658 - end of helix Processing helix chain 'E' and resid 2668 through 2685 Processing helix chain 'E' and resid 2692 through 2710 Proline residue: E2701 - end of helix Processing helix chain 'E' and resid 2748 through 2750 No H-bonds generated for 'chain 'E' and resid 2748 through 2750' Processing helix chain 'E' and resid 2751 through 2772 removed outlier: 3.722A pdb=" N LYS E2770 " --> pdb=" O TRP E2766 " (cutoff:3.500A) Processing helix chain 'E' and resid 2798 through 2819 removed outlier: 3.620A pdb=" N ILE E2804 " --> pdb=" O LYS E2800 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR E2805 " --> pdb=" O ASP E2801 " (cutoff:3.500A) Proline residue: E2808 - end of helix Processing helix chain 'E' and resid 2868 through 2898 Processing helix chain 'E' and resid 2907 through 2911 Processing helix chain 'E' and resid 2912 through 2933 removed outlier: 3.725A pdb=" N ARG E2918 " --> pdb=" O LYS E2914 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS E2922 " --> pdb=" O ARG E2918 " (cutoff:3.500A) Processing helix chain 'E' and resid 3018 through 3038 Processing helix chain 'E' and resid 3044 through 3061 Processing helix chain 'E' and resid 3069 through 3090 Proline residue: E3085 - end of helix removed outlier: 3.628A pdb=" N VAL E3088 " --> pdb=" O GLY E3084 " (cutoff:3.500A) Processing helix chain 'E' and resid 3096 through 3114 Processing helix chain 'E' and resid 3133 through 3152 Proline residue: E3138 - end of helix removed outlier: 3.621A pdb=" N HIS E3146 " --> pdb=" O THR E3142 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E3147 " --> pdb=" O LEU E3143 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA E3148 " --> pdb=" O PHE E3144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS E3150 " --> pdb=" O HIS E3146 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN E3151 " --> pdb=" O ILE E3147 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE E3152 " --> pdb=" O ALA E3148 " (cutoff:3.500A) Processing helix chain 'E' and resid 3159 through 3178 Processing helix chain 'E' and resid 3185 through 3199 removed outlier: 3.680A pdb=" N ALA E3199 " --> pdb=" O ALA E3195 " (cutoff:3.500A) 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 3300 through 3311 removed outlier: 3.516A pdb=" N CYS E3304 " --> pdb=" O ALA E3300 " (cutoff:3.500A) Processing helix chain 'E' and resid 3318 through 3337 Processing helix chain 'E' and resid 3338 through 3339 No H-bonds generated for 'chain 'E' and resid 3338 through 3339' Processing helix chain 'E' and resid 3346 through 3349 Processing helix chain 'E' and resid 3350 through 3362 Proline residue: E3360 - end of helix Processing helix chain 'E' and resid 3368 through 3396 removed outlier: 3.898A pdb=" N VAL E3373 " --> pdb=" O ALA E3369 " (cutoff:3.500A) Processing helix chain 'E' and resid 3403 through 3423 removed outlier: 3.808A pdb=" N LEU E3408 " --> pdb=" O ASP E3404 " (cutoff:3.500A) removed outlier: 3.968A 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 3433 Processing helix chain 'E' and resid 3438 through 3454 Processing helix chain 'E' and resid 3458 through 3469 removed outlier: 3.510A pdb=" N PHE E3469 " --> pdb=" O ASN E3465 " (cutoff:3.500A) Processing helix chain 'E' and resid 3479 through 3488 removed outlier: 3.519A pdb=" N GLY E3487 " --> pdb=" O ASP E3483 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY E3488 " --> pdb=" O ALA E3484 " (cutoff:3.500A) Processing helix chain 'E' and resid 3489 through 3491 No H-bonds generated for 'chain 'E' and resid 3489 through 3491' Processing helix chain 'E' and resid 3495 through 3502 Processing helix chain 'E' and resid 3516 through 3525 Processing helix chain 'E' and resid 3538 through 3543 Processing helix chain 'E' and resid 3550 through 3570 Proline residue: E3567 - end of helix Processing helix chain 'E' and resid 3646 through 3659 removed outlier: 3.626A pdb=" N ALA E3659 " --> pdb=" O GLU E3655 " (cutoff:3.500A) Processing helix chain 'E' and resid 3668 through 3677 removed outlier: 4.626A pdb=" N ARG E3672 " --> pdb=" O SER E3668 " (cutoff:3.500A) Processing helix chain 'E' and resid 3696 through 3711 Processing helix chain 'E' and resid 3719 through 3733 removed outlier: 3.950A pdb=" N CYS E3733 " --> pdb=" O MET E3729 " (cutoff:3.500A) Processing helix chain 'E' and resid 3751 through 3772 removed outlier: 3.788A pdb=" N LEU E3770 " --> pdb=" O GLN E3766 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR E3772 " --> pdb=" O SER E3768 " (cutoff:3.500A) Processing helix chain 'E' and resid 3774 through 3787 removed outlier: 3.894A pdb=" N LYS E3787 " --> pdb=" O ILE E3783 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3805 removed outlier: 3.781A pdb=" N SER E3795 " --> pdb=" O GLY E3791 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3823 removed outlier: 3.882A pdb=" N GLN E3813 " --> pdb=" O ASN E3809 " (cutoff:3.500A) Processing helix chain 'E' and resid 3826 through 3839 removed outlier: 3.807A pdb=" N GLN E3830 " --> pdb=" O VAL E3826 " (cutoff:3.500A) Processing helix chain 'E' and resid 3844 through 3852 removed outlier: 4.213A pdb=" N LYS E3852 " --> pdb=" O GLU E3848 " (cutoff:3.500A) Processing helix chain 'E' and resid 3878 through 3893 Processing helix chain 'E' and resid 3896 through 3906 removed outlier: 3.529A pdb=" N THR E3905 " --> pdb=" O ASN E3901 " (cutoff:3.500A) Processing helix chain 'E' and resid 3915 through 3938 Processing helix chain 'E' and resid 3945 through 3969 removed outlier: 4.020A pdb=" N PHE E3951 " --> pdb=" O GLY E3947 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3982 Processing helix chain 'E' and resid 3984 through 4001 removed outlier: 4.177A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) Processing helix chain 'E' and resid 4009 through 4032 Processing helix chain 'E' and resid 4040 through 4052 Processing helix chain 'E' and resid 4052 through 4063 removed outlier: 3.585A pdb=" N ASP E4063 " --> pdb=" O LEU E4059 " (cutoff:3.500A) Processing helix chain 'E' and resid 4074 through 4080 removed outlier: 3.967A pdb=" N GLN E4078 " --> pdb=" O SER E4074 " (cutoff:3.500A) Processing helix chain 'E' and resid 4090 through 4094 Processing helix chain 'E' and resid 4104 through 4115 Processing helix chain 'E' and resid 4136 through 4154 Processing helix chain 'E' and resid 4157 through 4167 Processing helix chain 'E' and resid 4167 through 4175 removed outlier: 3.663A pdb=" N LEU E4171 " --> pdb=" O ALA E4167 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR E4173 " --> pdb=" O SER E4169 " (cutoff:3.500A) Processing helix chain 'E' and resid 4198 through 4205 removed outlier: 3.656A pdb=" N TRP E4205 " --> pdb=" O ASN E4201 " (cutoff:3.500A) Processing helix chain 'E' and resid 4209 through 4225 removed outlier: 3.956A pdb=" N ARG E4215 " --> pdb=" O LYS E4211 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4251 removed outlier: 4.395A pdb=" N GLU E4232 " --> pdb=" O ALA E4228 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E4251 " --> pdb=" O ILE E4247 " (cutoff:3.500A) Processing helix chain 'E' and resid 4546 through 4558 Processing helix chain 'E' and resid 4558 through 4578 Processing helix chain 'E' and resid 4638 through 4663 removed outlier: 3.735A pdb=" N ALA E4642 " --> pdb=" O TYR E4638 " (cutoff:3.500A) Processing helix chain 'E' and resid 4664 through 4683 removed outlier: 4.267A pdb=" N LEU E4668 " --> pdb=" O LEU E4664 " (cutoff:3.500A) Processing helix chain 'E' and resid 4697 through 4702 removed outlier: 3.559A pdb=" N ASP E4702 " --> pdb=" O LYS E4698 " (cutoff:3.500A) Processing helix chain 'E' and resid 4703 through 4708 removed outlier: 4.114A pdb=" N LEU E4706 " --> pdb=" O ARG E4703 " (cutoff:3.500A) Processing helix chain 'E' and resid 4719 through 4729 Processing helix chain 'E' and resid 4733 through 4741 Processing helix chain 'E' and resid 4766 through 4771 removed outlier: 3.940A pdb=" N ILE E4771 " --> pdb=" O TRP E4767 " (cutoff:3.500A) Processing helix chain 'E' and resid 4772 through 4785 Processing helix chain 'E' and resid 4786 through 4805 Processing helix chain 'E' and resid 4807 through 4819 Processing helix chain 'E' and resid 4820 through 4832 removed outlier: 3.683A pdb=" N ARG E4824 " --> pdb=" O VAL E4820 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR E4825 " --> pdb=" O LYS E4821 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 Processing helix chain 'E' and resid 4878 through 4889 Processing helix chain 'E' and resid 4896 through 4901 removed outlier: 3.556A pdb=" N ASP E4899 " --> pdb=" O GLY E4896 " (cutoff:3.500A) removed outlier: 3.924A 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 4957 removed outlier: 3.563A pdb=" N ILE E4937 " --> pdb=" O GLN E4933 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E4955 " --> pdb=" O LYS E4951 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E4957 " --> pdb=" O ASP E4953 " (cutoff:3.500A) Processing helix chain 'E' and resid 4964 through 4969 removed outlier: 3.990A pdb=" N PHE E4968 " --> pdb=" O GLY E4964 " (cutoff:3.500A) Processing helix chain 'E' and resid 4974 through 4981 Processing helix chain 'E' and resid 4985 through 4998 removed outlier: 3.754A pdb=" N MET E4989 " --> pdb=" O LEU E4985 " (cutoff:3.500A) Processing helix chain 'E' and resid 4999 through 5003 removed outlier: 3.506A 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 56 through 66 removed outlier: 4.436A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.681A pdb=" N ILE G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 84 removed outlier: 3.502A pdb=" N GLN G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU G 80 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 146 removed outlier: 3.925A 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 255 through 258 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 394 through 421 Processing helix chain 'G' and resid 438 through 452 Processing helix chain 'G' and resid 460 through 481 Processing helix chain 'G' and resid 482 through 495 Processing helix chain 'G' and resid 514 through 531 removed outlier: 3.929A pdb=" N ILE G 530 " --> pdb=" O LEU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 539 Processing helix chain 'G' and resid 540 through 542 No H-bonds generated for 'chain 'G' and resid 540 through 542' Processing helix chain 'G' and resid 543 through 550 Processing helix chain 'G' and resid 557 through 570 removed outlier: 4.066A pdb=" N GLU G 570 " --> pdb=" O CYS G 566 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 575 Processing helix chain 'G' and resid 579 through 593 removed outlier: 3.578A pdb=" N ILE G 583 " --> pdb=" O GLN G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 608 removed outlier: 3.582A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 626 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 810 through 816 Processing helix chain 'G' and resid 864 through 888 removed outlier: 4.165A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) Processing helix chain 'G' and resid 905 through 908 Processing helix chain 'G' and resid 918 through 935 removed outlier: 4.376A pdb=" N MET G 924 " --> pdb=" O TYR G 920 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER G 925 " --> pdb=" O ASN G 921 " (cutoff:3.500A) Processing helix chain 'G' and resid 971 through 975 removed outlier: 3.939A pdb=" N VAL G 975 " --> pdb=" O LEU G 972 " (cutoff:3.500A) Processing helix chain 'G' and resid 978 through 1000 Processing helix chain 'G' and resid 1001 through 1003 No H-bonds generated for 'chain 'G' and resid 1001 through 1003' Processing helix chain 'G' and resid 1028 through 1049 removed outlier: 5.138A pdb=" N SER G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN G1035 " --> pdb=" O THR G1031 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP G1037 " --> pdb=" O ARG G1033 " (cutoff:3.500A) Processing helix chain 'G' and resid 1079 through 1082 Processing helix chain 'G' and resid 1211 through 1216 removed outlier: 3.974A pdb=" N ILE G1216 " --> pdb=" O ARG G1212 " (cutoff:3.500A) Processing helix chain 'G' and resid 1216 through 1221 removed outlier: 4.324A pdb=" N GLN G1220 " --> pdb=" O ILE G1216 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU G1221 " --> pdb=" O CYS G1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1216 through 1221' Processing helix chain 'G' and resid 1225 through 1229 Processing helix chain 'G' and resid 1580 through 1585 removed outlier: 3.950A pdb=" N LYS G1585 " --> pdb=" O LEU G1581 " (cutoff:3.500A) Processing helix chain 'G' and resid 1642 through 1645 removed outlier: 3.805A pdb=" N ASN G1645 " --> pdb=" O PRO G1642 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1642 through 1645' Processing helix chain 'G' and resid 1650 through 1654 removed outlier: 3.628A pdb=" N SER G1654 " --> pdb=" O ILE G1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1650 through 1654' Processing helix chain 'G' and resid 1656 through 1674 removed outlier: 3.819A pdb=" N CYS G1674 " --> pdb=" O TYR G1670 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1690 removed outlier: 4.453A pdb=" N ALA G1684 " --> pdb=" O ARG G1680 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER G1687 " --> pdb=" O HIS G1683 " (cutoff:3.500A) Processing helix chain 'G' and resid 1691 through 1698 Processing helix chain 'G' and resid 1704 through 1716 Processing helix chain 'G' and resid 1721 through 1727 Processing helix chain 'G' and resid 1728 through 1733 Processing helix chain 'G' and resid 1739 through 1744 removed outlier: 4.084A pdb=" N ALA G1744 " --> pdb=" O GLU G1741 " (cutoff:3.500A) Processing helix chain 'G' and resid 1803 through 1824 removed outlier: 3.769A pdb=" N ASP G1809 " --> pdb=" O GLU G1805 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G1818 " --> pdb=" O MET G1814 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP G1821 " --> pdb=" O GLU G1817 " (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: 3.632A pdb=" N ARG G1974 " --> pdb=" O GLN G1970 " (cutoff:3.500A) Processing helix chain 'G' and resid 2034 through 2044 Processing helix chain 'G' and resid 2058 through 2071 removed outlier: 4.187A pdb=" N ARG G2062 " --> pdb=" O SER G2058 " (cutoff:3.500A) Processing helix chain 'G' and resid 2094 through 2110 removed outlier: 4.111A pdb=" N ASP G2109 " --> pdb=" O TRP G2105 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR G2110 " --> pdb=" O ALA G2106 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2129 removed outlier: 3.906A pdb=" N TYR G2128 " --> pdb=" O LEU G2124 " (cutoff:3.500A) Processing helix chain 'G' and resid 2131 through 2138 Processing helix chain 'G' and resid 2145 through 2147 No H-bonds generated for 'chain 'G' and resid 2145 through 2147' Processing helix chain 'G' and resid 2148 through 2166 removed outlier: 3.919A pdb=" N THR G2152 " --> pdb=" O SER G2148 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU G2157 " --> pdb=" O MET G2153 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS G2158 " --> pdb=" O SER G2154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G2165 " --> pdb=" O GLN G2161 " (cutoff:3.500A) Processing helix chain 'G' and resid 2174 through 2188 Processing helix chain 'G' and resid 2194 through 2202 removed outlier: 3.745A pdb=" N GLY G2202 " --> pdb=" O MET G2198 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2215 Processing helix chain 'G' and resid 2227 through 2242 Processing helix chain 'G' and resid 2246 through 2252 removed outlier: 3.767A pdb=" N MET G2250 " --> pdb=" O ASN G2246 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2261 Processing helix chain 'G' and resid 2272 through 2281 Processing helix chain 'G' and resid 2283 through 2290 Processing helix chain 'G' and resid 2291 through 2304 removed outlier: 4.099A pdb=" N LEU G2295 " --> pdb=" O GLN G2291 " (cutoff:3.500A) Processing helix chain 'G' and resid 2327 through 2341 removed outlier: 3.741A pdb=" N VAL G2341 " --> pdb=" O PHE G2337 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2358 removed outlier: 3.772A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) Processing helix chain 'G' and resid 2376 through 2386 Processing helix chain 'G' and resid 2420 through 2435 Processing helix chain 'G' and resid 2451 through 2459 removed outlier: 3.569A pdb=" N ALA G2455 " --> pdb=" O LEU G2451 " (cutoff:3.500A) Processing helix chain 'G' and resid 2466 through 2472 Processing helix chain 'G' and resid 2495 through 2510 Processing helix chain 'G' and resid 2515 through 2522 Processing helix chain 'G' and resid 2526 through 2533 Processing helix chain 'G' and resid 2534 through 2537 removed outlier: 4.073A pdb=" N LEU G2537 " --> pdb=" O ALA G2534 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2534 through 2537' Processing helix chain 'G' and resid 2544 through 2544 No H-bonds generated for 'chain 'G' and resid 2544 through 2544' Processing helix chain 'G' and resid 2545 through 2556 removed outlier: 3.690A pdb=" N ASN G2551 " --> pdb=" O ALA G2547 " (cutoff:3.500A) Processing helix chain 'G' and resid 2557 through 2562 removed outlier: 4.087A pdb=" N LEU G2561 " --> pdb=" O ALA G2557 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE G2562 " --> pdb=" O VAL G2558 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2557 through 2562' Processing helix chain 'G' and resid 2568 through 2585 Processing helix chain 'G' and resid 2592 through 2609 Processing helix chain 'G' and resid 2616 through 2633 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 2685 Processing helix chain 'G' and resid 2692 through 2710 Proline residue: G2701 - end of helix Processing helix chain 'G' and resid 2748 through 2750 No H-bonds generated for 'chain 'G' and resid 2748 through 2750' Processing helix chain 'G' and resid 2751 through 2772 removed outlier: 3.751A pdb=" N LYS G2770 " --> pdb=" O TRP G2766 " (cutoff:3.500A) Processing helix chain 'G' and resid 2798 through 2819 removed outlier: 3.617A pdb=" N ILE G2804 " --> pdb=" O LYS G2800 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR G2805 " --> pdb=" O ASP G2801 " (cutoff:3.500A) Proline residue: G2808 - end of helix Processing helix chain 'G' and resid 2861 through 2865 Processing helix chain 'G' and resid 2868 through 2896 removed outlier: 3.596A pdb=" N TRP G2886 " --> pdb=" O TYR G2882 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY G2887 " --> pdb=" O HIS G2883 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS G2891 " --> pdb=" O GLY G2887 " (cutoff:3.500A) Processing helix chain 'G' and resid 2907 through 2911 Processing helix chain 'G' and resid 2912 through 2933 removed outlier: 3.610A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS G2922 " --> pdb=" O ARG G2918 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU G2926 " --> pdb=" O LYS G2922 " (cutoff:3.500A) Processing helix chain 'G' and resid 3018 through 3038 Processing helix chain 'G' and resid 3044 through 3061 removed outlier: 4.127A pdb=" N ARG G3053 " --> pdb=" O LEU G3049 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL G3054 " --> pdb=" O VAL G3050 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR G3059 " --> pdb=" O SER G3055 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP G3060 " --> pdb=" O LEU G3056 " (cutoff:3.500A) Processing helix chain 'G' and resid 3070 through 3090 removed outlier: 3.852A pdb=" N SER G3074 " --> pdb=" O ILE G3070 " (cutoff:3.500A) Proline residue: G3085 - end of helix removed outlier: 4.625A pdb=" N VAL G3088 " --> pdb=" O GLY G3084 " (cutoff:3.500A) Processing helix chain 'G' and resid 3096 through 3115 removed outlier: 3.775A pdb=" N SER G3100 " --> pdb=" O PHE G3096 " (cutoff:3.500A) Processing helix chain 'G' and resid 3133 through 3150 Proline residue: G3138 - end of helix removed outlier: 3.646A pdb=" N HIS G3146 " --> pdb=" O THR G3142 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE G3147 " --> pdb=" O LEU G3143 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G3148 " --> pdb=" O PHE G3144 " (cutoff:3.500A) Processing helix chain 'G' and resid 3159 through 3177 removed outlier: 3.699A pdb=" N SER G3164 " --> pdb=" O ASP G3160 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS G3165 " --> pdb=" O VAL G3161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR G3177 " --> pdb=" O TYR G3173 " (cutoff:3.500A) Processing helix chain 'G' and resid 3185 through 3199 removed outlier: 3.561A pdb=" N LEU G3190 " --> pdb=" O LEU G3186 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY G3191 " --> pdb=" O ARG G3187 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU G3192 " --> pdb=" O PRO G3188 " (cutoff:3.500A) Processing helix chain 'G' and resid 3205 through 3216 removed outlier: 3.533A pdb=" N ASN G3211 " --> pdb=" O GLU G3207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU G3212 " --> pdb=" O PRO G3208 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR G3213 " --> pdb=" O GLN G3209 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G3214 " --> pdb=" O LEU G3210 " (cutoff:3.500A) Processing helix chain 'G' and resid 3274 through 3288 removed outlier: 4.195A pdb=" N SER G3279 " --> pdb=" O PRO G3275 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G3281 " --> pdb=" O LEU G3277 " (cutoff:3.500A) Proline residue: G3282 - end of helix removed outlier: 3.881A pdb=" N TRP G3285 " --> pdb=" O LEU G3281 " (cutoff:3.500A) Processing helix chain 'G' and resid 3295 through 3299 Processing helix chain 'G' and resid 3300 through 3311 removed outlier: 3.519A pdb=" N CYS G3304 " --> pdb=" O ALA G3300 " (cutoff:3.500A) Processing helix chain 'G' and resid 3318 through 3337 removed outlier: 3.536A pdb=" N ILE G3322 " --> pdb=" O ASN G3318 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET G3335 " --> pdb=" O GLU G3331 " (cutoff:3.500A) Processing helix chain 'G' and resid 3338 through 3339 No H-bonds generated for 'chain 'G' and resid 3338 through 3339' Processing helix chain 'G' and resid 3346 through 3347 No H-bonds generated for 'chain 'G' and resid 3346 through 3347' Processing helix chain 'G' and resid 3348 through 3363 removed outlier: 3.749A pdb=" N LEU G3354 " --> pdb=" O ARG G3350 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS G3355 " --> pdb=" O PRO G3351 " (cutoff:3.500A) Proline residue: G3360 - end of helix Processing helix chain 'G' and resid 3368 through 3395 removed outlier: 3.796A pdb=" N VAL G3372 " --> pdb=" O ARG G3368 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL G3373 " --> pdb=" O ALA G3369 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA G3387 " --> pdb=" O ALA G3383 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU G3392 " --> pdb=" O GLU G3388 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG G3395 " --> pdb=" O GLU G3391 " (cutoff:3.500A) Processing helix chain 'G' and resid 3396 through 3397 No H-bonds generated for 'chain 'G' and resid 3396 through 3397' Processing helix chain 'G' and resid 3402 through 3402 No H-bonds generated for 'chain 'G' and resid 3402 through 3402' Processing helix chain 'G' and resid 3403 through 3423 removed outlier: 3.700A pdb=" N ALA G3407 " --> pdb=" O ARG G3403 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU G3408 " --> pdb=" O ASP G3404 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR G3409 " --> pdb=" O LEU G3405 " (cutoff:3.500A) Proline residue: G3410 - end of helix Processing helix chain 'G' and resid 3428 through 3432 removed outlier: 3.642A pdb=" N GLU G3432 " --> pdb=" O ASN G3428 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3428 through 3432' Processing helix chain 'G' and resid 3433 through 3435 No H-bonds generated for 'chain 'G' and resid 3433 through 3435' Processing helix chain 'G' and resid 3437 through 3437 No H-bonds generated for 'chain 'G' and resid 3437 through 3437' Processing helix chain 'G' and resid 3438 through 3454 Processing helix chain 'G' and resid 3458 through 3469 removed outlier: 3.529A pdb=" N ILE G3464 " --> pdb=" O VAL G3460 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN G3465 " --> pdb=" O GLN G3461 " (cutoff:3.500A) Processing helix chain 'G' and resid 3479 through 3487 removed outlier: 3.946A pdb=" N GLN G3485 " --> pdb=" O ALA G3481 " (cutoff:3.500A) Processing helix chain 'G' and resid 3488 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 3503 removed outlier: 3.603A pdb=" N ARG G3499 " --> pdb=" O LYS G3495 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G3501 " --> pdb=" O LYS G3497 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG G3502 " --> pdb=" O ARG G3498 " (cutoff:3.500A) Processing helix chain 'G' and resid 3514 through 3525 Proline residue: G3519 - end of helix removed outlier: 3.505A pdb=" N MET G3524 " --> pdb=" O ILE G3520 " (cutoff:3.500A) Processing helix chain 'G' and resid 3538 through 3543 removed outlier: 3.531A pdb=" N LYS G3543 " --> pdb=" O ARG G3539 " (cutoff:3.500A) Processing helix chain 'G' and resid 3552 through 3571 removed outlier: 3.663A pdb=" N HIS G3558 " --> pdb=" O GLN G3554 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G3559 " --> pdb=" O ASN G3555 " (cutoff:3.500A) Proline residue: G3567 - end of helix removed outlier: 3.702A pdb=" N TRP G3571 " --> pdb=" O PRO G3567 " (cutoff:3.500A) Processing helix chain 'G' and resid 3646 through 3659 removed outlier: 3.641A pdb=" N LEU G3654 " --> pdb=" O CYS G3650 " (cutoff:3.500A) Processing helix chain 'G' and resid 3669 through 3675 removed outlier: 3.510A pdb=" N ASP G3675 " --> pdb=" O ASP G3671 " (cutoff:3.500A) Processing helix chain 'G' and resid 3676 through 3679 removed outlier: 3.890A pdb=" N LYS G3679 " --> pdb=" O ASP G3676 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3676 through 3679' Processing helix chain 'G' and resid 3696 through 3711 removed outlier: 3.597A pdb=" N HIS G3704 " --> pdb=" O GLN G3700 " (cutoff:3.500A) Processing helix chain 'G' and resid 3719 through 3733 removed outlier: 3.662A pdb=" N TYR G3725 " --> pdb=" O LEU G3721 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP G3727 " --> pdb=" O MET G3723 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G3730 " --> pdb=" O ALA G3726 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS G3733 " --> pdb=" O MET G3729 " (cutoff:3.500A) Processing helix chain 'G' and resid 3751 through 3772 removed outlier: 3.614A pdb=" N GLU G3757 " --> pdb=" O PHE G3753 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU G3770 " --> pdb=" O GLN G3766 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR G3772 " --> pdb=" O SER G3768 " (cutoff:3.500A) Processing helix chain 'G' and resid 3774 through 3787 removed outlier: 3.663A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER G3784 " --> pdb=" O LEU G3780 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS G3787 " --> pdb=" O ILE G3783 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3804 removed outlier: 3.771A pdb=" N SER G3795 " --> pdb=" O GLY G3791 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS G3799 " --> pdb=" O SER G3795 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU G3800 " --> pdb=" O SER G3796 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3823 removed outlier: 3.789A pdb=" N GLN G3813 " --> pdb=" O ASN G3809 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP G3818 " --> pdb=" O GLN G3814 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G3820 " --> pdb=" O MET G3816 " (cutoff:3.500A) Processing helix chain 'G' and resid 3826 through 3839 removed outlier: 3.598A pdb=" N GLN G3830 " --> pdb=" O VAL G3826 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G3834 " --> pdb=" O GLN G3830 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3852 removed outlier: 3.951A pdb=" N ARG G3849 " --> pdb=" O ASN G3845 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS G3852 " --> pdb=" O GLU G3848 " (cutoff:3.500A) Processing helix chain 'G' and resid 3878 through 3893 Processing helix chain 'G' and resid 3896 through 3906 removed outlier: 3.579A pdb=" N TYR G3902 " --> pdb=" O ASP G3898 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG G3904 " --> pdb=" O GLN G3900 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR G3905 " --> pdb=" O ASN G3901 " (cutoff:3.500A) Processing helix chain 'G' and resid 3915 through 3939 removed outlier: 3.566A pdb=" N VAL G3920 " --> pdb=" O ILE G3916 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY G3939 " --> pdb=" O TRP G3935 " (cutoff:3.500A) Processing helix chain 'G' and resid 3945 through 3950 Processing helix chain 'G' and resid 3951 through 3970 removed outlier: 4.054A pdb=" N VAL G3957 " --> pdb=" O LYS G3953 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE G3962 " --> pdb=" O ALA G3958 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR G3968 " --> pdb=" O SER G3964 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G3969 " --> pdb=" O LEU G3965 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3982 Processing helix chain 'G' and resid 3984 through 4004 removed outlier: 3.608A pdb=" N VAL G3990 " --> pdb=" O TRP G3986 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS G3998 " --> pdb=" O HIS G3994 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET G4001 " --> pdb=" O ALA G3997 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS G4002 " --> pdb=" O HIS G3998 " (cutoff:3.500A) Processing helix chain 'G' and resid 4009 through 4029 removed outlier: 3.611A pdb=" N GLU G4015 " --> pdb=" O GLU G4011 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP G4022 " --> pdb=" O ASP G4018 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL G4024 " --> pdb=" O GLN G4020 " (cutoff:3.500A) Processing helix chain 'G' and resid 4040 through 4051 removed outlier: 3.506A pdb=" N MET G4047 " --> pdb=" O GLN G4043 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4062 removed outlier: 4.116A pdb=" N MET G4057 " --> pdb=" O SER G4053 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G4060 " --> pdb=" O GLU G4056 " (cutoff:3.500A) Processing helix chain 'G' and resid 4073 through 4080 removed outlier: 3.556A pdb=" N TYR G4080 " --> pdb=" O PHE G4077 " (cutoff:3.500A) Processing helix chain 'G' and resid 4090 through 4094 Processing helix chain 'G' and resid 4104 through 4114 removed outlier: 4.303A pdb=" N PHE G4110 " --> pdb=" O PRO G4106 " (cutoff:3.500A) Processing helix chain 'G' and resid 4136 through 4154 Processing helix chain 'G' and resid 4157 through 4166 removed outlier: 3.797A pdb=" N PHE G4163 " --> pdb=" O ARG G4159 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU G4166 " --> pdb=" O ASN G4162 " (cutoff:3.500A) Processing helix chain 'G' and resid 4167 through 4175 removed outlier: 4.029A pdb=" N TYR G4173 " --> pdb=" O SER G4169 " (cutoff:3.500A) Processing helix chain 'G' and resid 4198 through 4203 Processing helix chain 'G' and resid 4209 through 4225 removed outlier: 3.937A pdb=" N ARG G4215 " --> pdb=" O LYS G4211 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G4224 " --> pdb=" O ASP G4220 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4251 removed outlier: 4.149A pdb=" N GLU G4232 " --> pdb=" O ALA G4228 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G4235 " --> pdb=" O MET G4231 " (cutoff:3.500A) Processing helix chain 'G' and resid 4546 through 4558 Processing helix chain 'G' and resid 4558 through 4578 removed outlier: 3.609A pdb=" N ALA G4570 " --> pdb=" O ALA G4566 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE G4576 " --> pdb=" O ALA G4572 " (cutoff:3.500A) Processing helix chain 'G' and resid 4638 through 4662 removed outlier: 3.604A pdb=" N ALA G4642 " --> pdb=" O TYR G4638 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU G4648 " --> pdb=" O TRP G4644 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G4651 " --> pdb=" O SER G4647 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE G4658 " --> pdb=" O ALA G4654 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY G4660 " --> pdb=" O LEU G4656 " (cutoff:3.500A) Processing helix chain 'G' and resid 4664 through 4683 removed outlier: 3.933A pdb=" N LEU G4668 " --> pdb=" O LEU G4664 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG G4679 " --> pdb=" O LYS G4675 " (cutoff:3.500A) Processing helix chain 'G' and resid 4697 through 4702 Processing helix chain 'G' and resid 4703 through 4708 removed outlier: 4.020A pdb=" N LEU G4706 " --> pdb=" O ARG G4703 " (cutoff:3.500A) Processing helix chain 'G' and resid 4719 through 4728 removed outlier: 4.187A pdb=" N LEU G4725 " --> pdb=" O LYS G4721 " (cutoff:3.500A) Processing helix chain 'G' and resid 4735 through 4741 Processing helix chain 'G' and resid 4766 through 4771 removed outlier: 3.934A pdb=" N ILE G4771 " --> pdb=" O TRP G4767 " (cutoff:3.500A) Processing helix chain 'G' and resid 4772 through 4784 Processing helix chain 'G' and resid 4786 through 4801 removed outlier: 3.891A pdb=" N TYR G4791 " --> pdb=" O ASN G4787 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) Processing helix chain 'G' and resid 4807 through 4819 removed outlier: 3.548A pdb=" N ALA G4811 " --> pdb=" O PHE G4808 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS G4812 " --> pdb=" O PHE G4809 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G4813 " --> pdb=" O ALA G4810 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4832 removed outlier: 3.556A pdb=" N ARG G4824 " --> pdb=" O VAL G4820 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR G4825 " --> pdb=" O LYS G4821 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 3.550A pdb=" N TYR G4849 " --> pdb=" O ALA G4845 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR G4851 " --> pdb=" O VAL G4847 " (cutoff:3.500A) Processing helix chain 'G' and resid 4878 through 4889 removed outlier: 3.722A pdb=" N MET G4887 " --> pdb=" O TYR G4883 " (cutoff:3.500A) Processing helix chain 'G' and resid 4896 through 4901 removed outlier: 3.927A pdb=" N ILE G4901 " --> pdb=" O GLY G4898 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4922 removed outlier: 3.675A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G4916 " --> pdb=" O TYR G4912 " (cutoff:3.500A) Processing helix chain 'G' and resid 4927 through 4957 removed outlier: 3.712A pdb=" N ILE G4936 " --> pdb=" O ILE G4932 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE G4937 " --> pdb=" O GLN G4933 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG G4944 " --> pdb=" O PHE G4940 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP G4945 " --> pdb=" O GLY G4941 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN G4946 " --> pdb=" O GLU G4942 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU G4955 " --> pdb=" O LYS G4951 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS G4957 " --> pdb=" O ASP G4953 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4969 removed outlier: 4.090A pdb=" N PHE G4968 " --> pdb=" O GLY G4964 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4980 removed outlier: 4.037A pdb=" N THR G4977 " --> pdb=" O HIS G4973 " (cutoff:3.500A) Processing helix chain 'G' and resid 4986 through 4998 removed outlier: 3.561A pdb=" N LYS G4998 " --> pdb=" O TYR G4994 " (cutoff:3.500A) Processing helix chain 'G' and resid 4999 through 5003 Processing helix chain 'G' and resid 5004 through 5017 Processing helix chain 'H' and resid 56 through 66 removed outlier: 4.375A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.939A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 124 removed outlier: 4.941A pdb=" N ASP A 134 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A 135 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 191 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA8, first strand: chain 'A' and resid 230 through 233 removed outlier: 5.605A pdb=" N VAL A 245 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 290 through 294 Processing sheet with id=AB1, first strand: chain 'A' and resid 634 through 639 removed outlier: 3.738A pdb=" N GLN A 634 " --> pdb=" O HIS A1640 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A1638 " --> pdb=" O ASN A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 642 through 643 Processing sheet with id=AB3, first strand: chain 'A' and resid 755 through 759 removed outlier: 3.786A pdb=" N SER A 756 " --> pdb=" O CYS A 747 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.528A pdb=" N TRP A 722 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 713 " --> pdb=" O TRP A 722 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 830 through 831 Processing sheet with id=AB6, first strand: chain 'A' and resid 892 through 893 removed outlier: 6.223A pdb=" N THR A 892 " --> pdb=" O HIS A 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1121 through 1125 removed outlier: 5.340A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A1239 " --> pdb=" O ILE A1074 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB9, first strand: chain 'A' and resid 1152 through 1154 removed outlier: 3.603A pdb=" N PHE A1179 " --> pdb=" O ILE A1160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1163 through 1164 Processing sheet with id=AC2, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC3, first strand: chain 'A' and resid 1259 through 1260 removed outlier: 3.591A pdb=" N MET A1260 " --> pdb=" O HIS A1274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1287 through 1290 Processing sheet with id=AC5, first strand: chain 'A' and resid 1438 through 1439 removed outlier: 3.652A pdb=" N ILE A1516 " --> pdb=" O THR A1530 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1735 through 1737 Processing sheet with id=AC7, first strand: chain 'A' and resid 2776 through 2777 removed outlier: 5.846A pdb=" N SER A2776 " --> pdb=" O HIS A2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 2822 through 2824 Processing sheet with id=AC9, first strand: chain 'A' and resid 4088 through 4089 Processing sheet with id=AD1, first strand: chain 'A' and resid 4178 through 4183 Processing sheet with id=AD2, first strand: chain 'B' and resid 3 through 8 removed outlier: 4.812A pdb=" N VAL B 4 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR B 75 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR B 6 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS B 73 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 27 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY B 28 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 3 through 8 removed outlier: 4.812A pdb=" N VAL B 4 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR B 75 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR B 6 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS B 73 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 23 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 19 through 20 removed outlier: 6.939A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AD7, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AD8, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AD9, first strand: chain 'C' and resid 117 through 124 removed outlier: 4.941A pdb=" N ASP C 134 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL C 135 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 191 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AE2, first strand: chain 'C' and resid 230 through 233 removed outlier: 5.607A pdb=" N VAL C 245 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 290 through 294 Processing sheet with id=AE4, first strand: chain 'C' and resid 634 through 639 removed outlier: 3.752A pdb=" N GLN C 634 " --> pdb=" O HIS C1640 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C1638 " --> pdb=" O ASN C 636 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 642 through 643 Processing sheet with id=AE6, first strand: chain 'C' and resid 755 through 759 removed outlier: 3.787A pdb=" N SER C 756 " --> pdb=" O CYS C 747 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 664 " --> pdb=" O CYS C 746 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 721 through 722 removed outlier: 3.511A pdb=" N TRP C 722 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER C 713 " --> pdb=" O TRP C 722 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 830 through 831 Processing sheet with id=AE9, first strand: chain 'C' and resid 892 through 893 removed outlier: 6.218A pdb=" N THR C 892 " --> pdb=" O HIS C 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 1131 through 1132 removed outlier: 5.327A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C1239 " --> pdb=" O ILE C1074 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AF3, first strand: chain 'C' and resid 1152 through 1154 removed outlier: 3.616A pdb=" N PHE C1179 " --> pdb=" O ILE C1160 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1163 through 1164 Processing sheet with id=AF5, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AF6, first strand: chain 'C' and resid 1259 through 1260 removed outlier: 3.592A pdb=" N MET C1260 " --> pdb=" O HIS C1274 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1287 through 1290 Processing sheet with id=AF8, first strand: chain 'C' and resid 1438 through 1439 removed outlier: 3.646A pdb=" N ILE C1516 " --> pdb=" O THR C1530 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1735 through 1737 Processing sheet with id=AG1, first strand: chain 'C' and resid 2776 through 2777 removed outlier: 5.837A pdb=" N SER C2776 " --> pdb=" O HIS C2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 2822 through 2824 Processing sheet with id=AG3, first strand: chain 'C' and resid 4088 through 4089 Processing sheet with id=AG4, first strand: chain 'C' and resid 4178 through 4183 Processing sheet with id=AG5, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.807A pdb=" N VAL D 4 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR D 75 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR D 6 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS D 73 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 27 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY D 28 " --> pdb=" O PHE D 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.807A pdb=" N VAL D 4 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR D 75 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR D 6 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS D 73 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 23 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 19 through 20 removed outlier: 6.935A pdb=" N GLU E 19 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AG9, first strand: chain 'E' and resid 36 through 38 Processing sheet with id=AH1, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AH2, first strand: chain 'E' and resid 72 through 73 Processing sheet with id=AH3, first strand: chain 'E' and resid 117 through 124 removed outlier: 4.949A pdb=" N ASP E 134 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL E 135 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 191 " --> pdb=" O VAL E 135 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AH5, first strand: chain 'E' and resid 230 through 233 removed outlier: 5.603A pdb=" N VAL E 245 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 290 through 294 Processing sheet with id=AH7, first strand: chain 'E' and resid 634 through 639 removed outlier: 3.756A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA E1638 " --> pdb=" O ASN E 636 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 642 through 643 Processing sheet with id=AH9, first strand: chain 'E' and resid 755 through 759 removed outlier: 3.785A pdb=" N SER E 756 " --> pdb=" O CYS E 747 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS E 788 " --> pdb=" O ASP E 669 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 721 through 722 removed outlier: 3.525A pdb=" N TRP E 722 " --> pdb=" O SER E 713 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER E 713 " --> pdb=" O TRP E 722 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 830 through 831 Processing sheet with id=AI3, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.231A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'E' and resid 1121 through 1125 removed outlier: 5.356A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER E1239 " --> pdb=" O ILE E1074 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E1240 " --> pdb=" O MET E1608 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET E1608 " --> pdb=" O LYS E1240 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 1091 through 1094 Processing sheet with id=AI6, first strand: chain 'E' and resid 1152 through 1154 removed outlier: 3.605A pdb=" N PHE E1179 " --> pdb=" O ILE E1160 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 1163 through 1164 Processing sheet with id=AI8, first strand: chain 'E' and resid 1244 through 1246 Processing sheet with id=AI9, first strand: chain 'E' and resid 1259 through 1260 removed outlier: 3.590A pdb=" N MET E1260 " --> pdb=" O HIS E1274 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 1287 through 1290 Processing sheet with id=AJ2, first strand: chain 'E' and resid 1438 through 1439 removed outlier: 3.651A pdb=" N ILE E1516 " --> pdb=" O THR E1530 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 1735 through 1737 Processing sheet with id=AJ4, first strand: chain 'E' and resid 2776 through 2777 removed outlier: 5.842A pdb=" N SER E2776 " --> pdb=" O HIS E2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'E' and resid 2822 through 2824 Processing sheet with id=AJ6, first strand: chain 'E' and resid 4088 through 4089 Processing sheet with id=AJ7, first strand: chain 'E' and resid 4178 through 4183 Processing sheet with id=AJ8, first strand: chain 'F' and resid 3 through 8 removed outlier: 4.814A pdb=" N VAL F 4 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR F 75 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR F 6 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS F 73 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY F 28 " --> pdb=" O PHE F 36 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 3 through 8 removed outlier: 4.814A pdb=" N VAL F 4 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR F 75 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR F 6 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS F 73 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL F 23 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G' and resid 19 through 20 removed outlier: 6.934A pdb=" N GLU G 19 " --> pdb=" O ILE G 205 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=AK3, first strand: chain 'G' and resid 36 through 38 Processing sheet with id=AK4, first strand: chain 'G' and resid 67 through 68 Processing sheet with id=AK5, first strand: chain 'G' and resid 72 through 73 Processing sheet with id=AK6, first strand: chain 'G' and resid 117 through 124 removed outlier: 4.943A pdb=" N ASP G 134 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL G 135 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL G 191 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 347 through 350 Processing sheet with id=AK8, first strand: chain 'G' and resid 230 through 233 removed outlier: 5.606A pdb=" N VAL G 245 " --> pdb=" O ALA G 376 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 290 through 294 Processing sheet with id=AL1, first strand: chain 'G' and resid 634 through 639 removed outlier: 3.752A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA G1638 " --> pdb=" O ASN G 636 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 642 through 643 Processing sheet with id=AL3, first strand: chain 'G' and resid 762 through 763 removed outlier: 3.785A pdb=" N SER G 756 " --> pdb=" O CYS G 747 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS G 788 " --> pdb=" O ASP G 669 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 721 through 722 removed outlier: 3.522A pdb=" N TRP G 722 " --> pdb=" O SER G 713 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER G 713 " --> pdb=" O TRP G 722 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'G' and resid 830 through 831 Processing sheet with id=AL6, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.236A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'G' and resid 1131 through 1132 removed outlier: 5.325A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER G1239 " --> pdb=" O ILE G1074 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'G' and resid 1091 through 1094 Processing sheet with id=AL9, first strand: chain 'G' and resid 1152 through 1154 removed outlier: 3.609A pdb=" N PHE G1179 " --> pdb=" O ILE G1160 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'G' and resid 1163 through 1164 Processing sheet with id=AM2, first strand: chain 'G' and resid 1244 through 1246 Processing sheet with id=AM3, first strand: chain 'G' and resid 1259 through 1260 removed outlier: 3.588A pdb=" N MET G1260 " --> pdb=" O HIS G1274 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'G' and resid 1287 through 1290 Processing sheet with id=AM5, first strand: chain 'G' and resid 1438 through 1439 removed outlier: 3.655A pdb=" N ILE G1516 " --> pdb=" O THR G1530 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 1735 through 1737 Processing sheet with id=AM7, first strand: chain 'G' and resid 2776 through 2777 removed outlier: 5.841A pdb=" N SER G2776 " --> pdb=" O HIS G2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM7 Processing sheet with id=AM8, first strand: chain 'G' and resid 4088 through 4089 Processing sheet with id=AM9, first strand: chain 'G' and resid 4178 through 4179 Processing sheet with id=AN1, first strand: chain 'G' and resid 4182 through 4183 Processing sheet with id=AN2, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.791A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 74 " --> pdb=" O PHE H 99 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE H 99 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL H 23 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'H' and resid 27 through 29 6154 hydrogen bonds defined for protein. 17460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 78.18 Time building geometry restraints manager: 37.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 16092 1.25 - 1.42: 31246 1.42 - 1.58: 64497 1.58 - 1.75: 164 1.75 - 1.91: 945 Bond restraints: 112944 Sorted by residual: bond pdb=" CA ARG C4180 " pdb=" C ARG C4180 " ideal model delta sigma weight residual 1.523 1.376 0.146 1.10e-02 8.26e+03 1.77e+02 bond pdb=" CA ARG A4180 " pdb=" C ARG A4180 " ideal model delta sigma weight residual 1.523 1.381 0.142 1.10e-02 8.26e+03 1.66e+02 bond pdb=" CG TYR G4988 " pdb=" CD1 TYR G4988 " ideal model delta sigma weight residual 1.389 1.120 0.269 2.10e-02 2.27e+03 1.64e+02 bond pdb=" CA ARG E4180 " pdb=" C ARG E4180 " ideal model delta sigma weight residual 1.523 1.382 0.141 1.10e-02 8.26e+03 1.64e+02 bond pdb=" C ILE E4190 " pdb=" O ILE E4190 " ideal model delta sigma weight residual 1.234 1.118 0.116 9.50e-03 1.11e+04 1.50e+02 ... (remaining 112939 not shown) Histogram of bond angle deviations from ideal: 85.86 - 97.24: 87 97.24 - 108.61: 10079 108.61 - 119.99: 89859 119.99 - 131.37: 52606 131.37 - 142.75: 377 Bond angle restraints: 153008 Sorted by residual: angle pdb=" C ASP G4083 " pdb=" N PRO G4084 " pdb=" CA PRO G4084 " ideal model delta sigma weight residual 119.84 142.75 -22.91 1.25e+00 6.40e-01 3.36e+02 angle pdb=" C GLU E 915 " pdb=" N PRO E 916 " pdb=" CA PRO E 916 " ideal model delta sigma weight residual 119.84 142.71 -22.87 1.25e+00 6.40e-01 3.35e+02 angle pdb=" C GLU G 915 " pdb=" N PRO G 916 " pdb=" CA PRO G 916 " ideal model delta sigma weight residual 119.84 142.69 -22.85 1.25e+00 6.40e-01 3.34e+02 angle pdb=" C GLU C 915 " pdb=" N PRO C 916 " pdb=" CA PRO C 916 " ideal model delta sigma weight residual 119.84 142.56 -22.72 1.25e+00 6.40e-01 3.30e+02 angle pdb=" C GLU A 915 " pdb=" N PRO A 916 " pdb=" CA PRO A 916 " ideal model delta sigma weight residual 119.84 142.56 -22.72 1.25e+00 6.40e-01 3.30e+02 ... (remaining 153003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.51: 65993 26.51 - 53.02: 1085 53.02 - 79.54: 99 79.54 - 106.05: 29 106.05 - 132.56: 40 Dihedral angle restraints: 67246 sinusoidal: 23798 harmonic: 43448 Sorted by residual: dihedral pdb=" CA PRO A2361 " pdb=" C PRO A2361 " pdb=" N GLU A2362 " pdb=" CA GLU A2362 " ideal model delta harmonic sigma weight residual -180.00 -47.44 -132.56 0 5.00e+00 4.00e-02 7.03e+02 dihedral pdb=" CA PRO G2361 " pdb=" C PRO G2361 " pdb=" N GLU G2362 " pdb=" CA GLU G2362 " ideal model delta harmonic sigma weight residual -180.00 -47.48 -132.52 0 5.00e+00 4.00e-02 7.02e+02 dihedral pdb=" CA PRO C2361 " pdb=" C PRO C2361 " pdb=" N GLU C2362 " pdb=" CA GLU C2362 " ideal model delta harmonic sigma weight residual -180.00 -47.51 -132.49 0 5.00e+00 4.00e-02 7.02e+02 ... (remaining 67243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 16191 0.193 - 0.387: 1199 0.387 - 0.580: 96 0.580 - 0.774: 18 0.774 - 0.967: 4 Chirality restraints: 17508 Sorted by residual: chirality pdb=" CA TYR G4177 " pdb=" N TYR G4177 " pdb=" C TYR G4177 " pdb=" CB TYR G4177 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA TYR E4177 " pdb=" N TYR E4177 " pdb=" C TYR E4177 " pdb=" CB TYR E4177 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" CA TYR C4177 " pdb=" N TYR C4177 " pdb=" C TYR C4177 " pdb=" CB TYR C4177 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.22e+01 ... (remaining 17505 not shown) Planarity restraints: 19816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E4205 " -0.125 2.00e-02 2.50e+03 7.85e-02 1.54e+02 pdb=" CG TRP E4205 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP E4205 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP E4205 " 0.082 2.00e-02 2.50e+03 pdb=" NE1 TRP E4205 " 0.084 2.00e-02 2.50e+03 pdb=" CE2 TRP E4205 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP E4205 " 0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP E4205 " -0.108 2.00e-02 2.50e+03 pdb=" CZ3 TRP E4205 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP E4205 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A4205 " -0.125 2.00e-02 2.50e+03 7.83e-02 1.53e+02 pdb=" CG TRP A4205 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A4205 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A4205 " 0.082 2.00e-02 2.50e+03 pdb=" NE1 TRP A4205 " 0.083 2.00e-02 2.50e+03 pdb=" CE2 TRP A4205 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP A4205 " 0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4205 " -0.107 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4205 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A4205 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C4205 " -0.125 2.00e-02 2.50e+03 7.83e-02 1.53e+02 pdb=" CG TRP C4205 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP C4205 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP C4205 " 0.082 2.00e-02 2.50e+03 pdb=" NE1 TRP C4205 " 0.084 2.00e-02 2.50e+03 pdb=" CE2 TRP C4205 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP C4205 " 0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP C4205 " -0.108 2.00e-02 2.50e+03 pdb=" CZ3 TRP C4205 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP C4205 " -0.084 2.00e-02 2.50e+03 ... (remaining 19813 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 354 2.38 - 3.01: 59589 3.01 - 3.64: 178237 3.64 - 4.27: 258773 4.27 - 4.90: 400387 Nonbonded interactions: 897340 Sorted by model distance: nonbonded pdb=" O PHE G1782 " pdb=" OH TYR H 82 " model vdw 1.755 2.440 nonbonded pdb=" O PHE A1782 " pdb=" OH TYR B 82 " model vdw 1.765 2.440 nonbonded pdb=" O PHE E1782 " pdb=" OH TYR F 82 " model vdw 1.773 2.440 nonbonded pdb=" O PHE C1782 " pdb=" OH TYR D 82 " model vdw 1.777 2.440 nonbonded pdb=" O TYR G3936 " pdb=" NZ LYS G3940 " model vdw 1.985 2.520 ... (remaining 897335 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 14.450 Check model and map are aligned: 1.230 Set scattering table: 0.800 Process input model: 275.340 Find NCS groups from input model: 5.730 Set up NCS constraints: 0.630 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 302.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.019 0.269 112944 Z= 1.253 Angle : 1.711 23.564 153008 Z= 1.082 Chirality : 0.106 0.967 17508 Planarity : 0.009 0.119 19816 Dihedral : 11.287 132.562 38958 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 2.34 % Allowed : 6.51 % Favored : 91.16 % Rotamer: Outliers : 0.51 % Allowed : 1.80 % Favored : 97.69 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.20 % 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: -2.89 (0.06), residues: 14404 helix: -2.52 (0.04), residues: 7924 sheet: -2.97 (0.14), residues: 1176 loop : -0.18 (0.09), residues: 5304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.125 0.012 TRP A4205 HIS 0.038 0.005 HIS A4983 PHE 0.093 0.011 PHE G3899 TYR 0.087 0.011 TYR C4988 ARG 0.060 0.003 ARG G4180 *********************** 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 3276 residues out of total 13160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 3198 time to evaluate : 9.587 Fit side-chains 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