Starting phenix.real_space_refine on Thu Mar 14 11:06:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv6_20486/03_2024/6pv6_20486_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv6_20486/03_2024/6pv6_20486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv6_20486/03_2024/6pv6_20486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv6_20486/03_2024/6pv6_20486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv6_20486/03_2024/6pv6_20486_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv6_20486/03_2024/6pv6_20486_neut.pdb" } resolution = 4.5 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 S 644 5.16 5 C 76496 2.51 5 N 21384 2.21 5 O 22224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 1271": "NH1" <-> "NH2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B ARG 1607": "NH1" <-> "NH2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1743": "NH1" <-> "NH2" Residue "B ARG 1797": "NH1" <-> "NH2" Residue "B ARG 1827": "NH1" <-> "NH2" Residue "B ARG 1996": "NH1" <-> "NH2" Residue "B ARG 2140": "NH1" <-> "NH2" Residue "B ARG 2355": "NH1" <-> "NH2" Residue "B ARG 2452": "NH1" <-> "NH2" Residue "B ARG 3648": "NH1" <-> "NH2" Residue "B ARG 3886": "NH1" <-> "NH2" Residue "B ARG 3904": "NH1" <-> "NH2" Residue "B ARG 3949": "NH1" <-> "NH2" Residue "B ARG 3984": "NH1" <-> "NH2" Residue "B ARG 4042": "NH1" <-> "NH2" Residue "B ARG 4137": "NH1" <-> "NH2" Residue "B ARG 4159": "NH1" <-> "NH2" Residue "B ARG 4175": "NH1" <-> "NH2" Residue "B ARG 4192": "NH1" <-> "NH2" Residue "B ARG 4548": "NH1" <-> "NH2" Residue "B ARG 4557": "NH1" <-> "NH2" Residue "B ARG 4563": "NH1" <-> "NH2" Residue "B ARG 4673": "NH1" <-> "NH2" Residue "B ARG 4703": "NH1" <-> "NH2" Residue "B ARG 4722": "NH1" <-> "NH2" Residue "B ARG 4734": "NH1" <-> "NH2" Residue "B ARG 4736": "NH1" <-> "NH2" Residue "B PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4824": "NH1" <-> "NH2" Residue "B ARG 4860": "NH1" <-> "NH2" Residue "B ARG 4892": "NH1" <-> "NH2" Residue "B ARG 4913": "NH1" <-> "NH2" Residue "B ARG 5017": "NH1" <-> "NH2" Residue "B ARG 5029": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E ARG 1271": "NH1" <-> "NH2" Residue "E ARG 1594": "NH1" <-> "NH2" Residue "E ARG 1607": "NH1" <-> "NH2" Residue "E ARG 1656": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1743": "NH1" <-> "NH2" Residue "E ARG 1797": "NH1" <-> "NH2" Residue "E ARG 1827": "NH1" <-> "NH2" Residue "E ARG 1996": "NH1" <-> "NH2" Residue "E ARG 2140": "NH1" <-> "NH2" Residue "E ARG 2355": "NH1" <-> "NH2" Residue "E ARG 2452": "NH1" <-> "NH2" Residue "E ARG 3648": "NH1" <-> "NH2" Residue "E ARG 3886": "NH1" <-> "NH2" Residue "E ARG 3904": "NH1" <-> "NH2" Residue "E ARG 3949": "NH1" <-> "NH2" Residue "E ARG 3984": "NH1" <-> "NH2" Residue "E ARG 4042": "NH1" <-> "NH2" Residue "E ARG 4137": "NH1" <-> "NH2" Residue "E ARG 4159": "NH1" <-> "NH2" Residue "E ARG 4175": "NH1" <-> "NH2" Residue "E ARG 4192": "NH1" <-> "NH2" Residue "E ARG 4548": "NH1" <-> "NH2" Residue "E ARG 4557": "NH1" <-> "NH2" Residue "E ARG 4563": "NH1" <-> "NH2" Residue "E ARG 4673": "NH1" <-> "NH2" Residue "E ARG 4703": "NH1" <-> "NH2" Residue "E ARG 4722": "NH1" <-> "NH2" Residue "E ARG 4734": "NH1" <-> "NH2" Residue "E ARG 4736": "NH1" <-> "NH2" Residue "E PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4824": "NH1" <-> "NH2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E ARG 4913": "NH1" <-> "NH2" Residue "E ARG 5017": "NH1" <-> "NH2" Residue "E ARG 5029": "NH1" <-> "NH2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 266": "NH1" <-> "NH2" Residue "I ARG 426": "NH1" <-> "NH2" Residue "I ARG 553": "NH1" <-> "NH2" Residue "I ARG 1271": "NH1" <-> "NH2" Residue "I ARG 1594": "NH1" <-> "NH2" Residue "I ARG 1607": "NH1" <-> "NH2" Residue "I ARG 1656": "NH1" <-> "NH2" Residue "I ARG 1725": "NH1" <-> "NH2" Residue "I ARG 1743": "NH1" <-> "NH2" Residue "I ARG 1797": "NH1" <-> "NH2" Residue "I ARG 1827": "NH1" <-> "NH2" Residue "I ARG 1996": "NH1" <-> "NH2" Residue "I ARG 2140": "NH1" <-> "NH2" Residue "I ARG 2355": "NH1" <-> "NH2" Residue "I ARG 2452": "NH1" <-> "NH2" Residue "I ARG 3648": "NH1" <-> "NH2" Residue "I ARG 3886": "NH1" <-> "NH2" Residue "I ARG 3904": "NH1" <-> "NH2" Residue "I ARG 3949": "NH1" <-> "NH2" Residue "I ARG 3984": "NH1" <-> "NH2" Residue "I ARG 4042": "NH1" <-> "NH2" Residue "I ARG 4137": "NH1" <-> "NH2" Residue "I ARG 4159": "NH1" <-> "NH2" Residue "I ARG 4175": "NH1" <-> "NH2" Residue "I ARG 4192": "NH1" <-> "NH2" Residue "I ARG 4548": "NH1" <-> "NH2" Residue "I ARG 4557": "NH1" <-> "NH2" Residue "I ARG 4563": "NH1" <-> "NH2" Residue "I ARG 4673": "NH1" <-> "NH2" Residue "I ARG 4703": "NH1" <-> "NH2" Residue "I ARG 4722": "NH1" <-> "NH2" Residue "I ARG 4734": "NH1" <-> "NH2" Residue "I ARG 4736": "NH1" <-> "NH2" Residue "I PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4824": "NH1" <-> "NH2" Residue "I ARG 4860": "NH1" <-> "NH2" Residue "I ARG 4892": "NH1" <-> "NH2" Residue "I ARG 4913": "NH1" <-> "NH2" Residue "I ARG 5017": "NH1" <-> "NH2" Residue "I ARG 5029": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 266": "NH1" <-> "NH2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 553": "NH1" <-> "NH2" Residue "G ARG 1271": "NH1" <-> "NH2" Residue "G ARG 1594": "NH1" <-> "NH2" Residue "G ARG 1607": "NH1" <-> "NH2" Residue "G ARG 1656": "NH1" <-> "NH2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 1743": "NH1" <-> "NH2" Residue "G ARG 1797": "NH1" <-> "NH2" Residue "G ARG 1827": "NH1" <-> "NH2" Residue "G ARG 1996": "NH1" <-> "NH2" Residue "G ARG 2140": "NH1" <-> "NH2" Residue "G ARG 2355": "NH1" <-> "NH2" Residue "G ARG 2452": "NH1" <-> "NH2" Residue "G ARG 3648": "NH1" <-> "NH2" Residue "G ARG 3886": "NH1" <-> "NH2" Residue "G ARG 3904": "NH1" <-> "NH2" Residue "G ARG 3949": "NH1" <-> "NH2" Residue "G ARG 3984": "NH1" <-> "NH2" Residue "G ARG 4042": "NH1" <-> "NH2" Residue "G ARG 4137": "NH1" <-> "NH2" Residue "G ARG 4159": "NH1" <-> "NH2" Residue "G ARG 4175": "NH1" <-> "NH2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4548": "NH1" <-> "NH2" Residue "G ARG 4557": "NH1" <-> "NH2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G ARG 4673": "NH1" <-> "NH2" Residue "G ARG 4703": "NH1" <-> "NH2" Residue "G ARG 4722": "NH1" <-> "NH2" Residue "G ARG 4734": "NH1" <-> "NH2" Residue "G ARG 4736": "NH1" <-> "NH2" Residue "G PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4824": "NH1" <-> "NH2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G ARG 4913": "NH1" <-> "NH2" Residue "G ARG 5017": "NH1" <-> "NH2" Residue "G ARG 5029": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 120756 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 29369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4168, 29369 Classifications: {'peptide': 4168} Incomplete info: {'truncation_to_alanine': 1246} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4010} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3027 Unresolved non-hydrogen angles: 4229 Unresolved non-hydrogen dihedrals: 1879 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "E" Number of atoms: 29369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4168, 29369 Classifications: {'peptide': 4168} Incomplete info: {'truncation_to_alanine': 1246} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4010} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3027 Unresolved non-hydrogen angles: 4229 Unresolved non-hydrogen dihedrals: 1879 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "I" Number of atoms: 29369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4168, 29369 Classifications: {'peptide': 4168} Incomplete info: {'truncation_to_alanine': 1246} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4010} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3027 Unresolved non-hydrogen angles: 4229 Unresolved non-hydrogen dihedrals: 1879 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "G" Number of atoms: 29369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4168, 29369 Classifications: {'peptide': 4168} Incomplete info: {'truncation_to_alanine': 1246} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4010} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3027 Unresolved non-hydrogen angles: 4229 Unresolved non-hydrogen dihedrals: 1879 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 83, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1760 Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28698 SG CYS B4958 177.430 204.856 88.631 1.00 0.00 S ATOM 28723 SG CYS B4961 179.507 204.537 92.126 1.00 0.00 S ATOM 58067 SG CYS E4958 203.954 207.068 88.665 1.00 0.00 S ATOM 58092 SG CYS E4961 203.638 204.989 92.159 1.00 0.00 S ATOM 87436 SG CYS I4958 179.518 178.382 88.559 1.00 0.00 S ATOM 87461 SG CYS I4961 179.836 180.447 92.062 1.00 0.00 S ATOM A0CYT SG CYS G4958 205.855 180.624 88.529 1.00 0.00 S ATOM A0CZI SG CYS G4961 203.794 180.935 92.034 1.00 0.00 S Time building chain proxies: 44.66, per 1000 atoms: 0.37 Number of scatterers: 120756 At special positions: 0 Unit cell: (385.285, 386.54, 213.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 644 16.00 O 22224 8.00 N 21384 7.00 C 76496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.71 Conformation dependent library (CDL) restraints added in 13.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" ND1 HIS E4983 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4961 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4958 " pdb="ZN ZN E5101 " - pdb=" NE2 HIS E4978 " pdb=" ZN G5101 " pdb="ZN ZN G5101 " - pdb=" ND1 HIS G4983 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4958 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4961 " pdb="ZN ZN G5101 " - pdb=" NE2 HIS G4978 " pdb=" ZN I5101 " pdb="ZN ZN I5101 " - pdb=" ND1 HIS I4983 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4958 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4961 " pdb="ZN ZN I5101 " - pdb=" NE2 HIS I4978 " Number of angles added : 8 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32360 Finding SS restraints... Secondary structure from input PDB file: 716 helices and 116 sheets defined 61.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.39 Creating SS restraints... Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.600A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.198A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 419 removed outlier: 3.814A pdb=" N GLN B 399 " --> pdb=" O GLN B 395 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 removed outlier: 4.091A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 481 removed outlier: 3.744A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 473 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.730A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 529 removed outlier: 4.395A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.823A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 596 through 608 removed outlier: 3.767A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.670A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 622 " --> pdb=" O GLN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 888 removed outlier: 3.733A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 934 removed outlier: 3.735A pdb=" N ASN B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 930 " --> pdb=" O GLY B 926 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 999 removed outlier: 3.772A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 989 " --> pdb=" O VAL B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1038 removed outlier: 3.663A pdb=" N LYS B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1049 removed outlier: 3.963A pdb=" N ARG B1044 " --> pdb=" O CYS B1040 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B1046 " --> pdb=" O ALA B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1575 through 1579 removed outlier: 3.576A pdb=" N MET B1579 " --> pdb=" O SER B1576 " (cutoff:3.500A) Processing helix chain 'B' and resid 1623 through 1627 Processing helix chain 'B' and resid 1652 through 1657 removed outlier: 3.572A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1674 removed outlier: 3.782A pdb=" N HIS B1665 " --> pdb=" O ARG B1661 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B1670 " --> pdb=" O THR B1666 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B1671 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1683 Processing helix chain 'B' and resid 1684 through 1688 Processing helix chain 'B' and resid 1692 through 1700 removed outlier: 4.223A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1711 Processing helix chain 'B' and resid 1715 through 1730 removed outlier: 4.898A pdb=" N GLU B1721 " --> pdb=" O SER B1717 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER B1722 " --> pdb=" O ILE B1718 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B1723 " --> pdb=" O HIS B1719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B1725 " --> pdb=" O GLU B1721 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1824 removed outlier: 3.651A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B1813 " --> pdb=" O ASP B1809 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B1814 " --> pdb=" O LYS B1810 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B1819 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B1820 " --> pdb=" O GLY B1816 " (cutoff:3.500A) Processing helix chain 'B' and resid 1829 through 1832 Processing helix chain 'B' and resid 1833 through 1838 Processing helix chain 'B' and resid 1840 through 1851 removed outlier: 3.606A pdb=" N LEU B1848 " --> pdb=" O LEU B1844 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1863 Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1933 through 1981 removed outlier: 3.580A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B1966 " --> pdb=" O ALA B1962 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B1978 " --> pdb=" O ARG B1974 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B1979 " --> pdb=" O SER B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1994 removed outlier: 3.772A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1995 through 1998 Processing helix chain 'B' and resid 2001 through 2014 removed outlier: 3.578A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE B2012 " --> pdb=" O MET B2008 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B2013 " --> pdb=" O LEU B2009 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B2014 " --> pdb=" O LEU B2010 " (cutoff:3.500A) Processing helix chain 'B' and resid 2026 through 2042 removed outlier: 3.619A pdb=" N ASP B2030 " --> pdb=" O ASP B2026 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2108 removed outlier: 3.630A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2127 removed outlier: 3.579A pdb=" N PHE B2121 " --> pdb=" O VAL B2117 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B2123 " --> pdb=" O ALA B2119 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B2124 " --> pdb=" O MET B2120 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2138 Processing helix chain 'B' and resid 2139 through 2141 No H-bonds generated for 'chain 'B' and resid 2139 through 2141' Processing helix chain 'B' and resid 2148 through 2165 removed outlier: 3.522A pdb=" N LEU B2155 " --> pdb=" O ASP B2151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B2165 " --> pdb=" O GLN B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2186 removed outlier: 3.649A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B2184 " --> pdb=" O GLN B2180 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2201 removed outlier: 3.925A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B2200 " --> pdb=" O ASN B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2216 removed outlier: 3.503A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2242 removed outlier: 3.557A pdb=" N CYS B2233 " --> pdb=" O VAL B2229 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B2235 " --> pdb=" O SER B2231 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B2238 " --> pdb=" O ARG B2234 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2253 removed outlier: 4.336A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2262 removed outlier: 3.981A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 Processing helix chain 'B' and resid 2294 through 2306 removed outlier: 3.515A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2317 removed outlier: 3.883A pdb=" N ALA B2315 " --> pdb=" O MET B2312 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B2316 " --> pdb=" O LEU B2313 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B2317 " --> pdb=" O LEU B2314 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2331 removed outlier: 3.722A pdb=" N TYR B2331 " --> pdb=" O GLY B2327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2335 through 2339 removed outlier: 4.092A pdb=" N ALA B2338 " --> pdb=" O LEU B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2350 through 2358 removed outlier: 3.706A pdb=" N LEU B2356 " --> pdb=" O VAL B2352 " (cutoff:3.500A) Processing helix chain 'B' and resid 2360 through 2364 Processing helix chain 'B' and resid 2377 through 2388 Processing helix chain 'B' and resid 2389 through 2393 Processing helix chain 'B' and resid 2417 through 2436 removed outlier: 3.792A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B2428 " --> pdb=" O SER B2424 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B2433 " --> pdb=" O LEU B2429 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2445 Processing helix chain 'B' and resid 2448 through 2459 Processing helix chain 'B' and resid 2466 through 2471 Processing helix chain 'B' and resid 2499 through 2507 removed outlier: 3.720A pdb=" N UNK B2503 " --> pdb=" O UNK B2499 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N UNK B2505 " --> pdb=" O UNK B2501 " (cutoff:3.500A) Processing helix chain 'B' and resid 2517 through 2530 removed outlier: 3.544A pdb=" N UNK B2522 " --> pdb=" O UNK B2518 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N UNK B2523 " --> pdb=" O UNK B2519 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N UNK B2526 " --> pdb=" O UNK B2522 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N UNK B2527 " --> pdb=" O UNK B2523 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNK B2528 " --> pdb=" O UNK B2524 " (cutoff:3.500A) Processing helix chain 'B' and resid 2542 through 2548 removed outlier: 3.781A pdb=" N UNK B2546 " --> pdb=" O UNK B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2557 removed outlier: 3.706A pdb=" N UNK B2555 " --> pdb=" O UNK B2551 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2581 Processing helix chain 'B' and resid 2587 through 2602 Processing helix chain 'B' and resid 2610 through 2618 removed outlier: 3.534A pdb=" N UNK B2617 " --> pdb=" O UNK B2613 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N UNK B2618 " --> pdb=" O UNK B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2626 through 2641 removed outlier: 3.915A pdb=" N UNK B2630 " --> pdb=" O UNK B2626 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK B2631 " --> pdb=" O UNK B2627 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N UNK B2639 " --> pdb=" O UNK B2635 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N UNK B2641 " --> pdb=" O UNK B2637 " (cutoff:3.500A) Processing helix chain 'B' and resid 2650 through 2666 removed outlier: 3.578A pdb=" N UNK B2666 " --> pdb=" O UNK B2662 " (cutoff:3.500A) Processing helix chain 'B' and resid 2677 through 2683 removed outlier: 3.880A pdb=" N UNK B2681 " --> pdb=" O UNK B2677 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N UNK B2683 " --> pdb=" O UNK B2679 " (cutoff:3.500A) Processing helix chain 'B' and resid 2684 through 2687 removed outlier: 3.861A pdb=" N UNK B2687 " --> pdb=" O UNK B2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2684 through 2687' Processing helix chain 'B' and resid 2748 through 2773 removed outlier: 4.244A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.614A pdb=" N PHE B2797 " --> pdb=" O TYR B2794 " (cutoff:3.500A) Processing helix chain 'B' and resid 2800 through 2804 removed outlier: 3.521A pdb=" N ILE B2804 " --> pdb=" O ASP B2801 " (cutoff:3.500A) Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 4.159A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B2816 " --> pdb=" O SER B2812 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B2817 " --> pdb=" O LEU B2813 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 3.831A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP B2886 " --> pdb=" O TYR B2882 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2911 removed outlier: 3.534A pdb=" N THR B2910 " --> pdb=" O PRO B2907 " (cutoff:3.500A) Processing helix chain 'B' and resid 2914 through 2932 removed outlier: 3.748A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B2920 " --> pdb=" O LYS B2916 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2976 removed outlier: 4.191A pdb=" N UNK B2956 " --> pdb=" O UNK B2952 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK B2968 " --> pdb=" O UNK B2964 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N UNK B2969 " --> pdb=" O UNK B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3015 removed outlier: 3.549A pdb=" N UNK B3001 " --> pdb=" O UNK B2997 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N UNK B3006 " --> pdb=" O UNK B3002 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) Processing helix chain 'B' and resid 3017 through 3022 Processing helix chain 'B' and resid 3029 through 3040 removed outlier: 3.558A pdb=" N UNK B3037 " --> pdb=" O UNK B3033 " (cutoff:3.500A) Processing helix chain 'B' and resid 3048 through 3051 removed outlier: 3.683A pdb=" N UNK B3051 " --> pdb=" O UNK B3048 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3048 through 3051' Processing helix chain 'B' and resid 3052 through 3063 removed outlier: 4.089A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N UNK B3057 " --> pdb=" O UNK B3053 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N UNK B3061 " --> pdb=" O UNK B3057 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N UNK B3062 " --> pdb=" O UNK B3058 " (cutoff:3.500A) Processing helix chain 'B' and resid 3141 through 3146 Processing helix chain 'B' and resid 3146 through 3163 removed outlier: 4.136A pdb=" N UNK B3154 " --> pdb=" O UNK B3150 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3186 removed outlier: 3.679A pdb=" N UNK B3182 " --> pdb=" O UNK B3178 " (cutoff:3.500A) Processing helix chain 'B' and resid 3198 through 3212 removed outlier: 3.513A pdb=" N UNK B3205 " --> pdb=" O UNK B3201 " (cutoff:3.500A) Processing helix chain 'B' and resid 3224 through 3230 removed outlier: 3.676A pdb=" N UNK B3228 " --> pdb=" O UNK B3224 " (cutoff:3.500A) Processing helix chain 'B' and resid 3231 through 3234 Processing helix chain 'B' and resid 3244 through 3248 removed outlier: 3.781A pdb=" N UNK B3248 " --> pdb=" O UNK B3245 " (cutoff:3.500A) Processing helix chain 'B' and resid 3249 through 3254 Processing helix chain 'B' and resid 3271 through 3285 removed outlier: 3.841A pdb=" N UNK B3281 " --> pdb=" O UNK B3277 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N UNK B3282 " --> pdb=" O UNK B3278 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK B3284 " --> pdb=" O UNK B3280 " (cutoff:3.500A) Processing helix chain 'B' and resid 3301 through 3304 Processing helix chain 'B' and resid 3305 through 3310 Processing helix chain 'B' and resid 3316 through 3331 removed outlier: 3.736A pdb=" N UNK B3323 " --> pdb=" O UNK B3319 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N UNK B3324 " --> pdb=" O UNK B3320 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N UNK B3325 " --> pdb=" O UNK B3321 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK B3330 " --> pdb=" O UNK B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3349 removed outlier: 3.701A pdb=" N UNK B3348 " --> pdb=" O UNK B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3361 through 3388 Processing helix chain 'B' and resid 3399 through 3409 removed outlier: 3.861A pdb=" N UNK B3405 " --> pdb=" O UNK B3401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N UNK B3407 " --> pdb=" O UNK B3403 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N UNK B3409 " --> pdb=" O UNK B3405 " (cutoff:3.500A) Processing helix chain 'B' and resid 3410 through 3425 removed outlier: 4.281A pdb=" N UNK B3416 " --> pdb=" O UNK B3412 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK B3417 " --> pdb=" O UNK B3413 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N UNK B3420 " --> pdb=" O UNK B3416 " (cutoff:3.500A) Processing helix chain 'B' and resid 3437 through 3443 removed outlier: 3.589A pdb=" N UNK B3441 " --> pdb=" O UNK B3437 " (cutoff:3.500A) Processing helix chain 'B' and resid 3445 through 3450 Processing helix chain 'B' and resid 3457 through 3460 Processing helix chain 'B' and resid 3461 through 3468 removed outlier: 3.510A pdb=" N UNK B3468 " --> pdb=" O UNK B3464 " (cutoff:3.500A) Processing helix chain 'B' and resid 3522 through 3527 Processing helix chain 'B' and resid 3541 through 3547 Processing helix chain 'B' and resid 3551 through 3560 Processing helix chain 'B' and resid 3574 through 3583 removed outlier: 3.661A pdb=" N UNK B3579 " --> pdb=" O UNK B3575 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N UNK B3580 " --> pdb=" O UNK B3576 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N UNK B3583 " --> pdb=" O UNK B3579 " (cutoff:3.500A) Processing helix chain 'B' and resid 3588 through 3611 removed outlier: 3.884A pdb=" N UNK B3592 " --> pdb=" O UNK B3588 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N UNK B3595 " --> pdb=" O UNK B3591 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N UNK B3598 " --> pdb=" O UNK B3594 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N UNK B3600 " --> pdb=" O UNK B3596 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N UNK B3601 " --> pdb=" O UNK B3597 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N UNK B3611 " --> pdb=" O UNK B3607 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 removed outlier: 3.536A pdb=" N ASN B3651 " --> pdb=" O HIS B3647 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) Processing helix chain 'B' and resid 3657 through 3661 Processing helix chain 'B' and resid 3671 through 3680 removed outlier: 4.312A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) Processing helix chain 'B' and resid 3681 through 3683 No H-bonds generated for 'chain 'B' and resid 3681 through 3683' Processing helix chain 'B' and resid 3696 through 3708 Processing helix chain 'B' and resid 3719 through 3734 removed outlier: 3.714A pdb=" N ASP B3727 " --> pdb=" O MET B3723 " (cutoff:3.500A) Processing helix chain 'B' and resid 3736 through 3741 removed outlier: 3.875A pdb=" N GLU B3740 " --> pdb=" O GLU B3736 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B3741 " --> pdb=" O GLU B3737 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3736 through 3741' Processing helix chain 'B' and resid 3752 through 3758 Processing helix chain 'B' and resid 3764 through 3769 Processing helix chain 'B' and resid 3770 through 3773 removed outlier: 4.658A pdb=" N ARG B3773 " --> pdb=" O LEU B3770 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3770 through 3773' Processing helix chain 'B' and resid 3774 through 3785 removed outlier: 4.501A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3805 removed outlier: 3.843A pdb=" N LEU B3805 " --> pdb=" O GLY B3801 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3828 through 3838 removed outlier: 3.519A pdb=" N ILE B3832 " --> pdb=" O PHE B3828 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3856 Processing helix chain 'B' and resid 3877 through 3892 removed outlier: 4.430A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3903 Processing helix chain 'B' and resid 3914 through 3938 removed outlier: 4.010A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B3920 " --> pdb=" O ILE B3916 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP B3921 " --> pdb=" O ILE B3917 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B3922 " --> pdb=" O CYS B3918 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B3923 " --> pdb=" O THR B3919 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B3929 " --> pdb=" O ARG B3925 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B3934 " --> pdb=" O ILE B3930 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3968 removed outlier: 3.673A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B3959 " --> pdb=" O MET B3955 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B3961 " --> pdb=" O VAL B3957 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B3966 " --> pdb=" O PHE B3962 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3981 Processing helix chain 'B' and resid 3984 through 4004 removed outlier: 3.663A pdb=" N VAL B3990 " --> pdb=" O TRP B3986 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B3992 " --> pdb=" O ALA B3988 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B3993 " --> pdb=" O VAL B3989 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B4004 " --> pdb=" O MET B4000 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4030 removed outlier: 3.836A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4051 removed outlier: 3.813A pdb=" N ASP B4046 " --> pdb=" O ARG B4042 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B4048 " --> pdb=" O MET B4044 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B4050 " --> pdb=" O ASP B4046 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4066 removed outlier: 3.701A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) Processing helix chain 'B' and resid 4066 through 4072 removed outlier: 4.142A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4079 Processing helix chain 'B' and resid 4090 through 4100 Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4117 through 4122 removed outlier: 3.510A pdb=" N GLU B4121 " --> pdb=" O ALA B4117 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B4122 " --> pdb=" O ASP B4118 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4117 through 4122' Processing helix chain 'B' and resid 4124 through 4129 Processing helix chain 'B' and resid 4132 through 4154 removed outlier: 3.551A pdb=" N ALA B4136 " --> pdb=" O PHE B4132 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU B4152 " --> pdb=" O THR B4148 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B4154 " --> pdb=" O LEU B4150 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 removed outlier: 4.253A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B4166 " --> pdb=" O ASN B4162 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B4167 " --> pdb=" O PHE B4163 " (cutoff:3.500A) Processing helix chain 'B' and resid 4167 through 4175 Processing helix chain 'B' and resid 4198 through 4206 Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 3.511A pdb=" N ASP B4220 " --> pdb=" O GLN B4216 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4250 removed outlier: 4.651A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B4235 " --> pdb=" O MET B4231 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B4249 " --> pdb=" O MET B4245 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B4250 " --> pdb=" O GLN B4246 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4556 removed outlier: 3.573A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4576 removed outlier: 3.869A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B4573 " --> pdb=" O LEU B4569 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B4574 " --> pdb=" O ALA B4570 " (cutoff:3.500A) Processing helix chain 'B' and resid 4641 through 4664 removed outlier: 3.885A pdb=" N ALA B4654 " --> pdb=" O HIS B4650 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B4655 " --> pdb=" O THR B4651 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B4658 " --> pdb=" O ALA B4654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) Processing helix chain 'B' and resid 4667 through 4683 removed outlier: 3.643A pdb=" N LEU B4677 " --> pdb=" O ARG B4673 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B4678 " --> pdb=" O GLU B4674 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4702 Processing helix chain 'B' and resid 4710 through 4714 removed outlier: 3.546A pdb=" N SER B4713 " --> pdb=" O SER B4710 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN B4714 " --> pdb=" O PHE B4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4710 through 4714' Processing helix chain 'B' and resid 4719 through 4729 Processing helix chain 'B' and resid 4733 through 4741 Processing helix chain 'B' and resid 4745 through 4753 removed outlier: 4.066A pdb=" N THR B4751 " --> pdb=" O SER B4747 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B4753 " --> pdb=" O GLU B4749 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4784 removed outlier: 3.547A pdb=" N GLY B4781 " --> pdb=" O ILE B4777 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4802 removed outlier: 3.888A pdb=" N LEU B4790 " --> pdb=" O ASP B4786 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B4798 " --> pdb=" O TRP B4794 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B4799 " --> pdb=" O TYR B4795 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B4800 " --> pdb=" O MET B4796 " (cutoff:3.500A) Processing helix chain 'B' and resid 4810 through 4816 removed outlier: 3.600A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4810 through 4816' Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.667A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 removed outlier: 3.952A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B4842 " --> pdb=" O VAL B4838 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B4843 " --> pdb=" O MET B4839 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B4845 " --> pdb=" O VAL B4841 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B4848 " --> pdb=" O LEU B4844 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B4853 " --> pdb=" O TYR B4849 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B4855 " --> pdb=" O TYR B4851 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B4857 " --> pdb=" O VAL B4853 " (cutoff:3.500A) Processing helix chain 'B' and resid 4859 through 4863 removed outlier: 3.915A pdb=" N PHE B4862 " --> pdb=" O PHE B4859 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4859 through 4863' Processing helix chain 'B' and resid 4878 through 4889 removed outlier: 3.554A pdb=" N TYR B4883 " --> pdb=" O MET B4879 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B4885 " --> pdb=" O THR B4881 " (cutoff:3.500A) Processing helix chain 'B' and resid 4889 through 4894 removed outlier: 4.384A pdb=" N GLY B4894 " --> pdb=" O GLY B4890 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 removed outlier: 3.806A pdb=" N ASP B4899 " --> pdb=" O GLY B4896 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B4900 " --> pdb=" O ILE B4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4896 through 4900' Processing helix chain 'B' and resid 4909 through 4924 removed outlier: 4.384A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP B4917 " --> pdb=" O ARG B4913 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B4918 " --> pdb=" O VAL B4914 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B4924 " --> pdb=" O PHE B4920 " (cutoff:3.500A) Processing helix chain 'B' and resid 4924 through 4955 removed outlier: 4.095A pdb=" N LEU B4929 " --> pdb=" O ILE B4925 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B4930 " --> pdb=" O VAL B4926 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B4937 " --> pdb=" O GLN B4933 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B4938 " --> pdb=" O GLY B4934 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B4939 " --> pdb=" O LEU B4935 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B4940 " --> pdb=" O ILE B4936 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP B4945 " --> pdb=" O GLY B4941 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B4948 " --> pdb=" O ARG B4944 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B4950 " --> pdb=" O GLN B4946 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP B4953 " --> pdb=" O GLN B4949 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B4954 " --> pdb=" O VAL B4950 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 3.905A pdb=" N TYR B4967 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP B4969 " --> pdb=" O ASP B4966 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B4970 " --> pdb=" O TYR B4967 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4982 Processing helix chain 'B' and resid 4985 through 4997 removed outlier: 3.594A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) Processing helix chain 'B' and resid 5006 through 5017 Processing helix chain 'B' and resid 5032 through 5037 Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.599A pdb=" N THR E 254 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 removed outlier: 4.197A pdb=" N LEU E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 419 removed outlier: 3.814A pdb=" N GLN E 399 " --> pdb=" O GLN E 395 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP E 419 " --> pdb=" O ILE E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 452 removed outlier: 4.092A pdb=" N GLY E 450 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 481 removed outlier: 3.743A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN E 473 " --> pdb=" O ARG E 469 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 478 " --> pdb=" O ARG E 474 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 493 removed outlier: 3.731A pdb=" N VAL E 487 " --> pdb=" O MET E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 529 removed outlier: 4.395A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU E 524 " --> pdb=" O ASN E 520 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 528 " --> pdb=" O GLU E 524 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 529 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 543 through 548 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 571 through 576 removed outlier: 3.824A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 594 Processing helix chain 'E' and resid 596 through 608 removed outlier: 3.767A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 625 removed outlier: 3.670A pdb=" N ASP E 619 " --> pdb=" O ARG E 615 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR E 622 " --> pdb=" O GLN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 888 removed outlier: 3.733A pdb=" N GLU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS E 873 " --> pdb=" O ARG E 869 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 887 " --> pdb=" O ALA E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 934 removed outlier: 3.735A pdb=" N ASN E 919 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU E 929 " --> pdb=" O SER E 925 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS E 930 " --> pdb=" O GLY E 926 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA E 934 " --> pdb=" O LYS E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 980 through 999 removed outlier: 3.772A pdb=" N LEU E 984 " --> pdb=" O ALA E 980 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA E 989 " --> pdb=" O VAL E 985 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1038 removed outlier: 3.661A pdb=" N LYS E1032 " --> pdb=" O ASP E1028 " (cutoff:3.500A) Processing helix chain 'E' and resid 1039 through 1049 removed outlier: 3.964A pdb=" N ARG E1044 " --> pdb=" O CYS E1040 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR E1045 " --> pdb=" O GLN E1041 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E1046 " --> pdb=" O ALA E1042 " (cutoff:3.500A) Processing helix chain 'E' and resid 1575 through 1579 removed outlier: 3.577A pdb=" N MET E1579 " --> pdb=" O SER E1576 " (cutoff:3.500A) Processing helix chain 'E' and resid 1623 through 1627 Processing helix chain 'E' and resid 1652 through 1657 removed outlier: 3.571A pdb=" N LEU E1657 " --> pdb=" O LEU E1653 " (cutoff:3.500A) Processing helix chain 'E' and resid 1658 through 1674 removed outlier: 3.781A pdb=" N HIS E1665 " --> pdb=" O ARG E1661 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR E1670 " --> pdb=" O THR E1666 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E1671 " --> pdb=" O LEU E1667 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1683 Processing helix chain 'E' and resid 1684 through 1688 Processing helix chain 'E' and resid 1692 through 1700 removed outlier: 4.223A pdb=" N LEU E1698 " --> pdb=" O LEU E1694 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU E1699 " --> pdb=" O LEU E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1707 through 1711 Processing helix chain 'E' and resid 1715 through 1730 removed outlier: 4.899A pdb=" N GLU E1721 " --> pdb=" O SER E1717 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER E1722 " --> pdb=" O ILE E1718 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA E1723 " --> pdb=" O HIS E1719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG E1725 " --> pdb=" O GLU E1721 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 Processing helix chain 'E' and resid 1803 through 1824 removed outlier: 3.650A pdb=" N LEU E1807 " --> pdb=" O PRO E1803 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG E1813 " --> pdb=" O ASP E1809 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET E1814 " --> pdb=" O LYS E1810 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E1819 " --> pdb=" O LEU E1815 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E1820 " --> pdb=" O GLY E1816 " (cutoff:3.500A) Processing helix chain 'E' and resid 1829 through 1832 Processing helix chain 'E' and resid 1833 through 1838 Processing helix chain 'E' and resid 1840 through 1851 removed outlier: 3.607A pdb=" N LEU E1848 " --> pdb=" O LEU E1844 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET E1851 " --> pdb=" O THR E1847 " (cutoff:3.500A) Processing helix chain 'E' and resid 1855 through 1863 Processing helix chain 'E' and resid 1866 through 1871 Processing helix chain 'E' and resid 1933 through 1981 removed outlier: 3.580A pdb=" N GLN E1938 " --> pdb=" O SER E1934 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR E1945 " --> pdb=" O ASN E1941 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE E1946 " --> pdb=" O LEU E1942 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU E1963 " --> pdb=" O ALA E1959 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA E1978 " --> pdb=" O ARG E1974 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E1979 " --> pdb=" O SER E1975 " (cutoff:3.500A) Processing helix chain 'E' and resid 1989 through 1994 removed outlier: 3.773A pdb=" N ARG E1994 " --> pdb=" O GLU E1990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1995 through 1998 Processing helix chain 'E' and resid 2001 through 2014 removed outlier: 3.579A pdb=" N ASN E2007 " --> pdb=" O GLN E2003 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS E2011 " --> pdb=" O ASN E2007 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE E2012 " --> pdb=" O MET E2008 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS E2013 " --> pdb=" O LEU E2009 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP E2014 " --> pdb=" O LEU E2010 " (cutoff:3.500A) Processing helix chain 'E' and resid 2026 through 2042 removed outlier: 3.618A pdb=" N ASP E2030 " --> pdb=" O ASP E2026 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU E2031 " --> pdb=" O ILE E2027 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN E2032 " --> pdb=" O ARG E2028 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2108 removed outlier: 3.630A pdb=" N VAL E2103 " --> pdb=" O SER E2099 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2127 removed outlier: 3.579A pdb=" N PHE E2121 " --> pdb=" O VAL E2117 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU E2123 " --> pdb=" O ALA E2119 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E2124 " --> pdb=" O MET E2120 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2138 Processing helix chain 'E' and resid 2139 through 2141 No H-bonds generated for 'chain 'E' and resid 2139 through 2141' Processing helix chain 'E' and resid 2148 through 2165 removed outlier: 3.521A pdb=" N LEU E2155 " --> pdb=" O ASP E2151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E2161 " --> pdb=" O GLU E2157 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E2165 " --> pdb=" O GLN E2161 " (cutoff:3.500A) Processing helix chain 'E' and resid 2171 through 2186 removed outlier: 3.647A pdb=" N LEU E2177 " --> pdb=" O GLN E2173 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN E2184 " --> pdb=" O GLN E2180 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E2185 " --> pdb=" O SER E2181 " (cutoff:3.500A) Processing helix chain 'E' and resid 2194 through 2201 removed outlier: 3.925A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E2200 " --> pdb=" O ASN E2196 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.504A pdb=" N ASN E2213 " --> pdb=" O GLU E2209 " (cutoff:3.500A) Processing helix chain 'E' and resid 2227 through 2242 removed outlier: 3.558A pdb=" N CYS E2233 " --> pdb=" O VAL E2229 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E2235 " --> pdb=" O SER E2231 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR E2238 " --> pdb=" O ARG E2234 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2253 removed outlier: 4.336A pdb=" N HIS E2253 " --> pdb=" O SER E2249 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2262 removed outlier: 3.981A pdb=" N ASN E2260 " --> pdb=" O TYR E2256 " (cutoff:3.500A) Processing helix chain 'E' and resid 2271 through 2279 Processing helix chain 'E' and resid 2294 through 2306 removed outlier: 3.515A pdb=" N VAL E2299 " --> pdb=" O LEU E2295 " (cutoff:3.500A) Processing helix chain 'E' and resid 2311 through 2317 removed outlier: 3.884A pdb=" N ALA E2315 " --> pdb=" O MET E2312 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS E2316 " --> pdb=" O LEU E2313 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY E2317 " --> pdb=" O LEU E2314 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2331 removed outlier: 3.723A pdb=" N TYR E2331 " --> pdb=" O GLY E2327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2335 through 2339 removed outlier: 4.090A pdb=" N ALA E2338 " --> pdb=" O LEU E2335 " (cutoff:3.500A) Processing helix chain 'E' and resid 2350 through 2358 removed outlier: 3.705A pdb=" N LEU E2356 " --> pdb=" O VAL E2352 " (cutoff:3.500A) Processing helix chain 'E' and resid 2360 through 2364 Processing helix chain 'E' and resid 2377 through 2388 Processing helix chain 'E' and resid 2389 through 2393 Processing helix chain 'E' and resid 2417 through 2436 removed outlier: 3.792A pdb=" N ALA E2421 " --> pdb=" O HIS E2417 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET E2423 " --> pdb=" O GLY E2419 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA E2428 " --> pdb=" O SER E2424 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU E2433 " --> pdb=" O LEU E2429 " (cutoff:3.500A) Processing helix chain 'E' and resid 2440 through 2445 Processing helix chain 'E' and resid 2448 through 2459 Processing helix chain 'E' and resid 2466 through 2471 Processing helix chain 'E' and resid 2499 through 2507 removed outlier: 3.642A pdb=" N UNK E2503 " --> pdb=" O UNK E2499 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N UNK E2505 " --> pdb=" O UNK E2501 " (cutoff:3.500A) Processing helix chain 'E' and resid 2517 through 2530 removed outlier: 3.547A pdb=" N UNK E2522 " --> pdb=" O UNK E2518 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N UNK E2523 " --> pdb=" O UNK E2519 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N UNK E2526 " --> pdb=" O UNK E2522 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N UNK E2527 " --> pdb=" O UNK E2523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK E2528 " --> pdb=" O UNK E2524 " (cutoff:3.500A) Processing helix chain 'E' and resid 2542 through 2548 removed outlier: 3.736A pdb=" N UNK E2546 " --> pdb=" O UNK E2542 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2557 removed outlier: 3.701A pdb=" N UNK E2555 " --> pdb=" O UNK E2551 " (cutoff:3.500A) Processing helix chain 'E' and resid 2567 through 2581 Processing helix chain 'E' and resid 2587 through 2602 removed outlier: 3.500A pdb=" N UNK E2602 " --> pdb=" O UNK E2598 " (cutoff:3.500A) Processing helix chain 'E' and resid 2610 through 2618 removed outlier: 3.530A pdb=" N UNK E2617 " --> pdb=" O UNK E2613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N UNK E2618 " --> pdb=" O UNK E2614 " (cutoff:3.500A) Processing helix chain 'E' and resid 2626 through 2641 removed outlier: 3.914A pdb=" N UNK E2630 " --> pdb=" O UNK E2626 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N UNK E2631 " --> pdb=" O UNK E2627 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK E2639 " --> pdb=" O UNK E2635 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N UNK E2641 " --> pdb=" O UNK E2637 " (cutoff:3.500A) Processing helix chain 'E' and resid 2650 through 2666 removed outlier: 3.568A pdb=" N UNK E2666 " --> pdb=" O UNK E2662 " (cutoff:3.500A) Processing helix chain 'E' and resid 2677 through 2683 removed outlier: 3.887A pdb=" N UNK E2681 " --> pdb=" O UNK E2677 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N UNK E2683 " --> pdb=" O UNK E2679 " (cutoff:3.500A) Processing helix chain 'E' and resid 2684 through 2687 removed outlier: 3.868A pdb=" N UNK E2687 " --> pdb=" O UNK E2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2684 through 2687' Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 4.244A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E2768 " --> pdb=" O GLU E2764 " (cutoff:3.500A) Processing helix chain 'E' and resid 2793 through 2797 removed outlier: 3.613A pdb=" N PHE E2797 " --> pdb=" O TYR E2794 " (cutoff:3.500A) Processing helix chain 'E' and resid 2800 through 2804 removed outlier: 3.523A pdb=" N ILE E2804 " --> pdb=" O ASP E2801 " (cutoff:3.500A) Processing helix chain 'E' and resid 2809 through 2820 removed outlier: 4.158A pdb=" N ALA E2815 " --> pdb=" O GLU E2811 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET E2816 " --> pdb=" O SER E2812 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE E2817 " --> pdb=" O LEU E2813 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2895 removed outlier: 3.831A pdb=" N MET E2874 " --> pdb=" O GLU E2870 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP E2886 " --> pdb=" O TYR E2882 " (cutoff:3.500A) Processing helix chain 'E' and resid 2907 through 2911 removed outlier: 3.535A pdb=" N THR E2910 " --> pdb=" O PRO E2907 " (cutoff:3.500A) Processing helix chain 'E' and resid 2914 through 2932 removed outlier: 3.749A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG E2920 " --> pdb=" O LYS E2916 " (cutoff:3.500A) Processing helix chain 'E' and resid 2950 through 2976 removed outlier: 4.189A pdb=" N UNK E2956 " --> pdb=" O UNK E2952 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N UNK E2968 " --> pdb=" O UNK E2964 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N UNK E2969 " --> pdb=" O UNK E2965 " (cutoff:3.500A) Processing helix chain 'E' and resid 2997 through 3015 removed outlier: 3.545A pdb=" N UNK E3001 " --> pdb=" O UNK E2997 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N UNK E3006 " --> pdb=" O UNK E3002 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N UNK E3009 " --> pdb=" O UNK E3005 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N UNK E3010 " --> pdb=" O UNK E3006 " (cutoff:3.500A) Processing helix chain 'E' and resid 3017 through 3022 Processing helix chain 'E' and resid 3024 through 3029 removed outlier: 4.126A pdb=" N UNK E3028 " --> pdb=" O UNK E3024 " (cutoff:3.500A) Processing helix chain 'E' and resid 3029 through 3040 removed outlier: 3.557A pdb=" N UNK E3037 " --> pdb=" O UNK E3033 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK E3040 " --> pdb=" O UNK E3036 " (cutoff:3.500A) Processing helix chain 'E' and resid 3048 through 3051 removed outlier: 3.732A pdb=" N UNK E3051 " --> pdb=" O UNK E3048 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3048 through 3051' Processing helix chain 'E' and resid 3052 through 3063 removed outlier: 4.153A pdb=" N UNK E3056 " --> pdb=" O UNK E3052 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK E3057 " --> pdb=" O UNK E3053 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N UNK E3061 " --> pdb=" O UNK E3057 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N UNK E3062 " --> pdb=" O UNK E3058 " (cutoff:3.500A) Processing helix chain 'E' and resid 3141 through 3146 Processing helix chain 'E' and resid 3146 through 3163 removed outlier: 4.125A pdb=" N UNK E3154 " --> pdb=" O UNK E3150 " (cutoff:3.500A) Processing helix chain 'E' and resid 3175 through 3186 removed outlier: 3.647A pdb=" N UNK E3182 " --> pdb=" O UNK E3178 " (cutoff:3.500A) Processing helix chain 'E' and resid 3198 through 3212 Processing helix chain 'E' and resid 3224 through 3230 removed outlier: 3.682A pdb=" N UNK E3228 " --> pdb=" O UNK E3224 " (cutoff:3.500A) Processing helix chain 'E' and resid 3231 through 3234 Processing helix chain 'E' and resid 3244 through 3248 removed outlier: 3.501A pdb=" N UNK E3247 " --> pdb=" O UNK E3244 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N UNK E3248 " --> pdb=" O UNK E3245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3244 through 3248' Processing helix chain 'E' and resid 3249 through 3254 Processing helix chain 'E' and resid 3271 through 3285 removed outlier: 3.826A pdb=" N UNK E3281 " --> pdb=" O UNK E3277 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N UNK E3282 " --> pdb=" O UNK E3278 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N UNK E3284 " --> pdb=" O UNK E3280 " (cutoff:3.500A) Processing helix chain 'E' and resid 3301 through 3304 Processing helix chain 'E' and resid 3305 through 3310 Processing helix chain 'E' and resid 3316 through 3331 removed outlier: 3.754A pdb=" N UNK E3323 " --> pdb=" O UNK E3319 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N UNK E3324 " --> pdb=" O UNK E3320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N UNK E3325 " --> pdb=" O UNK E3321 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N UNK E3330 " --> pdb=" O UNK E3326 " (cutoff:3.500A) Processing helix chain 'E' and resid 3344 through 3349 removed outlier: 3.667A pdb=" N UNK E3348 " --> pdb=" O UNK E3344 " (cutoff:3.500A) Processing helix chain 'E' and resid 3361 through 3388 Processing helix chain 'E' and resid 3393 through 3398 removed outlier: 4.174A pdb=" N UNK E3396 " --> pdb=" O UNK E3393 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N UNK E3397 " --> pdb=" O UNK E3394 " (cutoff:3.500A) Processing helix chain 'E' and resid 3399 through 3409 removed outlier: 3.505A pdb=" N UNK E3404 " --> pdb=" O UNK E3400 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N UNK E3405 " --> pdb=" O UNK E3401 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK E3407 " --> pdb=" O UNK E3403 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK E3409 " --> pdb=" O UNK E3405 " (cutoff:3.500A) Processing helix chain 'E' and resid 3410 through 3425 removed outlier: 4.234A pdb=" N UNK E3416 " --> pdb=" O UNK E3412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N UNK E3417 " --> pdb=" O UNK E3413 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N UNK E3420 " --> pdb=" O UNK E3416 " (cutoff:3.500A) Processing helix chain 'E' and resid 3437 through 3443 removed outlier: 3.548A pdb=" N UNK E3441 " --> pdb=" O UNK E3437 " (cutoff:3.500A) Processing helix chain 'E' and resid 3445 through 3450 Processing helix chain 'E' and resid 3457 through 3460 Processing helix chain 'E' and resid 3461 through 3468 Processing helix chain 'E' and resid 3522 through 3527 Processing helix chain 'E' and resid 3541 through 3547 Processing helix chain 'E' and resid 3551 through 3560 Processing helix chain 'E' and resid 3574 through 3579 removed outlier: 3.661A pdb=" N UNK E3579 " --> pdb=" O UNK E3575 " (cutoff:3.500A) Processing helix chain 'E' and resid 3588 through 3611 removed outlier: 3.907A pdb=" N UNK E3592 " --> pdb=" O UNK E3588 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N UNK E3595 " --> pdb=" O UNK E3591 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK E3598 " --> pdb=" O UNK E3594 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N UNK E3600 " --> pdb=" O UNK E3596 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N UNK E3601 " --> pdb=" O UNK E3597 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK E3611 " --> pdb=" O UNK E3607 " (cutoff:3.500A) Processing helix chain 'E' and resid 3645 through 3656 removed outlier: 3.537A pdb=" N ASN E3651 " --> pdb=" O HIS E3647 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU E3655 " --> pdb=" O ASN E3651 " (cutoff:3.500A) Processing helix chain 'E' and resid 3657 through 3661 Processing helix chain 'E' and resid 3671 through 3680 removed outlier: 4.312A pdb=" N LEU E3677 " --> pdb=" O MET E3673 " (cutoff:3.500A) Processing helix chain 'E' and resid 3681 through 3683 No H-bonds generated for 'chain 'E' and resid 3681 through 3683' Processing helix chain 'E' and resid 3696 through 3708 Processing helix chain 'E' and resid 3719 through 3734 removed outlier: 3.713A pdb=" N ASP E3727 " --> pdb=" O MET E3723 " (cutoff:3.500A) Processing helix chain 'E' and resid 3736 through 3741 removed outlier: 3.875A pdb=" N GLU E3740 " --> pdb=" O GLU E3736 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN E3741 " --> pdb=" O GLU E3737 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3736 through 3741' Processing helix chain 'E' and resid 3752 through 3758 Processing helix chain 'E' and resid 3764 through 3769 Processing helix chain 'E' and resid 3770 through 3773 removed outlier: 4.658A pdb=" N ARG E3773 " --> pdb=" O LEU E3770 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3770 through 3773' Processing helix chain 'E' and resid 3774 through 3785 removed outlier: 4.503A pdb=" N MET E3778 " --> pdb=" O GLY E3774 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU E3780 " --> pdb=" O ALA E3776 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3805 removed outlier: 3.844A pdb=" N LEU E3805 " --> pdb=" O GLY E3801 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3824 Processing helix chain 'E' and resid 3828 through 3838 removed outlier: 3.518A pdb=" N ILE E3832 " --> pdb=" O PHE E3828 " (cutoff:3.500A) Processing helix chain 'E' and resid 3843 through 3856 Processing helix chain 'E' and resid 3877 through 3892 removed outlier: 4.431A pdb=" N ASP E3883 " --> pdb=" O GLU E3879 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE E3885 " --> pdb=" O THR E3881 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS E3892 " --> pdb=" O LEU E3888 " (cutoff:3.500A) Processing helix chain 'E' and resid 3898 through 3903 Processing helix chain 'E' and resid 3914 through 3938 removed outlier: 4.010A pdb=" N CYS E3918 " --> pdb=" O ASN E3914 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL E3920 " --> pdb=" O ILE E3916 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E3921 " --> pdb=" O ILE E3917 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E3922 " --> pdb=" O CYS E3918 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E3923 " --> pdb=" O THR E3919 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E3929 " --> pdb=" O ARG E3925 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR E3934 " --> pdb=" O ILE E3930 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP E3935 " --> pdb=" O SER E3931 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR E3936 " --> pdb=" O ASP E3932 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E3937 " --> pdb=" O PHE E3933 " (cutoff:3.500A) Processing helix chain 'E' and resid 3944 through 3968 removed outlier: 3.671A pdb=" N LYS E3953 " --> pdb=" O ARG E3949 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS E3959 " --> pdb=" O MET E3955 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN E3960 " --> pdb=" O SER E3956 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E3961 " --> pdb=" O VAL E3957 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR E3966 " --> pdb=" O PHE E3962 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E3967 " --> pdb=" O ASN E3963 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3981 Processing helix chain 'E' and resid 3984 through 4004 removed outlier: 3.663A pdb=" N VAL E3990 " --> pdb=" O TRP E3986 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY E3991 " --> pdb=" O ASP E3987 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E3993 " --> pdb=" O VAL E3989 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E4004 " --> pdb=" O MET E4000 " (cutoff:3.500A) Processing helix chain 'E' and resid 4009 through 4030 removed outlier: 3.836A pdb=" N MET E4026 " --> pdb=" O ASP E4022 " (cutoff:3.500A) Processing helix chain 'E' and resid 4039 through 4051 removed outlier: 3.811A pdb=" N ASP E4046 " --> pdb=" O ARG E4042 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E4048 " --> pdb=" O MET E4044 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E4050 " --> pdb=" O ASP E4046 " (cutoff:3.500A) Processing helix chain 'E' and resid 4051 through 4066 removed outlier: 3.703A pdb=" N PHE E4065 " --> pdb=" O PHE E4061 " (cutoff:3.500A) Processing helix chain 'E' and resid 4066 through 4072 removed outlier: 4.141A pdb=" N ASP E4070 " --> pdb=" O LEU E4066 " (cutoff:3.500A) Processing helix chain 'E' and resid 4074 through 4079 Processing helix chain 'E' and resid 4090 through 4100 Processing helix chain 'E' and resid 4104 through 4115 Processing helix chain 'E' and resid 4117 through 4122 removed outlier: 3.510A pdb=" N GLU E4121 " --> pdb=" O ALA E4117 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET E4122 " --> pdb=" O ASP E4118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4117 through 4122' Processing helix chain 'E' and resid 4124 through 4129 Processing helix chain 'E' and resid 4132 through 4154 removed outlier: 3.551A pdb=" N ALA E4136 " --> pdb=" O PHE E4132 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP E4138 " --> pdb=" O GLU E4134 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU E4152 " --> pdb=" O THR E4148 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E4154 " --> pdb=" O LEU E4150 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4167 removed outlier: 4.253A pdb=" N GLU E4165 " --> pdb=" O ARG E4161 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU E4166 " --> pdb=" O ASN E4162 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E4167 " --> pdb=" O PHE E4163 " (cutoff:3.500A) Processing helix chain 'E' and resid 4167 through 4175 Processing helix chain 'E' and resid 4198 through 4206 Processing helix chain 'E' and resid 4207 through 4224 removed outlier: 3.511A pdb=" N ASP E4220 " --> pdb=" O GLN E4216 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL E4222 " --> pdb=" O ILE E4218 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4250 removed outlier: 4.651A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E4235 " --> pdb=" O MET E4231 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E4243 " --> pdb=" O GLU E4239 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E4249 " --> pdb=" O MET E4245 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN E4250 " --> pdb=" O GLN E4246 " (cutoff:3.500A) Processing helix chain 'E' and resid 4542 through 4556 removed outlier: 3.572A pdb=" N TYR E4554 " --> pdb=" O LYS E4550 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4576 removed outlier: 3.869A pdb=" N PHE E4571 " --> pdb=" O LEU E4567 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA E4572 " --> pdb=" O PHE E4568 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E4573 " --> pdb=" O LEU E4569 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN E4574 " --> pdb=" O ALA E4570 " (cutoff:3.500A) Processing helix chain 'E' and resid 4641 through 4664 removed outlier: 3.886A pdb=" N ALA E4654 " --> pdb=" O HIS E4650 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE E4655 " --> pdb=" O THR E4651 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E4658 " --> pdb=" O ALA E4654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E4659 " --> pdb=" O PHE E4655 " (cutoff:3.500A) Processing helix chain 'E' and resid 4667 through 4683 removed outlier: 3.644A pdb=" N LEU E4677 " --> pdb=" O ARG E4673 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA E4678 " --> pdb=" O GLU E4674 " (cutoff:3.500A) Processing helix chain 'E' and resid 4696 through 4702 Processing helix chain 'E' and resid 4710 through 4714 removed outlier: 3.544A pdb=" N SER E4713 " --> pdb=" O SER E4710 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN E4714 " --> pdb=" O PHE E4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4710 through 4714' Processing helix chain 'E' and resid 4719 through 4729 Processing helix chain 'E' and resid 4733 through 4741 Processing helix chain 'E' and resid 4745 through 4753 removed outlier: 4.067A pdb=" N THR E4751 " --> pdb=" O SER E4747 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS E4753 " --> pdb=" O GLU E4749 " (cutoff:3.500A) Processing helix chain 'E' and resid 4772 through 4784 removed outlier: 3.548A pdb=" N GLY E4781 " --> pdb=" O ILE E4777 " (cutoff:3.500A) Processing helix chain 'E' and resid 4786 through 4802 removed outlier: 3.888A pdb=" N LEU E4790 " --> pdb=" O ASP E4786 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET E4798 " --> pdb=" O TRP E4794 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER E4799 " --> pdb=" O TYR E4795 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E4800 " --> pdb=" O MET E4796 " (cutoff:3.500A) Processing helix chain 'E' and resid 4810 through 4816 removed outlier: 3.601A pdb=" N LEU E4814 " --> pdb=" O ALA E4810 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP E4815 " --> pdb=" O ALA E4811 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E4816 " --> pdb=" O HIS E4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4810 through 4816' Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.666A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN E4833 " --> pdb=" O SER E4829 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 removed outlier: 3.952A pdb=" N MET E4839 " --> pdb=" O LYS E4835 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E4842 " --> pdb=" O VAL E4838 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E4843 " --> pdb=" O MET E4839 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E4845 " --> pdb=" O VAL E4841 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E4848 " --> pdb=" O LEU E4844 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E4853 " --> pdb=" O TYR E4849 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E4854 " --> pdb=" O LEU E4850 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA E4855 " --> pdb=" O TYR E4851 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN E4857 " --> pdb=" O VAL E4853 " (cutoff:3.500A) Processing helix chain 'E' and resid 4859 through 4863 removed outlier: 3.914A pdb=" N PHE E4862 " --> pdb=" O PHE E4859 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E4863 " --> pdb=" O ARG E4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4859 through 4863' Processing helix chain 'E' and resid 4878 through 4889 removed outlier: 3.553A pdb=" N TYR E4883 " --> pdb=" O MET E4879 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE E4885 " --> pdb=" O THR E4881 " (cutoff:3.500A) Processing helix chain 'E' and resid 4889 through 4894 removed outlier: 4.385A pdb=" N GLY E4894 " --> pdb=" O GLY E4890 " (cutoff:3.500A) Processing helix chain 'E' and resid 4896 through 4900 removed outlier: 3.808A pdb=" N ASP E4899 " --> pdb=" O GLY E4896 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E4900 " --> pdb=" O ILE E4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4896 through 4900' Processing helix chain 'E' and resid 4909 through 4924 removed outlier: 4.384A pdb=" N VAL E4915 " --> pdb=" O LEU E4911 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP E4917 " --> pdb=" O ARG E4913 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE E4918 " --> pdb=" O VAL E4914 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E4924 " --> pdb=" O PHE E4920 " (cutoff:3.500A) Processing helix chain 'E' and resid 4924 through 4955 removed outlier: 4.096A pdb=" N LEU E4929 " --> pdb=" O ILE E4925 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E4930 " --> pdb=" O VAL E4926 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E4936 " --> pdb=" O ILE E4932 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE E4937 " --> pdb=" O GLN E4933 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP E4938 " --> pdb=" O GLY E4934 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA E4939 " --> pdb=" O LEU E4935 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE E4940 " --> pdb=" O ILE E4936 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP E4945 " --> pdb=" O GLY E4941 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E4948 " --> pdb=" O ARG E4944 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL E4950 " --> pdb=" O GLN E4946 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E4951 " --> pdb=" O GLN E4947 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP E4953 " --> pdb=" O GLN E4949 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET E4954 " --> pdb=" O VAL E4950 " (cutoff:3.500A) Processing helix chain 'E' and resid 4964 through 4970 removed outlier: 3.906A pdb=" N TYR E4967 " --> pdb=" O GLY E4964 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP E4969 " --> pdb=" O ASP E4966 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR E4970 " --> pdb=" O TYR E4967 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4982 Processing helix chain 'E' and resid 4985 through 4997 removed outlier: 3.596A pdb=" N MET E4989 " --> pdb=" O LEU E4985 " (cutoff:3.500A) Processing helix chain 'E' and resid 5006 through 5017 Processing helix chain 'E' and resid 5032 through 5037 Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 251 through 255 removed outlier: 3.599A pdb=" N THR I 254 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 369 removed outlier: 4.197A pdb=" N LEU I 369 " --> pdb=" O LYS I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 419 removed outlier: 3.814A pdb=" N GLN I 399 " --> pdb=" O GLN I 395 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET I 403 " --> pdb=" O GLN I 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY I 409 " --> pdb=" O HIS I 405 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN I 413 " --> pdb=" O GLY I 409 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE I 414 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS I 416 " --> pdb=" O ASN I 412 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY I 417 " --> pdb=" O GLN I 413 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP I 419 " --> pdb=" O ILE I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 452 removed outlier: 4.092A pdb=" N GLY I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 481 removed outlier: 3.745A pdb=" N SER I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN I 473 " --> pdb=" O ARG I 469 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU I 481 " --> pdb=" O LEU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 493 removed outlier: 3.730A pdb=" N VAL I 487 " --> pdb=" O MET I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 529 removed outlier: 4.395A pdb=" N LYS I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU I 517 " --> pdb=" O GLU I 513 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR I 523 " --> pdb=" O VAL I 519 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU I 524 " --> pdb=" O ASN I 520 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER I 528 " --> pdb=" O GLU I 524 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I 529 " --> pdb=" O LEU I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 534 through 539 Processing helix chain 'I' and resid 543 through 548 Processing helix chain 'I' and resid 559 through 568 Processing helix chain 'I' and resid 571 through 576 removed outlier: 3.822A pdb=" N LEU I 575 " --> pdb=" O SER I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 594 Processing helix chain 'I' and resid 596 through 608 removed outlier: 3.767A pdb=" N LEU I 600 " --> pdb=" O ASN I 596 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS I 607 " --> pdb=" O LEU I 603 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL I 608 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 615 through 625 removed outlier: 3.670A pdb=" N ASP I 619 " --> pdb=" O ARG I 615 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR I 622 " --> pdb=" O GLN I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 888 removed outlier: 3.732A pdb=" N GLU I 872 " --> pdb=" O GLU I 868 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS I 873 " --> pdb=" O ARG I 869 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG I 886 " --> pdb=" O TRP I 882 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE I 887 " --> pdb=" O ALA I 883 " (cutoff:3.500A) Processing helix chain 'I' and resid 914 through 934 removed outlier: 3.734A pdb=" N ASN I 919 " --> pdb=" O GLU I 915 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU I 929 " --> pdb=" O SER I 925 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS I 930 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA I 934 " --> pdb=" O LYS I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 999 removed outlier: 3.773A pdb=" N LEU I 984 " --> pdb=" O ALA I 980 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA I 989 " --> pdb=" O VAL I 985 " (cutoff:3.500A) Processing helix chain 'I' and resid 1028 through 1038 removed outlier: 3.663A pdb=" N LYS I1032 " --> pdb=" O ASP I1028 " (cutoff:3.500A) Processing helix chain 'I' and resid 1039 through 1049 removed outlier: 3.964A pdb=" N ARG I1044 " --> pdb=" O CYS I1040 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR I1045 " --> pdb=" O GLN I1041 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU I1046 " --> pdb=" O ALA I1042 " (cutoff:3.500A) Processing helix chain 'I' and resid 1575 through 1579 removed outlier: 3.577A pdb=" N MET I1579 " --> pdb=" O SER I1576 " (cutoff:3.500A) Processing helix chain 'I' and resid 1623 through 1627 Processing helix chain 'I' and resid 1652 through 1657 removed outlier: 3.572A pdb=" N LEU I1657 " --> pdb=" O LEU I1653 " (cutoff:3.500A) Processing helix chain 'I' and resid 1658 through 1674 removed outlier: 3.782A pdb=" N HIS I1665 " --> pdb=" O ARG I1661 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR I1670 " --> pdb=" O THR I1666 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG I1671 " --> pdb=" O LEU I1667 " (cutoff:3.500A) Processing helix chain 'I' and resid 1678 through 1683 Processing helix chain 'I' and resid 1684 through 1688 Processing helix chain 'I' and resid 1692 through 1700 removed outlier: 4.224A pdb=" N LEU I1698 " --> pdb=" O LEU I1694 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU I1699 " --> pdb=" O LEU I1695 " (cutoff:3.500A) Processing helix chain 'I' and resid 1707 through 1711 Processing helix chain 'I' and resid 1715 through 1730 removed outlier: 4.898A pdb=" N GLU I1721 " --> pdb=" O SER I1717 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER I1722 " --> pdb=" O ILE I1718 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA I1723 " --> pdb=" O HIS I1719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG I1725 " --> pdb=" O GLU I1721 " (cutoff:3.500A) Processing helix chain 'I' and resid 1739 through 1744 Processing helix chain 'I' and resid 1803 through 1824 removed outlier: 3.650A pdb=" N LEU I1807 " --> pdb=" O PRO I1803 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG I1813 " --> pdb=" O ASP I1809 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET I1814 " --> pdb=" O LYS I1810 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL I1819 " --> pdb=" O LEU I1815 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG I1820 " --> pdb=" O GLY I1816 " (cutoff:3.500A) Processing helix chain 'I' and resid 1829 through 1832 Processing helix chain 'I' and resid 1833 through 1838 Processing helix chain 'I' and resid 1840 through 1851 removed outlier: 3.606A pdb=" N LEU I1848 " --> pdb=" O LEU I1844 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET I1851 " --> pdb=" O THR I1847 " (cutoff:3.500A) Processing helix chain 'I' and resid 1855 through 1863 Processing helix chain 'I' and resid 1866 through 1871 Processing helix chain 'I' and resid 1933 through 1981 removed outlier: 3.580A pdb=" N GLN I1938 " --> pdb=" O SER I1934 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR I1945 " --> pdb=" O ASN I1941 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE I1946 " --> pdb=" O LEU I1942 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU I1963 " --> pdb=" O ALA I1959 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG I1964 " --> pdb=" O ALA I1960 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL I1966 " --> pdb=" O ALA I1962 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA I1978 " --> pdb=" O ARG I1974 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU I1979 " --> pdb=" O SER I1975 " (cutoff:3.500A) Processing helix chain 'I' and resid 1989 through 1994 removed outlier: 3.772A pdb=" N ARG I1994 " --> pdb=" O GLU I1990 " (cutoff:3.500A) Processing helix chain 'I' and resid 1995 through 1998 Processing helix chain 'I' and resid 2001 through 2014 removed outlier: 3.578A pdb=" N ASN I2007 " --> pdb=" O GLN I2003 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS I2011 " --> pdb=" O ASN I2007 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE I2012 " --> pdb=" O MET I2008 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS I2013 " --> pdb=" O LEU I2009 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP I2014 " --> pdb=" O LEU I2010 " (cutoff:3.500A) Processing helix chain 'I' and resid 2026 through 2042 removed outlier: 3.619A pdb=" N ASP I2030 " --> pdb=" O ASP I2026 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU I2031 " --> pdb=" O ILE I2027 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN I2032 " --> pdb=" O ARG I2028 " (cutoff:3.500A) Processing helix chain 'I' and resid 2094 through 2108 removed outlier: 3.630A pdb=" N VAL I2103 " --> pdb=" O SER I2099 " (cutoff:3.500A) Processing helix chain 'I' and resid 2113 through 2127 removed outlier: 3.580A pdb=" N PHE I2121 " --> pdb=" O VAL I2117 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU I2123 " --> pdb=" O ALA I2119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I2124 " --> pdb=" O MET I2120 " (cutoff:3.500A) Processing helix chain 'I' and resid 2129 through 2138 Processing helix chain 'I' and resid 2139 through 2141 No H-bonds generated for 'chain 'I' and resid 2139 through 2141' Processing helix chain 'I' and resid 2148 through 2165 removed outlier: 3.521A pdb=" N LEU I2155 " --> pdb=" O ASP I2151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN I2161 " --> pdb=" O GLU I2157 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU I2165 " --> pdb=" O GLN I2161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2171 through 2186 removed outlier: 3.648A pdb=" N LEU I2177 " --> pdb=" O GLN I2173 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN I2184 " --> pdb=" O GLN I2180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I2185 " --> pdb=" O SER I2181 " (cutoff:3.500A) Processing helix chain 'I' and resid 2194 through 2201 removed outlier: 3.925A pdb=" N MET I2198 " --> pdb=" O HIS I2194 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA I2200 " --> pdb=" O ASN I2196 " (cutoff:3.500A) Processing helix chain 'I' and resid 2202 through 2216 removed outlier: 3.503A pdb=" N ASN I2213 " --> pdb=" O GLU I2209 " (cutoff:3.500A) Processing helix chain 'I' and resid 2227 through 2242 removed outlier: 3.556A pdb=" N CYS I2233 " --> pdb=" O VAL I2229 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE I2235 " --> pdb=" O SER I2231 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR I2238 " --> pdb=" O ARG I2234 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2253 removed outlier: 4.336A pdb=" N HIS I2253 " --> pdb=" O SER I2249 " (cutoff:3.500A) Processing helix chain 'I' and resid 2253 through 2262 removed outlier: 3.981A pdb=" N ASN I2260 " --> pdb=" O TYR I2256 " (cutoff:3.500A) Processing helix chain 'I' and resid 2271 through 2279 Processing helix chain 'I' and resid 2294 through 2306 removed outlier: 3.516A pdb=" N VAL I2299 " --> pdb=" O LEU I2295 " (cutoff:3.500A) Processing helix chain 'I' and resid 2311 through 2317 removed outlier: 3.885A pdb=" N ALA I2315 " --> pdb=" O MET I2312 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I2316 " --> pdb=" O LEU I2313 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY I2317 " --> pdb=" O LEU I2314 " (cutoff:3.500A) Processing helix chain 'I' and resid 2326 through 2331 removed outlier: 3.722A pdb=" N TYR I2331 " --> pdb=" O GLY I2327 " (cutoff:3.500A) Processing helix chain 'I' and resid 2335 through 2339 removed outlier: 4.090A pdb=" N ALA I2338 " --> pdb=" O LEU I2335 " (cutoff:3.500A) Processing helix chain 'I' and resid 2350 through 2358 removed outlier: 3.707A pdb=" N LEU I2356 " --> pdb=" O VAL I2352 " (cutoff:3.500A) Processing helix chain 'I' and resid 2360 through 2364 Processing helix chain 'I' and resid 2377 through 2388 Processing helix chain 'I' and resid 2389 through 2393 Processing helix chain 'I' and resid 2417 through 2436 removed outlier: 3.792A pdb=" N ALA I2421 " --> pdb=" O HIS I2417 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET I2423 " --> pdb=" O GLY I2419 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA I2428 " --> pdb=" O SER I2424 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU I2433 " --> pdb=" O LEU I2429 " (cutoff:3.500A) Processing helix chain 'I' and resid 2440 through 2445 Processing helix chain 'I' and resid 2448 through 2459 Processing helix chain 'I' and resid 2466 through 2471 Processing helix chain 'I' and resid 2499 through 2507 removed outlier: 3.705A pdb=" N UNK I2503 " --> pdb=" O UNK I2499 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N UNK I2505 " --> pdb=" O UNK I2501 " (cutoff:3.500A) Processing helix chain 'I' and resid 2517 through 2530 removed outlier: 3.526A pdb=" N UNK I2522 " --> pdb=" O UNK I2518 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N UNK I2523 " --> pdb=" O UNK I2519 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N UNK I2526 " --> pdb=" O UNK I2522 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N UNK I2527 " --> pdb=" O UNK I2523 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N UNK I2528 " --> pdb=" O UNK I2524 " (cutoff:3.500A) Processing helix chain 'I' and resid 2542 through 2548 removed outlier: 3.775A pdb=" N UNK I2546 " --> pdb=" O UNK I2542 " (cutoff:3.500A) Processing helix chain 'I' and resid 2551 through 2557 removed outlier: 3.726A pdb=" N UNK I2555 " --> pdb=" O UNK I2551 " (cutoff:3.500A) Processing helix chain 'I' and resid 2567 through 2581 Processing helix chain 'I' and resid 2587 through 2602 Processing helix chain 'I' and resid 2610 through 2618 removed outlier: 3.563A pdb=" N UNK I2617 " --> pdb=" O UNK I2613 " (cutoff:3.500A) Processing helix chain 'I' and resid 2626 through 2641 removed outlier: 3.912A pdb=" N UNK I2630 " --> pdb=" O UNK I2626 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N UNK I2631 " --> pdb=" O UNK I2627 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK I2639 " --> pdb=" O UNK I2635 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK I2641 " --> pdb=" O UNK I2637 " (cutoff:3.500A) Processing helix chain 'I' and resid 2650 through 2666 removed outlier: 3.594A pdb=" N UNK I2666 " --> pdb=" O UNK I2662 " (cutoff:3.500A) Processing helix chain 'I' and resid 2677 through 2683 removed outlier: 3.818A pdb=" N UNK I2681 " --> pdb=" O UNK I2677 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N UNK I2683 " --> pdb=" O UNK I2679 " (cutoff:3.500A) Processing helix chain 'I' and resid 2748 through 2773 removed outlier: 4.245A pdb=" N SER I2753 " --> pdb=" O GLU I2749 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE I2754 " --> pdb=" O LYS I2750 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE I2768 " --> pdb=" O GLU I2764 " (cutoff:3.500A) Processing helix chain 'I' and resid 2793 through 2797 removed outlier: 3.613A pdb=" N PHE I2797 " --> pdb=" O TYR I2794 " (cutoff:3.500A) Processing helix chain 'I' and resid 2800 through 2804 removed outlier: 3.522A pdb=" N ILE I2804 " --> pdb=" O ASP I2801 " (cutoff:3.500A) Processing helix chain 'I' and resid 2809 through 2820 removed outlier: 4.159A pdb=" N ALA I2815 " --> pdb=" O GLU I2811 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET I2816 " --> pdb=" O SER I2812 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE I2817 " --> pdb=" O LEU I2813 " (cutoff:3.500A) Processing helix chain 'I' and resid 2868 through 2895 removed outlier: 3.832A pdb=" N MET I2874 " --> pdb=" O GLU I2870 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP I2886 " --> pdb=" O TYR I2882 " (cutoff:3.500A) Processing helix chain 'I' and resid 2907 through 2911 removed outlier: 3.534A pdb=" N THR I2910 " --> pdb=" O PRO I2907 " (cutoff:3.500A) Processing helix chain 'I' and resid 2914 through 2932 removed outlier: 3.747A pdb=" N ASP I2919 " --> pdb=" O GLU I2915 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG I2920 " --> pdb=" O LYS I2916 " (cutoff:3.500A) Processing helix chain 'I' and resid 2950 through 2976 removed outlier: 4.204A pdb=" N UNK I2956 " --> pdb=" O UNK I2952 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK I2968 " --> pdb=" O UNK I2964 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N UNK I2969 " --> pdb=" O UNK I2965 " (cutoff:3.500A) Processing helix chain 'I' and resid 2997 through 3015 removed outlier: 3.558A pdb=" N UNK I3001 " --> pdb=" O UNK I2997 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N UNK I3002 " --> pdb=" O UNK I2998 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK I3006 " --> pdb=" O UNK I3002 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N UNK I3009 " --> pdb=" O UNK I3005 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N UNK I3010 " --> pdb=" O UNK I3006 " (cutoff:3.500A) Processing helix chain 'I' and resid 3017 through 3022 Processing helix chain 'I' and resid 3029 through 3040 removed outlier: 3.613A pdb=" N UNK I3037 " --> pdb=" O UNK I3033 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N UNK I3040 " --> pdb=" O UNK I3036 " (cutoff:3.500A) Processing helix chain 'I' and resid 3048 through 3051 removed outlier: 3.735A pdb=" N UNK I3051 " --> pdb=" O UNK I3048 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3048 through 3051' Processing helix chain 'I' and resid 3052 through 3063 removed outlier: 4.097A pdb=" N UNK I3056 " --> pdb=" O UNK I3052 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK I3057 " --> pdb=" O UNK I3053 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N UNK I3061 " --> pdb=" O UNK I3057 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N UNK I3062 " --> pdb=" O UNK I3058 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N UNK I3063 " --> pdb=" O UNK I3059 " (cutoff:3.500A) Processing helix chain 'I' and resid 3141 through 3146 Processing helix chain 'I' and resid 3146 through 3163 removed outlier: 4.163A pdb=" N UNK I3154 " --> pdb=" O UNK I3150 " (cutoff:3.500A) Processing helix chain 'I' and resid 3175 through 3186 removed outlier: 3.729A pdb=" N UNK I3182 " --> pdb=" O UNK I3178 " (cutoff:3.500A) Processing helix chain 'I' and resid 3198 through 3212 removed outlier: 3.509A pdb=" N UNK I3205 " --> pdb=" O UNK I3201 " (cutoff:3.500A) Processing helix chain 'I' and resid 3224 through 3230 removed outlier: 3.671A pdb=" N UNK I3228 " --> pdb=" O UNK I3224 " (cutoff:3.500A) Processing helix chain 'I' and resid 3231 through 3234 Processing helix chain 'I' and resid 3244 through 3248 removed outlier: 3.763A pdb=" N UNK I3248 " --> pdb=" O UNK I3245 " (cutoff:3.500A) Processing helix chain 'I' and resid 3249 through 3254 Processing helix chain 'I' and resid 3271 through 3285 removed outlier: 3.885A pdb=" N UNK I3281 " --> pdb=" O UNK I3277 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N UNK I3282 " --> pdb=" O UNK I3278 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N UNK I3284 " --> pdb=" O UNK I3280 " (cutoff:3.500A) Processing helix chain 'I' and resid 3301 through 3304 Processing helix chain 'I' and resid 3305 through 3310 Processing helix chain 'I' and resid 3316 through 3331 removed outlier: 3.724A pdb=" N UNK I3323 " --> pdb=" O UNK I3319 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N UNK I3324 " --> pdb=" O UNK I3320 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNK I3325 " --> pdb=" O UNK I3321 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK I3330 " --> pdb=" O UNK I3326 " (cutoff:3.500A) Processing helix chain 'I' and resid 3344 through 3349 removed outlier: 3.715A pdb=" N UNK I3348 " --> pdb=" O UNK I3344 " (cutoff:3.500A) Processing helix chain 'I' and resid 3361 through 3388 Processing helix chain 'I' and resid 3399 through 3409 removed outlier: 3.830A pdb=" N UNK I3405 " --> pdb=" O UNK I3401 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK I3407 " --> pdb=" O UNK I3403 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK I3409 " --> pdb=" O UNK I3405 " (cutoff:3.500A) Processing helix chain 'I' and resid 3410 through 3425 removed outlier: 4.258A pdb=" N UNK I3416 " --> pdb=" O UNK I3412 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK I3417 " --> pdb=" O UNK I3413 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N UNK I3420 " --> pdb=" O UNK I3416 " (cutoff:3.500A) Processing helix chain 'I' and resid 3437 through 3443 removed outlier: 3.571A pdb=" N UNK I3441 " --> pdb=" O UNK I3437 " (cutoff:3.500A) Processing helix chain 'I' and resid 3445 through 3450 Processing helix chain 'I' and resid 3457 through 3460 Processing helix chain 'I' and resid 3461 through 3468 Processing helix chain 'I' and resid 3522 through 3527 Processing helix chain 'I' and resid 3541 through 3547 Processing helix chain 'I' and resid 3551 through 3560 Processing helix chain 'I' and resid 3574 through 3579 removed outlier: 3.648A pdb=" N UNK I3579 " --> pdb=" O UNK I3575 " (cutoff:3.500A) Processing helix chain 'I' and resid 3588 through 3611 removed outlier: 3.858A pdb=" N UNK I3592 " --> pdb=" O UNK I3588 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N UNK I3595 " --> pdb=" O UNK I3591 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK I3598 " --> pdb=" O UNK I3594 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N UNK I3600 " --> pdb=" O UNK I3596 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N UNK I3601 " --> pdb=" O UNK I3597 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N UNK I3611 " --> pdb=" O UNK I3607 " (cutoff:3.500A) Processing helix chain 'I' and resid 3645 through 3656 removed outlier: 3.537A pdb=" N ASN I3651 " --> pdb=" O HIS I3647 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU I3655 " --> pdb=" O ASN I3651 " (cutoff:3.500A) Processing helix chain 'I' and resid 3657 through 3661 Processing helix chain 'I' and resid 3671 through 3680 removed outlier: 4.313A pdb=" N LEU I3677 " --> pdb=" O MET I3673 " (cutoff:3.500A) Processing helix chain 'I' and resid 3681 through 3683 No H-bonds generated for 'chain 'I' and resid 3681 through 3683' Processing helix chain 'I' and resid 3696 through 3708 Processing helix chain 'I' and resid 3719 through 3734 removed outlier: 3.713A pdb=" N ASP I3727 " --> pdb=" O MET I3723 " (cutoff:3.500A) Processing helix chain 'I' and resid 3736 through 3741 removed outlier: 3.875A pdb=" N GLU I3740 " --> pdb=" O GLU I3736 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN I3741 " --> pdb=" O GLU I3737 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3736 through 3741' Processing helix chain 'I' and resid 3752 through 3758 Processing helix chain 'I' and resid 3764 through 3769 Processing helix chain 'I' and resid 3770 through 3773 removed outlier: 4.657A pdb=" N ARG I3773 " --> pdb=" O LEU I3770 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3770 through 3773' Processing helix chain 'I' and resid 3774 through 3785 removed outlier: 4.502A pdb=" N MET I3778 " --> pdb=" O GLY I3774 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU I3780 " --> pdb=" O ALA I3776 " (cutoff:3.500A) Processing helix chain 'I' and resid 3791 through 3805 removed outlier: 3.844A pdb=" N LEU I3805 " --> pdb=" O GLY I3801 " (cutoff:3.500A) Processing helix chain 'I' and resid 3809 through 3824 Processing helix chain 'I' and resid 3828 through 3838 removed outlier: 3.520A pdb=" N ILE I3832 " --> pdb=" O PHE I3828 " (cutoff:3.500A) Processing helix chain 'I' and resid 3843 through 3856 Processing helix chain 'I' and resid 3877 through 3892 removed outlier: 4.431A pdb=" N ASP I3883 " --> pdb=" O GLU I3879 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE I3885 " --> pdb=" O THR I3881 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS I3892 " --> pdb=" O LEU I3888 " (cutoff:3.500A) Processing helix chain 'I' and resid 3898 through 3903 Processing helix chain 'I' and resid 3914 through 3938 removed outlier: 4.009A pdb=" N CYS I3918 " --> pdb=" O ASN I3914 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL I3920 " --> pdb=" O ILE I3916 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP I3921 " --> pdb=" O ILE I3917 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR I3922 " --> pdb=" O CYS I3918 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU I3923 " --> pdb=" O THR I3919 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER I3929 " --> pdb=" O ARG I3925 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR I3934 " --> pdb=" O ILE I3930 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP I3935 " --> pdb=" O SER I3931 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR I3936 " --> pdb=" O ASP I3932 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR I3937 " --> pdb=" O PHE I3933 " (cutoff:3.500A) Processing helix chain 'I' and resid 3944 through 3968 removed outlier: 3.672A pdb=" N LYS I3953 " --> pdb=" O ARG I3949 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA I3954 " --> pdb=" O ASN I3950 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS I3959 " --> pdb=" O MET I3955 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN I3960 " --> pdb=" O SER I3956 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL I3961 " --> pdb=" O VAL I3957 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR I3966 " --> pdb=" O PHE I3962 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU I3967 " --> pdb=" O ASN I3963 " (cutoff:3.500A) Processing helix chain 'I' and resid 3973 through 3981 Processing helix chain 'I' and resid 3984 through 4004 removed outlier: 3.663A pdb=" N VAL I3990 " --> pdb=" O TRP I3986 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY I3991 " --> pdb=" O ASP I3987 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE I3992 " --> pdb=" O ALA I3988 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU I3993 " --> pdb=" O VAL I3989 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS I3998 " --> pdb=" O HIS I3994 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET I4000 " --> pdb=" O PHE I3996 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA I4004 " --> pdb=" O MET I4000 " (cutoff:3.500A) Processing helix chain 'I' and resid 4009 through 4030 removed outlier: 3.836A pdb=" N MET I4026 " --> pdb=" O ASP I4022 " (cutoff:3.500A) Processing helix chain 'I' and resid 4039 through 4051 removed outlier: 3.811A pdb=" N ASP I4046 " --> pdb=" O ARG I4042 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I4048 " --> pdb=" O MET I4044 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU I4050 " --> pdb=" O ASP I4046 " (cutoff:3.500A) Processing helix chain 'I' and resid 4051 through 4066 removed outlier: 3.703A pdb=" N PHE I4065 " --> pdb=" O PHE I4061 " (cutoff:3.500A) Processing helix chain 'I' and resid 4066 through 4072 removed outlier: 4.141A pdb=" N ASP I4070 " --> pdb=" O LEU I4066 " (cutoff:3.500A) Processing helix chain 'I' and resid 4074 through 4079 Processing helix chain 'I' and resid 4090 through 4100 Processing helix chain 'I' and resid 4104 through 4115 Processing helix chain 'I' and resid 4117 through 4122 removed outlier: 3.510A pdb=" N GLU I4121 " --> pdb=" O ALA I4117 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET I4122 " --> pdb=" O ASP I4118 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4117 through 4122' Processing helix chain 'I' and resid 4124 through 4129 Processing helix chain 'I' and resid 4132 through 4154 removed outlier: 3.550A pdb=" N ALA I4136 " --> pdb=" O PHE I4132 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP I4138 " --> pdb=" O GLU I4134 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU I4152 " --> pdb=" O THR I4148 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL I4154 " --> pdb=" O LEU I4150 " (cutoff:3.500A) Processing helix chain 'I' and resid 4157 through 4167 removed outlier: 4.254A pdb=" N GLU I4165 " --> pdb=" O ARG I4161 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU I4166 " --> pdb=" O ASN I4162 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA I4167 " --> pdb=" O PHE I4163 " (cutoff:3.500A) Processing helix chain 'I' and resid 4167 through 4175 Processing helix chain 'I' and resid 4198 through 4206 Processing helix chain 'I' and resid 4207 through 4224 removed outlier: 3.510A pdb=" N ASP I4220 " --> pdb=" O GLN I4216 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL I4222 " --> pdb=" O ILE I4218 " (cutoff:3.500A) Processing helix chain 'I' and resid 4228 through 4250 removed outlier: 4.652A pdb=" N PHE I4234 " --> pdb=" O LYS I4230 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL I4235 " --> pdb=" O MET I4231 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE I4243 " --> pdb=" O GLU I4239 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA I4249 " --> pdb=" O MET I4245 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN I4250 " --> pdb=" O GLN I4246 " (cutoff:3.500A) Processing helix chain 'I' and resid 4542 through 4556 removed outlier: 3.572A pdb=" N TYR I4554 " --> pdb=" O LYS I4550 " (cutoff:3.500A) Processing helix chain 'I' and resid 4558 through 4576 removed outlier: 3.869A pdb=" N PHE I4571 " --> pdb=" O LEU I4567 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA I4572 " --> pdb=" O PHE I4568 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE I4573 " --> pdb=" O LEU I4569 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN I4574 " --> pdb=" O ALA I4570 " (cutoff:3.500A) Processing helix chain 'I' and resid 4641 through 4664 removed outlier: 3.886A pdb=" N ALA I4654 " --> pdb=" O HIS I4650 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE I4655 " --> pdb=" O THR I4651 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE I4658 " --> pdb=" O ALA I4654 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE I4659 " --> pdb=" O PHE I4655 " (cutoff:3.500A) Processing helix chain 'I' and resid 4667 through 4683 removed outlier: 3.644A pdb=" N LEU I4677 " --> pdb=" O ARG I4673 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA I4678 " --> pdb=" O GLU I4674 " (cutoff:3.500A) Processing helix chain 'I' and resid 4696 through 4702 Processing helix chain 'I' and resid 4710 through 4714 removed outlier: 3.544A pdb=" N SER I4713 " --> pdb=" O SER I4710 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN I4714 " --> pdb=" O PHE I4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4710 through 4714' Processing helix chain 'I' and resid 4719 through 4729 Processing helix chain 'I' and resid 4733 through 4741 Processing helix chain 'I' and resid 4745 through 4753 removed outlier: 4.067A pdb=" N THR I4751 " --> pdb=" O SER I4747 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS I4753 " --> pdb=" O GLU I4749 " (cutoff:3.500A) Processing helix chain 'I' and resid 4772 through 4784 removed outlier: 3.548A pdb=" N GLY I4781 " --> pdb=" O ILE I4777 " (cutoff:3.500A) Processing helix chain 'I' and resid 4786 through 4802 removed outlier: 3.889A pdb=" N LEU I4790 " --> pdb=" O ASP I4786 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET I4798 " --> pdb=" O TRP I4794 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I4799 " --> pdb=" O TYR I4795 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I4800 " --> pdb=" O MET I4796 " (cutoff:3.500A) Processing helix chain 'I' and resid 4810 through 4816 removed outlier: 3.603A pdb=" N LEU I4814 " --> pdb=" O ALA I4810 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP I4815 " --> pdb=" O ALA I4811 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE I4816 " --> pdb=" O HIS I4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4810 through 4816' Processing helix chain 'I' and resid 4820 through 4833 removed outlier: 3.665A pdb=" N ILE I4826 " --> pdb=" O THR I4822 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN I4833 " --> pdb=" O SER I4829 " (cutoff:3.500A) Processing helix chain 'I' and resid 4833 through 4858 removed outlier: 3.952A pdb=" N MET I4839 " --> pdb=" O LYS I4835 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY I4842 " --> pdb=" O VAL I4838 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU I4843 " --> pdb=" O MET I4839 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA I4845 " --> pdb=" O VAL I4841 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL I4848 " --> pdb=" O LEU I4844 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL I4853 " --> pdb=" O TYR I4849 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I4854 " --> pdb=" O LEU I4850 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA I4855 " --> pdb=" O TYR I4851 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN I4857 " --> pdb=" O VAL I4853 " (cutoff:3.500A) Processing helix chain 'I' and resid 4859 through 4863 removed outlier: 3.914A pdb=" N PHE I4862 " --> pdb=" O PHE I4859 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR I4863 " --> pdb=" O ARG I4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4859 through 4863' Processing helix chain 'I' and resid 4878 through 4889 removed outlier: 3.553A pdb=" N TYR I4883 " --> pdb=" O MET I4879 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE I4885 " --> pdb=" O THR I4881 " (cutoff:3.500A) Processing helix chain 'I' and resid 4889 through 4894 removed outlier: 4.386A pdb=" N GLY I4894 " --> pdb=" O GLY I4890 " (cutoff:3.500A) Processing helix chain 'I' and resid 4896 through 4900 removed outlier: 3.807A pdb=" N ASP I4899 " --> pdb=" O GLY I4896 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I4900 " --> pdb=" O ILE I4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4896 through 4900' Processing helix chain 'I' and resid 4909 through 4924 removed outlier: 4.383A pdb=" N VAL I4915 " --> pdb=" O LEU I4911 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP I4917 " --> pdb=" O ARG I4913 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE I4918 " --> pdb=" O VAL I4914 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I4924 " --> pdb=" O PHE I4920 " (cutoff:3.500A) Processing helix chain 'I' and resid 4924 through 4955 removed outlier: 4.095A pdb=" N LEU I4929 " --> pdb=" O ILE I4925 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA I4930 " --> pdb=" O VAL I4926 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE I4936 " --> pdb=" O ILE I4932 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE I4937 " --> pdb=" O GLN I4933 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP I4938 " --> pdb=" O GLY I4934 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA I4939 " --> pdb=" O LEU I4935 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE I4940 " --> pdb=" O ILE I4936 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP I4945 " --> pdb=" O GLY I4941 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU I4948 " --> pdb=" O ARG I4944 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL I4950 " --> pdb=" O GLN I4946 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS I4951 " --> pdb=" O GLN I4947 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP I4953 " --> pdb=" O GLN I4949 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET I4954 " --> pdb=" O VAL I4950 " (cutoff:3.500A) Processing helix chain 'I' and resid 4964 through 4970 removed outlier: 3.906A pdb=" N TYR I4967 " --> pdb=" O GLY I4964 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP I4969 " --> pdb=" O ASP I4966 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR I4970 " --> pdb=" O TYR I4967 " (cutoff:3.500A) Processing helix chain 'I' and resid 4973 through 4982 Processing helix chain 'I' and resid 4985 through 4997 removed outlier: 3.595A pdb=" N MET I4989 " --> pdb=" O LEU I4985 " (cutoff:3.500A) Processing helix chain 'I' and resid 5006 through 5017 Processing helix chain 'I' and resid 5032 through 5037 Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 251 through 255 removed outlier: 3.599A pdb=" N THR G 254 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 369 removed outlier: 4.198A pdb=" N LEU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 419 removed outlier: 3.815A pdb=" N GLN G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET G 403 " --> pdb=" O GLN G 399 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY G 409 " --> pdb=" O HIS G 405 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN G 413 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS G 416 " --> pdb=" O ASN G 412 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY G 417 " --> pdb=" O GLN G 413 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP G 419 " --> pdb=" O ILE G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 452 removed outlier: 4.092A pdb=" N GLY G 450 " --> pdb=" O GLN G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 481 removed outlier: 3.743A pdb=" N SER G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN G 473 " --> pdb=" O ARG G 469 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE G 478 " --> pdb=" O ARG G 474 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU G 481 " --> pdb=" O LEU G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 483 through 493 removed outlier: 3.730A pdb=" N VAL G 487 " --> pdb=" O MET G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 529 removed outlier: 4.396A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR G 523 " --> pdb=" O VAL G 519 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU G 524 " --> pdb=" O ASN G 520 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 528 " --> pdb=" O GLU G 524 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU G 529 " --> pdb=" O LEU G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 539 Processing helix chain 'G' and resid 543 through 548 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'G' and resid 571 through 576 removed outlier: 3.824A pdb=" N LEU G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 594 Processing helix chain 'G' and resid 596 through 608 removed outlier: 3.767A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 615 through 625 removed outlier: 3.670A pdb=" N ASP G 619 " --> pdb=" O ARG G 615 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR G 622 " --> pdb=" O GLN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 888 removed outlier: 3.731A pdb=" N GLU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 873 " --> pdb=" O ARG G 869 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE G 887 " --> pdb=" O ALA G 883 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 934 removed outlier: 3.735A pdb=" N ASN G 919 " --> pdb=" O GLU G 915 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU G 929 " --> pdb=" O SER G 925 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS G 930 " --> pdb=" O GLY G 926 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 934 " --> pdb=" O LYS G 930 " (cutoff:3.500A) Processing helix chain 'G' and resid 980 through 999 removed outlier: 3.771A pdb=" N LEU G 984 " --> pdb=" O ALA G 980 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA G 989 " --> pdb=" O VAL G 985 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1038 removed outlier: 3.662A pdb=" N LYS G1032 " --> pdb=" O ASP G1028 " (cutoff:3.500A) Processing helix chain 'G' and resid 1039 through 1049 removed outlier: 3.964A pdb=" N ARG G1044 " --> pdb=" O CYS G1040 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR G1045 " --> pdb=" O GLN G1041 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU G1046 " --> pdb=" O ALA G1042 " (cutoff:3.500A) Processing helix chain 'G' and resid 1575 through 1579 removed outlier: 3.576A pdb=" N MET G1579 " --> pdb=" O SER G1576 " (cutoff:3.500A) Processing helix chain 'G' and resid 1623 through 1627 Processing helix chain 'G' and resid 1652 through 1657 removed outlier: 3.572A pdb=" N LEU G1657 " --> pdb=" O LEU G1653 " (cutoff:3.500A) Processing helix chain 'G' and resid 1658 through 1674 removed outlier: 3.781A pdb=" N HIS G1665 " --> pdb=" O ARG G1661 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR G1670 " --> pdb=" O THR G1666 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG G1671 " --> pdb=" O LEU G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1683 Processing helix chain 'G' and resid 1684 through 1688 Processing helix chain 'G' and resid 1692 through 1700 removed outlier: 4.223A pdb=" N LEU G1698 " --> pdb=" O LEU G1694 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU G1699 " --> pdb=" O LEU G1695 " (cutoff:3.500A) Processing helix chain 'G' and resid 1707 through 1711 Processing helix chain 'G' and resid 1715 through 1730 removed outlier: 4.898A pdb=" N GLU G1721 " --> pdb=" O SER G1717 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER G1722 " --> pdb=" O ILE G1718 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA G1723 " --> pdb=" O HIS G1719 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG G1725 " --> pdb=" O GLU G1721 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 Processing helix chain 'G' and resid 1803 through 1824 removed outlier: 3.651A pdb=" N LEU G1807 " --> pdb=" O PRO G1803 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G1813 " --> pdb=" O ASP G1809 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET G1814 " --> pdb=" O LYS G1810 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G1819 " --> pdb=" O LEU G1815 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG G1820 " --> pdb=" O GLY G1816 " (cutoff:3.500A) Processing helix chain 'G' and resid 1829 through 1832 Processing helix chain 'G' and resid 1833 through 1838 Processing helix chain 'G' and resid 1840 through 1851 removed outlier: 3.605A pdb=" N LEU G1848 " --> pdb=" O LEU G1844 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET G1851 " --> pdb=" O THR G1847 " (cutoff:3.500A) Processing helix chain 'G' and resid 1855 through 1863 Processing helix chain 'G' and resid 1866 through 1871 Processing helix chain 'G' and resid 1933 through 1981 removed outlier: 3.580A pdb=" N GLN G1938 " --> pdb=" O SER G1934 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR G1945 " --> pdb=" O ASN G1941 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE G1946 " --> pdb=" O LEU G1942 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU G1963 " --> pdb=" O ALA G1959 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG G1964 " --> pdb=" O ALA G1960 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA G1978 " --> pdb=" O ARG G1974 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU G1979 " --> pdb=" O SER G1975 " (cutoff:3.500A) Processing helix chain 'G' and resid 1989 through 1994 removed outlier: 3.774A pdb=" N ARG G1994 " --> pdb=" O GLU G1990 " (cutoff:3.500A) Processing helix chain 'G' and resid 1995 through 1998 Processing helix chain 'G' and resid 2001 through 2014 removed outlier: 3.579A pdb=" N ASN G2007 " --> pdb=" O GLN G2003 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE G2012 " --> pdb=" O MET G2008 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS G2013 " --> pdb=" O LEU G2009 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP G2014 " --> pdb=" O LEU G2010 " (cutoff:3.500A) Processing helix chain 'G' and resid 2026 through 2042 removed outlier: 3.620A pdb=" N ASP G2030 " --> pdb=" O ASP G2026 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU G2031 " --> pdb=" O ILE G2027 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN G2032 " --> pdb=" O ARG G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2094 through 2108 removed outlier: 3.631A pdb=" N VAL G2103 " --> pdb=" O SER G2099 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2127 removed outlier: 3.579A pdb=" N PHE G2121 " --> pdb=" O VAL G2117 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G2123 " --> pdb=" O ALA G2119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU G2124 " --> pdb=" O MET G2120 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2138 Processing helix chain 'G' and resid 2139 through 2141 No H-bonds generated for 'chain 'G' and resid 2139 through 2141' Processing helix chain 'G' and resid 2148 through 2165 removed outlier: 3.521A pdb=" N LEU G2155 " --> pdb=" O ASP G2151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN G2161 " --> pdb=" O GLU G2157 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G2165 " --> pdb=" O GLN G2161 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2186 removed outlier: 3.649A pdb=" N LEU G2177 " --> pdb=" O GLN G2173 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN G2184 " --> pdb=" O GLN G2180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G2185 " --> pdb=" O SER G2181 " (cutoff:3.500A) Processing helix chain 'G' and resid 2194 through 2201 removed outlier: 3.925A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G2200 " --> pdb=" O ASN G2196 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.503A pdb=" N ASN G2213 " --> pdb=" O GLU G2209 " (cutoff:3.500A) Processing helix chain 'G' and resid 2227 through 2242 removed outlier: 3.557A pdb=" N CYS G2233 " --> pdb=" O VAL G2229 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE G2235 " --> pdb=" O SER G2231 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR G2238 " --> pdb=" O ARG G2234 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2253 removed outlier: 4.337A pdb=" N HIS G2253 " --> pdb=" O SER G2249 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2262 removed outlier: 3.980A pdb=" N ASN G2260 " --> pdb=" O TYR G2256 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2279 Processing helix chain 'G' and resid 2294 through 2306 removed outlier: 3.516A pdb=" N VAL G2299 " --> pdb=" O LEU G2295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2311 through 2317 removed outlier: 3.883A pdb=" N ALA G2315 " --> pdb=" O MET G2312 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS G2316 " --> pdb=" O LEU G2313 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY G2317 " --> pdb=" O LEU G2314 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2331 removed outlier: 3.721A pdb=" N TYR G2331 " --> pdb=" O GLY G2327 " (cutoff:3.500A) Processing helix chain 'G' and resid 2335 through 2339 removed outlier: 4.092A pdb=" N ALA G2338 " --> pdb=" O LEU G2335 " (cutoff:3.500A) Processing helix chain 'G' and resid 2350 through 2358 removed outlier: 3.704A pdb=" N LEU G2356 " --> pdb=" O VAL G2352 " (cutoff:3.500A) Processing helix chain 'G' and resid 2360 through 2364 Processing helix chain 'G' and resid 2377 through 2388 Processing helix chain 'G' and resid 2389 through 2393 Processing helix chain 'G' and resid 2417 through 2436 removed outlier: 3.790A pdb=" N ALA G2421 " --> pdb=" O HIS G2417 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET G2423 " --> pdb=" O GLY G2419 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA G2428 " --> pdb=" O SER G2424 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G2433 " --> pdb=" O LEU G2429 " (cutoff:3.500A) Processing helix chain 'G' and resid 2440 through 2445 Processing helix chain 'G' and resid 2448 through 2459 Processing helix chain 'G' and resid 2466 through 2471 Processing helix chain 'G' and resid 2499 through 2507 removed outlier: 3.785A pdb=" N UNK G2503 " --> pdb=" O UNK G2499 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N UNK G2505 " --> pdb=" O UNK G2501 " (cutoff:3.500A) Processing helix chain 'G' and resid 2517 through 2530 removed outlier: 3.532A pdb=" N UNK G2522 " --> pdb=" O UNK G2518 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N UNK G2523 " --> pdb=" O UNK G2519 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N UNK G2526 " --> pdb=" O UNK G2522 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N UNK G2527 " --> pdb=" O UNK G2523 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N UNK G2528 " --> pdb=" O UNK G2524 " (cutoff:3.500A) Processing helix chain 'G' and resid 2542 through 2548 removed outlier: 3.756A pdb=" N UNK G2546 " --> pdb=" O UNK G2542 " (cutoff:3.500A) Processing helix chain 'G' and resid 2551 through 2557 removed outlier: 3.732A pdb=" N UNK G2555 " --> pdb=" O UNK G2551 " (cutoff:3.500A) Processing helix chain 'G' and resid 2567 through 2581 Processing helix chain 'G' and resid 2587 through 2602 Processing helix chain 'G' and resid 2610 through 2618 removed outlier: 3.556A pdb=" N UNK G2617 " --> pdb=" O UNK G2613 " (cutoff:3.500A) Processing helix chain 'G' and resid 2626 through 2641 removed outlier: 3.929A pdb=" N UNK G2630 " --> pdb=" O UNK G2626 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N UNK G2631 " --> pdb=" O UNK G2627 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK G2639 " --> pdb=" O UNK G2635 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK G2641 " --> pdb=" O UNK G2637 " (cutoff:3.500A) Processing helix chain 'G' and resid 2650 through 2666 removed outlier: 3.560A pdb=" N UNK G2666 " --> pdb=" O UNK G2662 " (cutoff:3.500A) Processing helix chain 'G' and resid 2677 through 2683 removed outlier: 3.820A pdb=" N UNK G2681 " --> pdb=" O UNK G2677 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N UNK G2683 " --> pdb=" O UNK G2679 " (cutoff:3.500A) Processing helix chain 'G' and resid 2684 through 2687 removed outlier: 3.731A pdb=" N UNK G2687 " --> pdb=" O UNK G2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2684 through 2687' Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 4.243A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G2768 " --> pdb=" O GLU G2764 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2797 removed outlier: 3.614A pdb=" N PHE G2797 " --> pdb=" O TYR G2794 " (cutoff:3.500A) Processing helix chain 'G' and resid 2800 through 2804 removed outlier: 3.523A pdb=" N ILE G2804 " --> pdb=" O ASP G2801 " (cutoff:3.500A) Processing helix chain 'G' and resid 2809 through 2820 removed outlier: 4.159A pdb=" N ALA G2815 " --> pdb=" O GLU G2811 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET G2816 " --> pdb=" O SER G2812 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE G2817 " --> pdb=" O LEU G2813 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2895 removed outlier: 3.831A pdb=" N MET G2874 " --> pdb=" O GLU G2870 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP G2886 " --> pdb=" O TYR G2882 " (cutoff:3.500A) Processing helix chain 'G' and resid 2907 through 2911 removed outlier: 3.534A pdb=" N THR G2910 " --> pdb=" O PRO G2907 " (cutoff:3.500A) Processing helix chain 'G' and resid 2914 through 2932 removed outlier: 3.747A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG G2920 " --> pdb=" O LYS G2916 " (cutoff:3.500A) Processing helix chain 'G' and resid 2950 through 2976 removed outlier: 4.210A pdb=" N UNK G2956 " --> pdb=" O UNK G2952 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK G2968 " --> pdb=" O UNK G2964 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N UNK G2969 " --> pdb=" O UNK G2965 " (cutoff:3.500A) Processing helix chain 'G' and resid 2997 through 3015 removed outlier: 3.588A pdb=" N UNK G3001 " --> pdb=" O UNK G2997 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK G3002 " --> pdb=" O UNK G2998 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N UNK G3006 " --> pdb=" O UNK G3002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N UNK G3009 " --> pdb=" O UNK G3005 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK G3010 " --> pdb=" O UNK G3006 " (cutoff:3.500A) Processing helix chain 'G' and resid 3017 through 3022 Processing helix chain 'G' and resid 3024 through 3029 removed outlier: 4.138A pdb=" N UNK G3028 " --> pdb=" O UNK G3024 " (cutoff:3.500A) Processing helix chain 'G' and resid 3029 through 3040 removed outlier: 3.607A pdb=" N UNK G3037 " --> pdb=" O UNK G3033 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N UNK G3040 " --> pdb=" O UNK G3036 " (cutoff:3.500A) Processing helix chain 'G' and resid 3048 through 3051 removed outlier: 3.771A pdb=" N UNK G3051 " --> pdb=" O UNK G3048 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3048 through 3051' Processing helix chain 'G' and resid 3052 through 3063 removed outlier: 4.164A pdb=" N UNK G3056 " --> pdb=" O UNK G3052 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N UNK G3057 " --> pdb=" O UNK G3053 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N UNK G3061 " --> pdb=" O UNK G3057 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N UNK G3062 " --> pdb=" O UNK G3058 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N UNK G3063 " --> pdb=" O UNK G3059 " (cutoff:3.500A) Processing helix chain 'G' and resid 3141 through 3146 Processing helix chain 'G' and resid 3146 through 3163 removed outlier: 4.149A pdb=" N UNK G3154 " --> pdb=" O UNK G3150 " (cutoff:3.500A) Processing helix chain 'G' and resid 3175 through 3186 removed outlier: 3.702A pdb=" N UNK G3182 " --> pdb=" O UNK G3178 " (cutoff:3.500A) Processing helix chain 'G' and resid 3198 through 3212 Processing helix chain 'G' and resid 3224 through 3230 removed outlier: 3.676A pdb=" N UNK G3228 " --> pdb=" O UNK G3224 " (cutoff:3.500A) Processing helix chain 'G' and resid 3231 through 3234 Processing helix chain 'G' and resid 3244 through 3248 removed outlier: 3.763A pdb=" N UNK G3248 " --> pdb=" O UNK G3245 " (cutoff:3.500A) Processing helix chain 'G' and resid 3249 through 3254 Processing helix chain 'G' and resid 3271 through 3285 removed outlier: 3.874A pdb=" N UNK G3281 " --> pdb=" O UNK G3277 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N UNK G3282 " --> pdb=" O UNK G3278 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N UNK G3284 " --> pdb=" O UNK G3280 " (cutoff:3.500A) Processing helix chain 'G' and resid 3301 through 3304 Processing helix chain 'G' and resid 3305 through 3310 Processing helix chain 'G' and resid 3316 through 3331 removed outlier: 3.720A pdb=" N UNK G3323 " --> pdb=" O UNK G3319 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N UNK G3324 " --> pdb=" O UNK G3320 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK G3325 " --> pdb=" O UNK G3321 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N UNK G3330 " --> pdb=" O UNK G3326 " (cutoff:3.500A) Processing helix chain 'G' and resid 3344 through 3349 removed outlier: 3.712A pdb=" N UNK G3348 " --> pdb=" O UNK G3344 " (cutoff:3.500A) Processing helix chain 'G' and resid 3361 through 3388 Processing helix chain 'G' and resid 3393 through 3398 removed outlier: 4.156A pdb=" N UNK G3396 " --> pdb=" O UNK G3393 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK G3397 " --> pdb=" O UNK G3394 " (cutoff:3.500A) Processing helix chain 'G' and resid 3399 through 3404 Processing helix chain 'G' and resid 3404 through 3409 removed outlier: 3.773A pdb=" N UNK G3409 " --> pdb=" O UNK G3405 " (cutoff:3.500A) Processing helix chain 'G' and resid 3410 through 3425 removed outlier: 4.266A pdb=" N UNK G3416 " --> pdb=" O UNK G3412 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N UNK G3417 " --> pdb=" O UNK G3413 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N UNK G3420 " --> pdb=" O UNK G3416 " (cutoff:3.500A) Processing helix chain 'G' and resid 3437 through 3443 removed outlier: 3.543A pdb=" N UNK G3441 " --> pdb=" O UNK G3437 " (cutoff:3.500A) Processing helix chain 'G' and resid 3445 through 3450 Processing helix chain 'G' and resid 3457 through 3460 Processing helix chain 'G' and resid 3461 through 3468 removed outlier: 3.532A pdb=" N UNK G3468 " --> pdb=" O UNK G3464 " (cutoff:3.500A) Processing helix chain 'G' and resid 3522 through 3527 Processing helix chain 'G' and resid 3541 through 3547 Processing helix chain 'G' and resid 3551 through 3560 Processing helix chain 'G' and resid 3574 through 3579 removed outlier: 3.651A pdb=" N UNK G3579 " --> pdb=" O UNK G3575 " (cutoff:3.500A) Processing helix chain 'G' and resid 3588 through 3611 removed outlier: 3.870A pdb=" N UNK G3592 " --> pdb=" O UNK G3588 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N UNK G3595 " --> pdb=" O UNK G3591 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK G3598 " --> pdb=" O UNK G3594 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N UNK G3600 " --> pdb=" O UNK G3596 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N UNK G3601 " --> pdb=" O UNK G3597 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N UNK G3611 " --> pdb=" O UNK G3607 " (cutoff:3.500A) Processing helix chain 'G' and resid 3645 through 3656 removed outlier: 3.537A pdb=" N ASN G3651 " --> pdb=" O HIS G3647 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU G3655 " --> pdb=" O ASN G3651 " (cutoff:3.500A) Processing helix chain 'G' and resid 3657 through 3661 Processing helix chain 'G' and resid 3671 through 3680 removed outlier: 4.312A pdb=" N LEU G3677 " --> pdb=" O MET G3673 " (cutoff:3.500A) Processing helix chain 'G' and resid 3681 through 3683 No H-bonds generated for 'chain 'G' and resid 3681 through 3683' Processing helix chain 'G' and resid 3696 through 3708 Processing helix chain 'G' and resid 3719 through 3734 removed outlier: 3.713A pdb=" N ASP G3727 " --> pdb=" O MET G3723 " (cutoff:3.500A) Processing helix chain 'G' and resid 3736 through 3741 removed outlier: 3.875A pdb=" N GLU G3740 " --> pdb=" O GLU G3736 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN G3741 " --> pdb=" O GLU G3737 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3736 through 3741' Processing helix chain 'G' and resid 3752 through 3758 Processing helix chain 'G' and resid 3764 through 3769 Processing helix chain 'G' and resid 3770 through 3773 removed outlier: 4.657A pdb=" N ARG G3773 " --> pdb=" O LEU G3770 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3770 through 3773' Processing helix chain 'G' and resid 3774 through 3785 removed outlier: 4.503A pdb=" N MET G3778 " --> pdb=" O GLY G3774 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3805 removed outlier: 3.843A pdb=" N LEU G3805 " --> pdb=" O GLY G3801 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3824 Processing helix chain 'G' and resid 3828 through 3838 removed outlier: 3.520A pdb=" N ILE G3832 " --> pdb=" O PHE G3828 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3856 Processing helix chain 'G' and resid 3877 through 3892 removed outlier: 4.430A pdb=" N ASP G3883 " --> pdb=" O GLU G3879 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE G3885 " --> pdb=" O THR G3881 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N CYS G3892 " --> pdb=" O LEU G3888 " (cutoff:3.500A) Processing helix chain 'G' and resid 3898 through 3903 Processing helix chain 'G' and resid 3914 through 3938 removed outlier: 4.010A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL G3920 " --> pdb=" O ILE G3916 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP G3921 " --> pdb=" O ILE G3917 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR G3922 " --> pdb=" O CYS G3918 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G3923 " --> pdb=" O THR G3919 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G3929 " --> pdb=" O ARG G3925 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR G3934 " --> pdb=" O ILE G3930 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP G3935 " --> pdb=" O SER G3931 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3968 removed outlier: 3.671A pdb=" N LYS G3953 " --> pdb=" O ARG G3949 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA G3954 " --> pdb=" O ASN G3950 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS G3959 " --> pdb=" O MET G3955 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN G3960 " --> pdb=" O SER G3956 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL G3961 " --> pdb=" O VAL G3957 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G3966 " --> pdb=" O PHE G3962 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G3967 " --> pdb=" O ASN G3963 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3981 Processing helix chain 'G' and resid 3984 through 4004 removed outlier: 3.662A pdb=" N VAL G3990 " --> pdb=" O TRP G3986 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU G3993 " --> pdb=" O VAL G3989 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS G3998 " --> pdb=" O HIS G3994 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA G4004 " --> pdb=" O MET G4000 " (cutoff:3.500A) Processing helix chain 'G' and resid 4009 through 4030 removed outlier: 3.835A pdb=" N MET G4026 " --> pdb=" O ASP G4022 " (cutoff:3.500A) Processing helix chain 'G' and resid 4039 through 4051 removed outlier: 3.811A pdb=" N ASP G4046 " --> pdb=" O ARG G4042 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G4048 " --> pdb=" O MET G4044 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU G4050 " --> pdb=" O ASP G4046 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4066 removed outlier: 3.703A pdb=" N PHE G4065 " --> pdb=" O PHE G4061 " (cutoff:3.500A) Processing helix chain 'G' and resid 4066 through 4072 removed outlier: 4.142A pdb=" N ASP G4070 " --> pdb=" O LEU G4066 " (cutoff:3.500A) Processing helix chain 'G' and resid 4074 through 4079 Processing helix chain 'G' and resid 4090 through 4100 Processing helix chain 'G' and resid 4104 through 4115 Processing helix chain 'G' and resid 4117 through 4122 removed outlier: 3.510A pdb=" N GLU G4121 " --> pdb=" O ALA G4117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET G4122 " --> pdb=" O ASP G4118 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4117 through 4122' Processing helix chain 'G' and resid 4124 through 4129 Processing helix chain 'G' and resid 4132 through 4154 removed outlier: 3.552A pdb=" N ALA G4136 " --> pdb=" O PHE G4132 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP G4138 " --> pdb=" O GLU G4134 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G4152 " --> pdb=" O THR G4148 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL G4154 " --> pdb=" O LEU G4150 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4167 removed outlier: 4.255A pdb=" N GLU G4165 " --> pdb=" O ARG G4161 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU G4166 " --> pdb=" O ASN G4162 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA G4167 " --> pdb=" O PHE G4163 " (cutoff:3.500A) Processing helix chain 'G' and resid 4167 through 4175 Processing helix chain 'G' and resid 4198 through 4206 Processing helix chain 'G' and resid 4207 through 4224 removed outlier: 3.510A pdb=" N ASP G4220 " --> pdb=" O GLN G4216 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL G4222 " --> pdb=" O ILE G4218 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4250 removed outlier: 4.652A pdb=" N PHE G4234 " --> pdb=" O LYS G4230 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL G4235 " --> pdb=" O MET G4231 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE G4243 " --> pdb=" O GLU G4239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA G4249 " --> pdb=" O MET G4245 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN G4250 " --> pdb=" O GLN G4246 " (cutoff:3.500A) Processing helix chain 'G' and resid 4542 through 4556 removed outlier: 3.571A pdb=" N TYR G4554 " --> pdb=" O LYS G4550 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4576 removed outlier: 3.869A pdb=" N PHE G4571 " --> pdb=" O LEU G4567 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA G4572 " --> pdb=" O PHE G4568 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE G4573 " --> pdb=" O LEU G4569 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN G4574 " --> pdb=" O ALA G4570 " (cutoff:3.500A) Processing helix chain 'G' and resid 4641 through 4664 removed outlier: 3.885A pdb=" N ALA G4654 " --> pdb=" O HIS G4650 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE G4655 " --> pdb=" O THR G4651 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE G4658 " --> pdb=" O ALA G4654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) Processing helix chain 'G' and resid 4667 through 4683 removed outlier: 3.644A pdb=" N LEU G4677 " --> pdb=" O ARG G4673 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA G4678 " --> pdb=" O GLU G4674 " (cutoff:3.500A) Processing helix chain 'G' and resid 4696 through 4702 Processing helix chain 'G' and resid 4710 through 4714 removed outlier: 3.545A pdb=" N SER G4713 " --> pdb=" O SER G4710 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN G4714 " --> pdb=" O PHE G4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4710 through 4714' Processing helix chain 'G' and resid 4719 through 4729 Processing helix chain 'G' and resid 4733 through 4741 Processing helix chain 'G' and resid 4745 through 4753 removed outlier: 4.067A pdb=" N THR G4751 " --> pdb=" O SER G4747 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS G4753 " --> pdb=" O GLU G4749 " (cutoff:3.500A) Processing helix chain 'G' and resid 4772 through 4784 removed outlier: 3.548A pdb=" N GLY G4781 " --> pdb=" O ILE G4777 " (cutoff:3.500A) Processing helix chain 'G' and resid 4786 through 4802 removed outlier: 3.889A pdb=" N LEU G4790 " --> pdb=" O ASP G4786 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET G4798 " --> pdb=" O TRP G4794 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G4800 " --> pdb=" O MET G4796 " (cutoff:3.500A) Processing helix chain 'G' and resid 4810 through 4816 removed outlier: 3.602A pdb=" N LEU G4814 " --> pdb=" O ALA G4810 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP G4815 " --> pdb=" O ALA G4811 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G4816 " --> pdb=" O HIS G4812 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4810 through 4816' Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.666A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 3.952A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY G4842 " --> pdb=" O VAL G4838 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G4843 " --> pdb=" O MET G4839 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G4845 " --> pdb=" O VAL G4841 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL G4848 " --> pdb=" O LEU G4844 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL G4853 " --> pdb=" O TYR G4849 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL G4854 " --> pdb=" O LEU G4850 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA G4855 " --> pdb=" O TYR G4851 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN G4857 " --> pdb=" O VAL G4853 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4863 removed outlier: 3.915A pdb=" N PHE G4862 " --> pdb=" O PHE G4859 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR G4863 " --> pdb=" O ARG G4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4859 through 4863' Processing helix chain 'G' and resid 4878 through 4889 removed outlier: 3.554A pdb=" N TYR G4883 " --> pdb=" O MET G4879 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G4885 " --> pdb=" O THR G4881 " (cutoff:3.500A) Processing helix chain 'G' and resid 4889 through 4894 removed outlier: 4.384A pdb=" N GLY G4894 " --> pdb=" O GLY G4890 " (cutoff:3.500A) Processing helix chain 'G' and resid 4896 through 4900 removed outlier: 3.807A pdb=" N ASP G4899 " --> pdb=" O GLY G4896 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G4900 " --> pdb=" O ILE G4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4896 through 4900' Processing helix chain 'G' and resid 4909 through 4924 removed outlier: 4.384A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP G4917 " --> pdb=" O ARG G4913 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE G4918 " --> pdb=" O VAL G4914 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G4924 " --> pdb=" O PHE G4920 " (cutoff:3.500A) Processing helix chain 'G' and resid 4924 through 4955 removed outlier: 4.094A pdb=" N LEU G4929 " --> pdb=" O ILE G4925 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA G4930 " --> pdb=" O VAL G4926 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G4936 " --> pdb=" O ILE G4932 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE G4937 " --> pdb=" O GLN G4933 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP G4938 " --> pdb=" O GLY G4934 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA G4939 " --> pdb=" O LEU G4935 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE G4940 " --> pdb=" O ILE G4936 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP G4945 " --> pdb=" O GLY G4941 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU G4948 " --> pdb=" O ARG G4944 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL G4950 " --> pdb=" O GLN G4946 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS G4951 " --> pdb=" O GLN G4947 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP G4953 " --> pdb=" O GLN G4949 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET G4954 " --> pdb=" O VAL G4950 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4970 removed outlier: 3.907A pdb=" N TYR G4967 " --> pdb=" O GLY G4964 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP G4969 " --> pdb=" O ASP G4966 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR G4970 " --> pdb=" O TYR G4967 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4982 Processing helix chain 'G' and resid 4985 through 4997 removed outlier: 3.593A pdb=" N MET G4989 " --> pdb=" O LEU G4985 " (cutoff:3.500A) Processing helix chain 'G' and resid 5006 through 5017 Processing helix chain 'G' and resid 5032 through 5037 Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 56 through 65 removed outlier: 4.083A pdb=" N GLY F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.748A pdb=" N VAL F 80 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 56 through 65 removed outlier: 4.081A pdb=" N GLY A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.748A pdb=" N VAL A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 Processing helix chain 'H' and resid 56 through 65 removed outlier: 4.082A pdb=" N GLY H 62 " --> pdb=" O GLY H 58 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.747A pdb=" N VAL H 80 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 43 Processing helix chain 'J' and resid 56 through 65 removed outlier: 4.083A pdb=" N GLY J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.749A pdb=" N VAL J 80 " --> pdb=" O THR J 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 25 removed outlier: 4.437A pdb=" N GLU B 40 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU B 46 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 73 removed outlier: 3.547A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 152 Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AA6, first strand: chain 'B' and resid 299 through 302 removed outlier: 4.004A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 292 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 291 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N LEU B 293 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 13.688A pdb=" N LEU B 280 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 230 through 233 Processing sheet with id=AA8, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 359 Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 614 removed outlier: 5.730A pdb=" N ALA B 613 " --> pdb=" O GLN B2169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 636 through 639 removed outlier: 3.515A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 644 through 646 Processing sheet with id=AB4, first strand: chain 'B' and resid 742 through 743 removed outlier: 3.517A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 664 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 746 " --> pdb=" O PHE B 664 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 742 through 743 removed outlier: 3.517A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B 665 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 714 through 716 Processing sheet with id=AB7, first strand: chain 'B' and resid 839 through 840 removed outlier: 4.006A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AB9, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.520A pdb=" N THR B 892 " --> pdb=" O HIS B 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 940 through 941 Processing sheet with id=AC2, first strand: chain 'B' and resid 1073 through 1075 Processing sheet with id=AC3, first strand: chain 'B' and resid 1238 through 1239 Processing sheet with id=AC4, first strand: chain 'B' and resid 1255 through 1259 Processing sheet with id=AC5, first strand: chain 'B' and resid 1459 through 1463 removed outlier: 3.829A pdb=" N UNK B1287 " --> pdb=" O UNK B1460 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1293 through 1294 Processing sheet with id=AC7, first strand: chain 'B' and resid 1515 through 1516 Processing sheet with id=AC8, first strand: chain 'B' and resid 4178 through 4183 Processing sheet with id=AC9, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AD1, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AD2, first strand: chain 'E' and resid 23 through 25 removed outlier: 4.438A pdb=" N GLU E 40 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU E 46 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 71 through 73 removed outlier: 3.547A pdb=" N GLN E 71 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 148 through 152 Processing sheet with id=AD5, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AD6, first strand: chain 'E' and resid 299 through 302 removed outlier: 4.006A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 292 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 291 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE E 282 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N LEU E 293 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 13.689A pdb=" N LEU E 280 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 230 through 233 Processing sheet with id=AD8, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AD9, first strand: chain 'E' and resid 356 through 359 Processing sheet with id=AE1, first strand: chain 'E' and resid 613 through 614 removed outlier: 5.730A pdb=" N ALA E 613 " --> pdb=" O GLN E2169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 636 through 639 removed outlier: 3.514A pdb=" N ARG E1646 " --> pdb=" O ILE E1641 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 644 through 646 Processing sheet with id=AE4, first strand: chain 'E' and resid 742 through 743 removed outlier: 3.516A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 664 " --> pdb=" O CYS E 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS E 746 " --> pdb=" O PHE E 664 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 742 through 743 removed outlier: 3.516A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU E 665 " --> pdb=" O LEU E 792 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 714 through 716 Processing sheet with id=AE7, first strand: chain 'E' and resid 839 through 840 removed outlier: 4.008A pdb=" N ASP E1147 " --> pdb=" O ALA E1094 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AE9, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.520A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'E' and resid 940 through 941 Processing sheet with id=AF2, first strand: chain 'E' and resid 1073 through 1075 Processing sheet with id=AF3, first strand: chain 'E' and resid 1238 through 1239 Processing sheet with id=AF4, first strand: chain 'E' and resid 1255 through 1259 Processing sheet with id=AF5, first strand: chain 'E' and resid 1459 through 1463 removed outlier: 3.714A pdb=" N UNK E1287 " --> pdb=" O UNK E1460 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1293 through 1294 Processing sheet with id=AF7, first strand: chain 'E' and resid 1515 through 1516 Processing sheet with id=AF8, first strand: chain 'E' and resid 4178 through 4183 Processing sheet with id=AF9, first strand: chain 'E' and resid 4580 through 4583 Processing sheet with id=AG1, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AG2, first strand: chain 'I' and resid 23 through 25 removed outlier: 4.438A pdb=" N GLU I 40 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU I 46 " --> pdb=" O GLU I 40 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 71 through 73 removed outlier: 3.547A pdb=" N GLN I 71 " --> pdb=" O LEU I 108 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 148 through 152 Processing sheet with id=AG5, first strand: chain 'I' and resid 181 through 184 Processing sheet with id=AG6, first strand: chain 'I' and resid 299 through 302 removed outlier: 4.006A pdb=" N VAL I 300 " --> pdb=" O ALA I 292 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA I 292 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 291 " --> pdb=" O ILE I 282 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE I 282 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N LEU I 293 " --> pdb=" O LEU I 280 " (cutoff:3.500A) removed outlier: 13.688A pdb=" N LEU I 280 " --> pdb=" O LEU I 293 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 230 through 233 Processing sheet with id=AG8, first strand: chain 'I' and resid 314 through 317 Processing sheet with id=AG9, first strand: chain 'I' and resid 356 through 359 Processing sheet with id=AH1, first strand: chain 'I' and resid 613 through 614 removed outlier: 5.731A pdb=" N ALA I 613 " --> pdb=" O GLN I2169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'I' and resid 636 through 639 removed outlier: 3.515A pdb=" N ARG I1646 " --> pdb=" O ILE I1641 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 644 through 646 Processing sheet with id=AH4, first strand: chain 'I' and resid 742 through 743 removed outlier: 3.518A pdb=" N ASP I 742 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE I 664 " --> pdb=" O CYS I 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS I 746 " --> pdb=" O PHE I 664 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 742 through 743 removed outlier: 3.518A pdb=" N ASP I 742 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU I 665 " --> pdb=" O LEU I 792 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 714 through 716 Processing sheet with id=AH7, first strand: chain 'I' and resid 839 through 840 removed outlier: 4.006A pdb=" N ASP I1147 " --> pdb=" O ALA I1094 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AH9, first strand: chain 'I' and resid 892 through 893 removed outlier: 6.520A pdb=" N THR I 892 " --> pdb=" O HIS I 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'I' and resid 940 through 941 Processing sheet with id=AI2, first strand: chain 'I' and resid 1073 through 1075 Processing sheet with id=AI3, first strand: chain 'I' and resid 1238 through 1239 Processing sheet with id=AI4, first strand: chain 'I' and resid 1255 through 1259 Processing sheet with id=AI5, first strand: chain 'I' and resid 1459 through 1463 removed outlier: 3.911A pdb=" N UNK I1287 " --> pdb=" O UNK I1460 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 1293 through 1294 Processing sheet with id=AI7, first strand: chain 'I' and resid 1515 through 1516 Processing sheet with id=AI8, first strand: chain 'I' and resid 4178 through 4183 Processing sheet with id=AI9, first strand: chain 'I' and resid 4580 through 4583 Processing sheet with id=AJ1, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AJ2, first strand: chain 'G' and resid 23 through 25 removed outlier: 4.438A pdb=" N GLU G 40 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU G 46 " --> pdb=" O GLU G 40 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 71 through 73 removed outlier: 3.547A pdb=" N GLN G 71 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 148 through 152 Processing sheet with id=AJ5, first strand: chain 'G' and resid 181 through 184 Processing sheet with id=AJ6, first strand: chain 'G' and resid 299 through 302 removed outlier: 4.004A pdb=" N VAL G 300 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA G 292 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 291 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE G 282 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N LEU G 293 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 13.689A pdb=" N LEU G 280 " --> pdb=" O LEU G 293 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 230 through 233 Processing sheet with id=AJ8, first strand: chain 'G' and resid 314 through 317 Processing sheet with id=AJ9, first strand: chain 'G' and resid 356 through 359 Processing sheet with id=AK1, first strand: chain 'G' and resid 613 through 614 removed outlier: 5.730A pdb=" N ALA G 613 " --> pdb=" O GLN G2169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'G' and resid 636 through 639 removed outlier: 3.514A pdb=" N ARG G1646 " --> pdb=" O ILE G1641 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 644 through 646 Processing sheet with id=AK4, first strand: chain 'G' and resid 742 through 743 removed outlier: 3.517A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE G 664 " --> pdb=" O CYS G 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS G 746 " --> pdb=" O PHE G 664 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 742 through 743 removed outlier: 3.517A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU G 665 " --> pdb=" O LEU G 792 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 714 through 716 Processing sheet with id=AK7, first strand: chain 'G' and resid 839 through 840 removed outlier: 4.006A pdb=" N ASP G1147 " --> pdb=" O ALA G1094 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AK9, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.520A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK9 Processing sheet with id=AL1, first strand: chain 'G' and resid 940 through 941 Processing sheet with id=AL2, first strand: chain 'G' and resid 1073 through 1075 Processing sheet with id=AL3, first strand: chain 'G' and resid 1238 through 1239 Processing sheet with id=AL4, first strand: chain 'G' and resid 1255 through 1259 Processing sheet with id=AL5, first strand: chain 'G' and resid 1459 through 1463 removed outlier: 3.785A pdb=" N UNK G1287 " --> pdb=" O UNK G1460 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'G' and resid 1293 through 1294 Processing sheet with id=AL7, first strand: chain 'G' and resid 1515 through 1517 Processing sheet with id=AL8, first strand: chain 'G' and resid 4178 through 4183 Processing sheet with id=AL9, first strand: chain 'G' and resid 4580 through 4583 Processing sheet with id=AM1, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AM2, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.536A pdb=" N PHE F 99 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AM4, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.537A pdb=" N PHE A 99 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AM6, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.537A pdb=" N PHE H 99 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'J' and resid 21 through 22 Processing sheet with id=AM8, first strand: chain 'J' and resid 27 through 30 removed outlier: 3.537A pdb=" N PHE J 99 " --> pdb=" O LEU J 74 " (cutoff:3.500A) 5023 hydrogen bonds defined for protein. 14373 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: 84.89 Time building geometry restraints manager: 36.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 39284 1.34 - 1.46: 21931 1.46 - 1.58: 60773 1.58 - 1.70: 4 1.70 - 1.82: 1020 Bond restraints: 123012 Sorted by residual: bond pdb=" N GLU G4871 " pdb=" CA GLU G4871 " ideal model delta sigma weight residual 1.462 1.489 -0.027 9.90e-03 1.02e+04 7.49e+00 bond pdb=" N GLU I4871 " pdb=" CA GLU I4871 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.90e-03 1.02e+04 6.77e+00 bond pdb=" N GLU B4871 " pdb=" CA GLU B4871 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.05e-02 9.07e+03 5.80e+00 bond pdb=" N GLU E4871 " pdb=" CA GLU E4871 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.05e-02 9.07e+03 5.73e+00 bond pdb=" C LEU B2023 " pdb=" N PRO B2024 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.28e+00 ... (remaining 123007 not shown) Histogram of bond angle deviations from ideal: 97.67 - 105.85: 2761 105.85 - 114.03: 70736 114.03 - 122.22: 70130 122.22 - 130.40: 23493 130.40 - 138.58: 600 Bond angle restraints: 167720 Sorted by residual: angle pdb=" C HIS B4153 " pdb=" N VAL B4154 " pdb=" CA VAL B4154 " ideal model delta sigma weight residual 123.33 116.68 6.65 8.70e-01 1.32e+00 5.85e+01 angle pdb=" C HIS E4153 " pdb=" N VAL E4154 " pdb=" CA VAL E4154 " ideal model delta sigma weight residual 123.33 116.74 6.59 8.70e-01 1.32e+00 5.73e+01 angle pdb=" C HIS G4153 " pdb=" N VAL G4154 " pdb=" CA VAL G4154 " ideal model delta sigma weight residual 123.33 116.75 6.58 8.70e-01 1.32e+00 5.71e+01 angle pdb=" C HIS I4153 " pdb=" N VAL I4154 " pdb=" CA VAL I4154 " ideal model delta sigma weight residual 123.33 116.79 6.54 8.70e-01 1.32e+00 5.66e+01 angle pdb=" N PRO I4872 " pdb=" CA PRO I4872 " pdb=" C PRO I4872 " ideal model delta sigma weight residual 113.53 103.15 10.38 1.39e+00 5.18e-01 5.57e+01 ... (remaining 167715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 69381 15.57 - 31.14: 3108 31.14 - 46.71: 774 46.71 - 62.28: 61 62.28 - 77.84: 100 Dihedral angle restraints: 73424 sinusoidal: 23656 harmonic: 49768 Sorted by residual: dihedral pdb=" CA GLY G2343 " pdb=" C GLY G2343 " pdb=" N GLU G2344 " pdb=" CA GLU G2344 " ideal model delta harmonic sigma weight residual 180.00 -120.06 -59.94 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA GLY E2343 " pdb=" C GLY E2343 " pdb=" N GLU E2344 " pdb=" CA GLU E2344 " ideal model delta harmonic sigma weight residual -180.00 -120.15 -59.85 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA GLY I2343 " pdb=" C GLY I2343 " pdb=" N GLU I2344 " pdb=" CA GLU I2344 " ideal model delta harmonic sigma weight residual -180.00 -120.16 -59.84 0 5.00e+00 4.00e-02 1.43e+02 ... (remaining 73421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 16421 0.066 - 0.132: 2766 0.132 - 0.198: 356 0.198 - 0.264: 41 0.264 - 0.330: 16 Chirality restraints: 19600 Sorted by residual: chirality pdb=" CB ILE E 826 " pdb=" CA ILE E 826 " pdb=" CG1 ILE E 826 " pdb=" CG2 ILE E 826 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE G 826 " pdb=" CA ILE G 826 " pdb=" CG1 ILE G 826 " pdb=" CG2 ILE G 826 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE I 826 " pdb=" CA ILE I 826 " pdb=" CG1 ILE I 826 " pdb=" CG2 ILE I 826 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 19597 not shown) Planarity restraints: 22092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E4666 " 0.065 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO E4667 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO E4667 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO E4667 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G4666 " -0.065 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO G4667 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO G4667 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO G4667 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I4666 " -0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO I4667 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO I4667 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO I4667 " -0.053 5.00e-02 4.00e+02 ... (remaining 22089 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 16 2.08 - 2.78: 29544 2.78 - 3.49: 168307 3.49 - 4.19: 286012 4.19 - 4.90: 467488 Nonbonded interactions: 951367 Sorted by model distance: nonbonded pdb=" O UNK B1487 " pdb=" CB UNK B1551 " model vdw 1.373 3.440 nonbonded pdb=" O UNK E3557 " pdb=" CB UNK E3561 " model vdw 1.373 3.440 nonbonded pdb=" O UNK E1487 " pdb=" CB UNK E1551 " model vdw 1.373 3.440 nonbonded pdb=" CB UNK E1297 " pdb=" O UNK E1452 " model vdw 1.373 3.440 nonbonded pdb=" CB UNK G1297 " pdb=" O UNK G1452 " model vdw 1.374 3.440 ... (remaining 951362 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 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'H' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 2.520 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: 0.120 Extract box with map and model: 17.040 Check model and map are aligned: 1.320 Set scattering table: 0.830 Process input model: 280.910 Find NCS groups from input model: 5.900 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 311.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 123012 Z= 0.363 Angle : 1.044 14.338 167720 Z= 0.577 Chirality : 0.051 0.330 19600 Planarity : 0.007 0.099 22092 Dihedral : 10.652 77.844 41064 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.95 % Favored : 88.90 % Rotamer: Outliers : 0.31 % Allowed : 3.25 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.53 % 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: -4.72 (0.06), residues: 13356 helix: -3.23 (0.05), residues: 5296 sheet: -2.92 (0.15), residues: 944 loop : -3.13 (0.06), residues: 7116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP G5019 HIS 0.015 0.003 HIS G1665 PHE 0.033 0.003 PHE E4163 TYR 0.040 0.003 TYR E4863 ARG 0.016 0.001 ARG G1671 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.074 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.3875 time to fit residues: 3.6825 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.075 Evaluate side-chains 428 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 420 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 VAL cc_start: 0.5750 (t) cc_final: 0.4598 (t) REVERT: B 2423 MET cc_start: 0.6709 (ppp) cc_final: 0.6172 (tmm) REVERT: B 3783 ILE cc_start: 0.6763 (mm) cc_final: 0.6504 (mm) REVERT: B 4048 LEU cc_start: 0.7796 (mt) cc_final: 0.7333 (mt) REVERT: B 4145 VAL cc_start: 0.7163 (p) cc_final: 0.6929 (p) REVERT: B 4146 LEU cc_start: 0.7546 (tp) cc_final: 0.7101 (tt) outliers start: 8 outliers final: 0 residues processed: 428 average time/residue: 0.3619 time to fit residues: 236.6422 Evaluate side-chains 228 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.0030 chunk 10 optimal weight: 0.0030 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0020 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 0.1486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 57 ASN B 71 GLN B 79 GLN B 105 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 218 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS B 405 HIS B 465 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN B1158 ASN B1598 GLN B1611 HIS ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1702 HIS B1775 HIS B1941 ASN B1970 GLN B2005 GLN B2100 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2184 ASN B2291 GLN B2884 ASN B3766 GLN B3809 ASN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4005 GLN B4054 ASN ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4156 HIS B4553 ASN B4691 GLN B4728 HIS B4806 ASN B5031 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4152 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 123012 Z= 0.210 Angle : 0.734 10.570 167720 Z= 0.377 Chirality : 0.040 0.253 19600 Planarity : 0.006 0.130 22092 Dihedral : 6.632 54.766 18056 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.09 % Favored : 89.76 % Rotamer: Outliers : 0.12 % Allowed : 2.60 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.22 % 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: -3.78 (0.06), residues: 13356 helix: -2.08 (0.06), residues: 5804 sheet: -2.36 (0.16), residues: 996 loop : -2.95 (0.07), residues: 6556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 515 HIS 0.007 0.001 HIS J 87 PHE 0.026 0.002 PHE B4780 TYR 0.025 0.002 TYR G3936 ARG 0.014 0.001 ARG E3672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.3565 time to fit residues: 1.5646 Evaluate side-chains 2 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.078 Evaluate side-chains 340 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 337 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 LEU cc_start: 0.5507 (mt) cc_final: 0.5267 (mt) REVERT: B 2123 LEU cc_start: 0.6878 (pt) cc_final: 0.6347 (tt) REVERT: B 2423 MET cc_start: 0.6935 (ppp) cc_final: 0.6234 (tmm) REVERT: B 3800 LEU cc_start: 0.8354 (tp) cc_final: 0.7949 (tt) REVERT: B 4163 PHE cc_start: 0.5093 (m-80) cc_final: 0.4828 (m-10) REVERT: B 4730 ASP cc_start: 0.6149 (p0) cc_final: 0.5837 (p0) REVERT: B 4989 MET cc_start: 0.5563 (mtp) cc_final: 0.5289 (mtp) REVERT: B 5020 ASP cc_start: 0.5936 (p0) cc_final: 0.5515 (p0) outliers start: 3 outliers final: 1 residues processed: 338 average time/residue: 0.3477 time to fit residues: 184.0086 Evaluate side-chains 232 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0770 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 0.0050 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 40.0000 overall best weight: 2.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 HIS B1660 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1719 HIS ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2036 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2184 ASN ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4130 ASN ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4553 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4214 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 123012 Z= 0.182 Angle : 0.679 13.453 167720 Z= 0.346 Chirality : 0.039 0.293 19600 Planarity : 0.005 0.109 22092 Dihedral : 6.122 53.470 18056 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.42 % Favored : 89.49 % Rotamer: Outliers : 0.12 % Allowed : 3.45 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.16 % 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: -3.11 (0.07), residues: 13356 helix: -1.39 (0.06), residues: 5816 sheet: -2.25 (0.16), residues: 916 loop : -2.69 (0.07), residues: 6624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP G3935 HIS 0.010 0.001 HIS E1663 PHE 0.046 0.002 PHE G 67 TYR 0.028 0.002 TYR G1711 ARG 0.013 0.001 ARG G2104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.3497 time to fit residues: 1.5460 Evaluate side-chains 2 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.079 Evaluate side-chains 292 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 289 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 961 MET cc_start: 0.1131 (ttm) cc_final: 0.0213 (mtm) REVERT: B 1935 VAL cc_start: 0.6780 (t) cc_final: 0.6575 (t) REVERT: B 2123 LEU cc_start: 0.7265 (pt) cc_final: 0.6932 (tt) REVERT: B 2423 MET cc_start: 0.6804 (ppp) cc_final: 0.6191 (tmm) REVERT: B 4931 ILE cc_start: 0.8432 (pt) cc_final: 0.8098 (pt) REVERT: B 4992 LEU cc_start: 0.7416 (tp) cc_final: 0.6949 (tp) REVERT: B 5001 THR cc_start: 0.8245 (m) cc_final: 0.7864 (m) REVERT: B 5020 ASP cc_start: 0.6232 (p0) cc_final: 0.5296 (p0) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.3242 time to fit residues: 152.4092 Evaluate side-chains 219 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 0.0370 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 0.0060 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 479 GLN ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 HIS ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2184 ASN ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4130 ASN ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4691 GLN B4806 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4156 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 123012 Z= 0.168 Angle : 0.660 14.019 167720 Z= 0.330 Chirality : 0.039 0.250 19600 Planarity : 0.005 0.081 22092 Dihedral : 5.704 52.705 18056 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.76 % Favored : 90.15 % Rotamer: Outliers : 0.15 % Allowed : 3.10 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.09 % 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: -2.78 (0.07), residues: 13356 helix: -1.05 (0.06), residues: 5964 sheet: -2.09 (0.16), residues: 948 loop : -2.60 (0.08), residues: 6444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E3935 HIS 0.005 0.001 HIS J 87 PHE 0.044 0.001 PHE E 67 TYR 0.025 0.002 TYR G1711 ARG 0.010 0.001 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2535 time to fit residues: 0.9154 Evaluate side-chains 2 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.084 Evaluate side-chains 291 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 287 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 961 MET cc_start: 0.0957 (ttm) cc_final: 0.0277 (mtm) REVERT: B 1730 MET cc_start: 0.5092 (ptt) cc_final: 0.4402 (ptm) REVERT: B 1935 VAL cc_start: 0.6731 (t) cc_final: 0.6361 (t) REVERT: B 2123 LEU cc_start: 0.7347 (pt) cc_final: 0.6989 (tt) REVERT: B 2423 MET cc_start: 0.6783 (ppp) cc_final: 0.6020 (tmm) REVERT: B 4880 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.5140 (mmp) REVERT: B 4931 ILE cc_start: 0.8310 (pt) cc_final: 0.8028 (pt) REVERT: B 4991 PHE cc_start: 0.5841 (t80) cc_final: 0.5425 (t80) REVERT: B 4992 LEU cc_start: 0.7330 (tp) cc_final: 0.6936 (tp) REVERT: B 5020 ASP cc_start: 0.6235 (p0) cc_final: 0.5278 (p0) outliers start: 4 outliers final: 0 residues processed: 290 average time/residue: 0.3230 time to fit residues: 151.7954 Evaluate side-chains 214 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 9 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.3012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2184 ASN ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3761 GLN B3781 GLN ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4691 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4141 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 123012 Z= 0.154 Angle : 0.641 13.882 167720 Z= 0.321 Chirality : 0.039 0.314 19600 Planarity : 0.005 0.081 22092 Dihedral : 5.487 51.518 18056 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.37 % Favored : 90.54 % Rotamer: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.09 % 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: -2.56 (0.07), residues: 13356 helix: -0.82 (0.06), residues: 5968 sheet: -1.92 (0.16), residues: 960 loop : -2.54 (0.07), residues: 6428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G4644 HIS 0.005 0.001 HIS G3667 PHE 0.042 0.001 PHE B 67 TYR 0.026 0.001 TYR I1089 ARG 0.013 0.000 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2328 time to fit residues: 0.8412 Evaluate side-chains 2 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.078 Evaluate side-chains 284 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 961 MET cc_start: 0.0940 (ttm) cc_final: 0.0307 (mtm) REVERT: B 1648 MET cc_start: 0.2282 (pmm) cc_final: 0.2072 (pmm) REVERT: B 1730 MET cc_start: 0.5172 (ptt) cc_final: 0.4476 (ptm) REVERT: B 1851 MET cc_start: 0.5744 (mpp) cc_final: 0.5330 (mpp) REVERT: B 1939 MET cc_start: 0.6173 (ptp) cc_final: 0.5931 (ptm) REVERT: B 2423 MET cc_start: 0.6672 (ppp) cc_final: 0.6078 (tmm) REVERT: B 3731 LYS cc_start: 0.8564 (pttp) cc_final: 0.7751 (ptpp) REVERT: B 4931 ILE cc_start: 0.7990 (pt) cc_final: 0.7783 (pt) REVERT: B 4991 PHE cc_start: 0.5798 (t80) cc_final: 0.5539 (t80) REVERT: B 4992 LEU cc_start: 0.7271 (tp) cc_final: 0.6929 (tp) REVERT: B 5020 ASP cc_start: 0.6106 (p0) cc_final: 0.5185 (p0) outliers start: 1 outliers final: 1 residues processed: 283 average time/residue: 0.3089 time to fit residues: 141.0904 Evaluate side-chains 208 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.0050 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 0.0030 chunk 37 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 overall best weight: 0.8806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2184 ASN B2933 ASN B3643 ASN ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4142 ASN B4946 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4149 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 123012 Z= 0.158 Angle : 0.636 13.810 167720 Z= 0.320 Chirality : 0.039 0.260 19600 Planarity : 0.005 0.090 22092 Dihedral : 5.308 49.149 18056 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.25 % Favored : 90.66 % Rotamer: Outliers : 0.08 % Allowed : 2.05 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.09 % 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: -2.35 (0.07), residues: 13356 helix: -0.63 (0.07), residues: 5976 sheet: -1.79 (0.15), residues: 1056 loop : -2.46 (0.08), residues: 6324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E4644 HIS 0.004 0.001 HIS F 87 PHE 0.083 0.002 PHE E2340 TYR 0.023 0.001 TYR G5009 ARG 0.012 0.000 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2435 time to fit residues: 0.8782 Evaluate side-chains 2 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.092 Evaluate side-chains 267 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 961 MET cc_start: 0.0738 (ttm) cc_final: 0.0166 (mtm) REVERT: B 1711 TYR cc_start: 0.2659 (m-80) cc_final: 0.2338 (m-10) REVERT: B 1730 MET cc_start: 0.5226 (ptt) cc_final: 0.4611 (ptm) REVERT: B 1939 MET cc_start: 0.6428 (ptp) cc_final: 0.6094 (ptm) REVERT: B 2423 MET cc_start: 0.6749 (ppp) cc_final: 0.6149 (tmm) REVERT: B 3731 LYS cc_start: 0.8485 (pttp) cc_final: 0.7753 (ptpp) REVERT: B 3782 MET cc_start: 0.7184 (tmm) cc_final: 0.6864 (tmm) REVERT: B 4919 THR cc_start: 0.6648 (p) cc_final: 0.6228 (p) REVERT: B 4991 PHE cc_start: 0.5761 (t80) cc_final: 0.5558 (t80) REVERT: B 4992 LEU cc_start: 0.7248 (tp) cc_final: 0.6762 (tp) REVERT: B 5020 ASP cc_start: 0.6018 (p0) cc_final: 0.5144 (p0) outliers start: 2 outliers final: 0 residues processed: 267 average time/residue: 0.3695 time to fit residues: 161.7202 Evaluate side-chains 201 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** 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 306, in __init__ self.caller(self.refine_xyz) 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 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4883 > 50: distance: 0 - 1: 40.860 distance: 1 - 4: 14.158 distance: 2 - 3: 7.139 distance: 6 - 7: 41.050 distance: 9 - 10: 39.161 distance: 10 - 11: 40.870 distance: 13 - 14: 33.766 distance: 14 - 15: 40.807 distance: 15 - 17: 38.789 distance: 17 - 18: 46.935 distance: 18 - 19: 46.625 distance: 18 - 21: 48.990 distance: 19 - 20: 40.195 distance: 21 - 22: 55.851 distance: 22 - 23: 54.277 distance: 22 - 24: 69.287 distance: 23 - 25: 33.493 distance: 24 - 26: 39.295 distance: 25 - 26: 69.819 distance: 27 - 28: 39.964 distance: 28 - 31: 39.423 distance: 29 - 30: 38.990 distance: 29 - 32: 57.315 distance: 32 - 33: 39.302 distance: 33 - 34: 41.270 distance: 33 - 36: 40.156 distance: 34 - 35: 56.511 distance: 34 - 39: 40.415 distance: 36 - 38: 40.782 distance: 40 - 43: 29.200 distance: 41 - 42: 56.536 distance: 43 - 44: 64.178 distance: 44 - 45: 39.359 distance: 44 - 46: 20.047 distance: 47 - 48: 40.864 distance: 48 - 49: 9.487 distance: 48 - 51: 50.314 distance: 51 - 52: 41.332 distance: 52 - 53: 35.196 distance: 52 - 54: 37.230 distance: 56 - 57: 40.571 distance: 56 - 59: 40.823 distance: 57 - 58: 41.086 distance: 57 - 67: 40.645 distance: 59 - 60: 54.677 distance: 60 - 61: 55.646 distance: 60 - 62: 38.329 distance: 62 - 64: 40.000 distance: 63 - 65: 39.887 distance: 64 - 65: 40.126 distance: 65 - 66: 57.107 distance: 67 - 68: 39.819 distance: 68 - 69: 40.431 distance: 69 - 70: 40.414 distance: 69 - 71: 38.461 distance: 71 - 72: 56.799 distance: 72 - 73: 39.245 distance: 73 - 74: 40.267 distance: 75 - 76: 40.589