Starting phenix.real_space_refine on Thu Mar 14 11:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmg_22393/03_2024/7jmg_22393_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmg_22393/03_2024/7jmg_22393.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/7jmg_22393/03_2024/7jmg_22393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmg_22393/03_2024/7jmg_22393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmg_22393/03_2024/7jmg_22393_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmg_22393/03_2024/7jmg_22393_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= 0.030 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 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 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 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 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: 0.27s 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 177.988 204.735 88.034 1.00 0.93 S ATOM 28723 SG CYS B4961 180.025 203.964 91.655 1.00 1.05 S ATOM 58067 SG CYS E4958 205.200 207.949 87.800 1.00 1.23 S ATOM 58092 SG CYS E4961 204.456 205.933 91.438 1.00 1.27 S ATOM 87436 SG CYS I4958 180.921 177.467 87.990 1.00 1.09 S ATOM 87461 SG CYS I4961 181.709 179.478 91.623 1.00 1.23 S ATOM A0CYT SG CYS G4958 208.233 180.592 87.820 1.00 1.33 S ATOM A0CZI SG CYS G4961 206.241 181.360 91.467 1.00 1.39 S Time building chain proxies: 46.77, per 1000 atoms: 0.39 Number of scatterers: 120756 At special positions: 0 Unit cell: (387.795, 386.54, 212.095, 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: 34.07 Conformation dependent library (CDL) restraints added in 14.8 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 B4958 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" ND1 HIS E4983 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4958 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4961 " 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 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 " 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: 694 helices and 107 sheets defined 60.7% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.51 Creating SS restraints... Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.593A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 395 through 419 removed outlier: 3.753A pdb=" N GLN B 399 " --> pdb=" O GLN B 395 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.844A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 481 removed outlier: 3.521A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 473 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 510 through 529 removed outlier: 4.076A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.820A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.825A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.714A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.994A 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: 4.116A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.987A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 622 " --> pdb=" O GLN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 890 removed outlier: 3.635A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B 879 " --> pdb=" O ALA B 875 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 934 removed outlier: 3.673A pdb=" N ASN B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 988 removed outlier: 3.734A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1001 removed outlier: 3.519A pdb=" N HIS B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B 996 " --> pdb=" O GLY B 992 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B1000 " --> pdb=" O TRP B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1041 removed outlier: 3.582A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.581A pdb=" N LEU B1046 " --> pdb=" O ALA B1042 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B1047 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B1048 " --> pdb=" O ARG B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1082 Processing helix chain 'B' and resid 1575 through 1579 removed outlier: 3.567A pdb=" N ALA B1578 " --> pdb=" O LEU B1575 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B1579 " --> pdb=" O SER B1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1575 through 1579' Processing helix chain 'B' and resid 1652 through 1657 removed outlier: 3.505A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1674 removed outlier: 3.809A pdb=" N HIS B1665 " --> pdb=" O ARG B1661 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B1670 " --> pdb=" O THR B1666 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG B1671 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1686 removed outlier: 3.654A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) Processing helix chain 'B' and resid 1692 through 1700 removed outlier: 4.201A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1710 through 1714 removed outlier: 3.805A pdb=" N ASP B1713 " --> pdb=" O GLY B1710 " (cutoff:3.500A) Processing helix chain 'B' and resid 1715 through 1720 Processing helix chain 'B' and resid 1720 through 1730 removed outlier: 3.930A pdb=" N ARG B1725 " --> pdb=" O GLU B1721 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1824 removed outlier: 3.665A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B1814 " --> pdb=" O LYS B1810 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B1816 " --> pdb=" O LEU B1812 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1838 Processing helix chain 'B' and resid 1840 through 1851 removed outlier: 3.579A 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 1982 removed outlier: 3.612A pdb=" N LEU B1937 " --> pdb=" O GLU B1933 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B1948 " --> pdb=" O GLU B1944 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B1966 " --> pdb=" O ALA B1962 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B1973 " --> pdb=" O LEU B1969 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B1978 " --> pdb=" O ARG B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1994 removed outlier: 3.614A 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 2011 removed outlier: 3.623A pdb=" N ILE B2006 " --> pdb=" O PRO B2002 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) Processing helix chain 'B' and resid 2029 through 2042 Processing helix chain 'B' and resid 2094 through 2108 removed outlier: 3.796A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2129 removed outlier: 3.513A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B2126 " --> pdb=" O SER B2122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2137 Processing helix chain 'B' and resid 2148 through 2165 removed outlier: 3.900A pdb=" N CYS B2158 " --> pdb=" O SER B2154 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B2165 " --> pdb=" O GLN B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2186 removed outlier: 3.691A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 Processing helix chain 'B' and resid 2194 through 2201 removed outlier: 4.017A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2216 removed outlier: 3.974A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2228 through 2242 removed outlier: 3.640A pdb=" N CYS B2233 " --> pdb=" O VAL B2229 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B2237 " --> pdb=" O CYS B2233 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B2238 " --> pdb=" O ARG B2234 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2252 removed outlier: 3.583A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2262 removed outlier: 4.074A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 Processing helix chain 'B' and resid 2294 through 2306 removed outlier: 3.543A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 4.307A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2331 removed outlier: 3.587A pdb=" N TYR B2331 " --> pdb=" O GLY B2327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2335 through 2339 removed outlier: 4.050A pdb=" N ALA B2338 " --> pdb=" O LEU B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2349 Processing helix chain 'B' and resid 2350 through 2358 removed outlier: 3.591A 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 2375 through 2388 removed outlier: 3.504A pdb=" N ARG B2385 " --> pdb=" O GLU B2381 " (cutoff:3.500A) Processing helix chain 'B' and resid 2389 through 2393 Processing helix chain 'B' and resid 2417 through 2436 removed outlier: 4.109A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B2422 " --> pdb=" O LEU B2418 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B2425 " --> pdb=" O ALA B2421 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B2428 " --> pdb=" O SER B2424 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B2433 " --> pdb=" O LEU B2429 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2445 removed outlier: 3.738A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2461 removed outlier: 3.860A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2471 Processing helix chain 'B' and resid 2502 through 2507 removed outlier: 3.546A pdb=" N UNK B2506 " --> pdb=" O UNK B2502 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2525 removed outlier: 4.272A pdb=" N UNK B2523 " --> pdb=" O UNK B2519 " (cutoff:3.500A) Processing helix chain 'B' and resid 2525 through 2530 Processing helix chain 'B' and resid 2542 through 2548 removed outlier: 3.697A pdb=" N UNK B2546 " --> pdb=" O UNK B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2557 removed outlier: 3.757A pdb=" N UNK B2555 " --> pdb=" O UNK B2551 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2581 removed outlier: 3.520A pdb=" N UNK B2578 " --> pdb=" O UNK B2574 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2602 removed outlier: 3.612A pdb=" N UNK B2597 " --> pdb=" O UNK B2593 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N UNK B2602 " --> pdb=" O UNK B2598 " (cutoff:3.500A) Processing helix chain 'B' and resid 2610 through 2618 removed outlier: 3.764A pdb=" N UNK B2618 " --> pdb=" O UNK B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2626 through 2640 removed outlier: 3.902A pdb=" N UNK B2630 " --> pdb=" O UNK B2626 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N UNK B2631 " --> pdb=" O UNK B2627 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK B2634 " --> pdb=" O UNK B2630 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK B2635 " --> pdb=" O UNK B2631 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N UNK B2639 " --> pdb=" O UNK B2635 " (cutoff:3.500A) Processing helix chain 'B' and resid 2641 through 2643 No H-bonds generated for 'chain 'B' and resid 2641 through 2643' Processing helix chain 'B' and resid 2650 through 2666 Processing helix chain 'B' and resid 2748 through 2773 removed outlier: 3.632A pdb=" N ASP B2752 " --> pdb=" O PRO B2748 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.769A pdb=" N PHE B2797 " --> pdb=" O TYR B2794 " (cutoff:3.500A) Processing helix chain 'B' and resid 2800 through 2804 Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 4.202A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B2816 " --> pdb=" O SER B2812 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B2817 " --> pdb=" O LEU B2813 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 3.966A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP B2886 " --> pdb=" O TYR B2882 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2911 Processing helix chain 'B' and resid 2914 through 2932 removed outlier: 3.546A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B2920 " --> pdb=" O LYS B2916 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2976 removed outlier: 4.269A pdb=" N UNK B2956 " --> pdb=" O UNK B2952 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK B2968 " --> pdb=" O UNK B2964 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N UNK B2969 " --> pdb=" O UNK B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3015 removed outlier: 3.714A pdb=" N UNK B3001 " --> pdb=" O UNK B2997 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N UNK B3002 " --> pdb=" O UNK B2998 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N UNK B3004 " --> pdb=" O UNK B3000 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N UNK B3006 " --> pdb=" O UNK B3002 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.802A 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 3025 through 3040 removed outlier: 4.254A pdb=" N UNK B3032 " --> pdb=" O UNK B3028 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N UNK B3040 " --> pdb=" O UNK B3036 " (cutoff:3.500A) Processing helix chain 'B' and resid 3052 through 3063 removed outlier: 4.336A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N UNK B3057 " --> pdb=" O UNK B3053 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N UNK B3061 " --> pdb=" O UNK B3057 " (cutoff:3.500A) removed outlier: 4.128A 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 3162 removed outlier: 4.087A pdb=" N UNK B3154 " --> pdb=" O UNK B3150 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3186 removed outlier: 3.742A pdb=" N UNK B3182 " --> pdb=" O UNK B3178 " (cutoff:3.500A) Processing helix chain 'B' and resid 3198 through 3212 Processing helix chain 'B' and resid 3224 through 3230 removed outlier: 3.899A pdb=" N UNK B3228 " --> pdb=" O UNK B3224 " (cutoff:3.500A) Processing helix chain 'B' and resid 3249 through 3254 Processing helix chain 'B' and resid 3271 through 3285 removed outlier: 3.588A pdb=" N UNK B3281 " --> pdb=" O UNK B3277 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N UNK B3282 " --> pdb=" O UNK B3278 " (cutoff:3.500A) removed outlier: 3.947A 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 3321 removed outlier: 3.634A pdb=" N UNK B3321 " --> pdb=" O UNK B3317 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3330 removed outlier: 3.572A pdb=" N UNK B3330 " --> pdb=" O UNK B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3349 removed outlier: 3.565A 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 3407 removed outlier: 3.594A pdb=" N UNK B3403 " --> pdb=" O UNK B3399 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N UNK B3404 " --> pdb=" O UNK B3400 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N UNK B3405 " --> pdb=" O UNK B3401 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N UNK B3407 " --> pdb=" O UNK B3403 " (cutoff:3.500A) Processing helix chain 'B' and resid 3410 through 3425 removed outlier: 4.113A pdb=" N UNK B3416 " --> pdb=" O UNK B3412 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N UNK B3417 " --> pdb=" O UNK B3413 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N UNK B3420 " --> pdb=" O UNK B3416 " (cutoff:3.500A) Processing helix chain 'B' and resid 3437 through 3443 Processing helix chain 'B' and resid 3445 through 3450 Processing helix chain 'B' and resid 3461 through 3468 removed outlier: 3.540A pdb=" N UNK B3468 " --> pdb=" O UNK B3464 " (cutoff:3.500A) Processing helix chain 'B' and resid 3518 through 3521 removed outlier: 3.706A pdb=" N UNK B3521 " --> pdb=" O UNK B3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3518 through 3521' Processing helix chain 'B' and resid 3522 through 3527 Processing helix chain 'B' and resid 3541 through 3547 removed outlier: 3.634A pdb=" N UNK B3547 " --> pdb=" O UNK B3543 " (cutoff:3.500A) Processing helix chain 'B' and resid 3551 through 3560 Processing helix chain 'B' and resid 3574 through 3579 removed outlier: 3.647A pdb=" N UNK B3579 " --> pdb=" O UNK B3575 " (cutoff:3.500A) Processing helix chain 'B' and resid 3589 through 3608 removed outlier: 4.148A pdb=" N UNK B3595 " --> pdb=" O UNK B3591 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK B3598 " --> pdb=" O UNK B3594 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N UNK B3600 " --> pdb=" O UNK B3596 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK B3601 " --> pdb=" O UNK B3597 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 Processing helix chain 'B' and resid 3657 through 3661 Processing helix chain 'B' and resid 3671 through 3680 removed outlier: 4.091A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (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 3738 removed outlier: 4.174A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3758 Processing helix chain 'B' and resid 3764 through 3769 Processing helix chain 'B' and resid 3774 through 3784 removed outlier: 4.055A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B3779 " --> pdb=" O ALA B3775 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B3783 " --> pdb=" O VAL B3779 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3805 removed outlier: 3.772A pdb=" N SER B3803 " --> pdb=" O LYS B3799 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.577A 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: 3.694A pdb=" N GLN B3882 " --> pdb=" O ASP B3878 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3905 Processing helix chain 'B' and resid 3914 through 3937 removed outlier: 3.951A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B3920 " --> pdb=" O ILE B3916 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B3921 " --> pdb=" O ILE B3917 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B3929 " --> pdb=" O ARG B3925 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B3934 " --> pdb=" O ILE B3930 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3968 removed outlier: 3.683A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS B3959 " --> pdb=" O MET B3955 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B3961 " --> pdb=" O VAL B3957 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.757A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 4004 removed outlier: 3.598A pdb=" N VAL B3990 " --> pdb=" O TRP B3986 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B3992 " --> pdb=" O ALA B3988 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B3993 " --> pdb=" O VAL B3989 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B3994 " --> pdb=" O VAL B3990 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B3999 " --> pdb=" O VAL B3995 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B4004 " --> pdb=" O MET B4000 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4030 removed outlier: 3.907A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4051 removed outlier: 3.840A pdb=" N ASP B4046 " --> pdb=" O ARG B4042 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B4048 " --> pdb=" O MET B4044 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4062 removed outlier: 3.541A pdb=" N PHE B4061 " --> pdb=" O MET B4057 " (cutoff:3.500A) Processing helix chain 'B' and resid 4067 through 4072 Processing helix chain 'B' and resid 4074 through 4079 Processing helix chain 'B' and resid 4090 through 4100 removed outlier: 3.524A pdb=" N MET B4097 " --> pdb=" O PHE B4093 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4124 through 4154 removed outlier: 4.633A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) Proline residue: B4135 - end of helix removed outlier: 6.010A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B4141 " --> pdb=" O ARG B4137 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B4142 " --> pdb=" O ASP B4138 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B4152 " --> pdb=" O THR B4148 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B4154 " --> pdb=" O LEU B4150 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 removed outlier: 3.609A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) Processing helix chain 'B' and resid 4167 through 4174 removed outlier: 3.539A pdb=" N LEU B4171 " --> pdb=" O ALA B4167 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4206 removed outlier: 3.641A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B4204 " --> pdb=" O THR B4200 " (cutoff:3.500A) Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 3.532A pdb=" N ASP B4220 " --> pdb=" O GLN B4216 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4250 removed outlier: 3.556A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B4249 " --> pdb=" O MET B4245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B4250 " --> pdb=" O GLN B4246 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4558 removed outlier: 3.700A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4576 removed outlier: 3.569A pdb=" N LEU B4562 " --> pdb=" O ASN B4558 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B4570 " --> pdb=" O ALA B4566 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) Processing helix chain 'B' and resid 4641 through 4664 removed outlier: 3.696A pdb=" N CYS B4657 " --> pdb=" O VAL B4653 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B4658 " --> pdb=" O ALA B4654 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B4664 " --> pdb=" O GLY B4660 " (cutoff:3.500A) Processing helix chain 'B' and resid 4667 through 4683 removed outlier: 3.612A pdb=" N GLU B4676 " --> pdb=" O LYS B4672 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B4678 " --> pdb=" O GLU B4674 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4702 removed outlier: 3.568A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4705 No H-bonds generated for 'chain 'B' and resid 4703 through 4705' Processing helix chain 'B' and resid 4710 through 4714 removed outlier: 3.549A pdb=" N SER B4713 " --> pdb=" O SER B4710 " (cutoff:3.500A) removed outlier: 4.683A 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 4728 Processing helix chain 'B' and resid 4733 through 4741 Processing helix chain 'B' and resid 4745 through 4753 removed outlier: 4.808A pdb=" N THR B4751 " --> pdb=" O SER B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.525A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4802 removed outlier: 3.577A pdb=" N LEU B4790 " --> pdb=" O ASP B4786 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B4799 " --> pdb=" O TYR B4795 " (cutoff:3.500A) Processing helix chain 'B' and resid 4811 through 4820 removed outlier: 3.999A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.769A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 removed outlier: 3.968A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B4846 " --> pdb=" O GLY B4842 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B4848 " --> pdb=" O LEU B4844 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B4853 " --> pdb=" O TYR B4849 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B4855 " --> pdb=" O TYR B4851 " (cutoff:3.500A) Processing helix chain 'B' and resid 4859 through 4863 removed outlier: 3.866A pdb=" N PHE B4862 " --> pdb=" O PHE B4859 " (cutoff:3.500A) removed outlier: 3.897A 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 4890 removed outlier: 3.546A pdb=" N TYR B4883 " --> pdb=" O MET B4879 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 removed outlier: 3.876A pdb=" N ASP B4899 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4913 through 4922 removed outlier: 3.774A pdb=" N ASP B4917 " --> pdb=" O ARG B4913 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B4918 " --> pdb=" O VAL B4914 " (cutoff:3.500A) Processing helix chain 'B' and resid 4924 through 4957 removed outlier: 3.953A pdb=" N LEU B4929 " --> pdb=" O ILE B4925 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B4930 " --> pdb=" O VAL B4926 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B4939 " --> pdb=" O LEU B4935 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B4944 " --> pdb=" O PHE B4940 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B4953 " --> pdb=" O GLN B4949 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET B4954 " --> pdb=" O VAL B4950 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B4955 " --> pdb=" O LYS B4951 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4968 removed outlier: 3.934A pdb=" N TYR B4967 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4982 Processing helix chain 'B' and resid 4986 through 4997 removed outlier: 3.549A pdb=" N ILE B4996 " --> pdb=" O LEU B4992 " (cutoff:3.500A) Processing helix chain 'B' and resid 5006 through 5017 Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.593A pdb=" N THR E 254 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 Processing helix chain 'E' and resid 395 through 419 removed outlier: 3.754A pdb=" N GLN E 399 " --> pdb=" O GLN E 395 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS E 405 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP E 419 " --> pdb=" O ILE E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 452 removed outlier: 3.844A pdb=" N GLY E 450 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 481 removed outlier: 3.520A pdb=" N GLN E 465 " --> pdb=" O HIS E 461 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN E 473 " --> pdb=" O ARG E 469 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE E 478 " --> pdb=" O ARG E 474 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN E 479 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 529 removed outlier: 4.076A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 524 " --> pdb=" O ASN E 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 528 " --> pdb=" O GLU E 524 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU E 529 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 removed outlier: 3.820A pdb=" N LEU E 539 " --> pdb=" O ALA E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 542 No H-bonds generated for 'chain 'E' and resid 540 through 542' Processing helix chain 'E' and resid 543 through 551 removed outlier: 3.827A pdb=" N VAL E 548 " --> pdb=" O LEU E 544 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS E 550 " --> pdb=" O TRP E 546 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 551 " --> pdb=" O VAL E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.714A pdb=" N TYR E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 568 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU E 570 " --> pdb=" O CYS E 566 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER E 571 " --> pdb=" O VAL E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 576 removed outlier: 3.994A 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: 4.118A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 603 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 625 removed outlier: 3.988A pdb=" N GLN E 618 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 619 " --> pdb=" O ARG E 615 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR E 622 " --> pdb=" O GLN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 890 removed outlier: 3.636A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS E 873 " --> pdb=" O ARG E 869 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS E 879 " --> pdb=" O ALA E 875 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 887 " --> pdb=" O ALA E 883 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN E 889 " --> pdb=" O THR E 885 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 934 removed outlier: 3.671A pdb=" N ASN E 919 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 929 " --> pdb=" O SER E 925 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA E 934 " --> pdb=" O LYS E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 980 through 988 removed outlier: 3.734A pdb=" N LEU E 984 " --> pdb=" O ALA E 980 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP E 986 " --> pdb=" O THR E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 1001 removed outlier: 3.518A pdb=" N HIS E 993 " --> pdb=" O ALA E 989 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP E 996 " --> pdb=" O GLY E 992 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG E1000 " --> pdb=" O TRP E 996 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1041 removed outlier: 3.582A pdb=" N LEU E1039 " --> pdb=" O ASN E1035 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN E1041 " --> pdb=" O ASP E1037 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1049 removed outlier: 3.582A pdb=" N LEU E1046 " --> pdb=" O ALA E1042 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU E1047 " --> pdb=" O VAL E1043 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E1048 " --> pdb=" O ARG E1044 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1082 Processing helix chain 'E' and resid 1575 through 1579 removed outlier: 3.566A pdb=" N ALA E1578 " --> pdb=" O LEU E1575 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET E1579 " --> pdb=" O SER E1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1575 through 1579' Processing helix chain 'E' and resid 1652 through 1657 removed outlier: 3.505A pdb=" N LEU E1657 " --> pdb=" O LEU E1653 " (cutoff:3.500A) Processing helix chain 'E' and resid 1658 through 1674 removed outlier: 3.809A pdb=" N HIS E1665 " --> pdb=" O ARG E1661 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR E1670 " --> pdb=" O THR E1666 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG E1671 " --> pdb=" O LEU E1667 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1686 removed outlier: 3.654A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS E1686 " --> pdb=" O ALA E1682 " (cutoff:3.500A) Processing helix chain 'E' and resid 1692 through 1700 removed outlier: 4.200A pdb=" N LEU E1698 " --> pdb=" O LEU E1694 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E1699 " --> pdb=" O LEU E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1710 through 1714 removed outlier: 3.804A pdb=" N ASP E1713 " --> pdb=" O GLY E1710 " (cutoff:3.500A) Processing helix chain 'E' and resid 1715 through 1720 Processing helix chain 'E' and resid 1720 through 1730 removed outlier: 3.929A pdb=" N ARG E1725 " --> pdb=" O GLU E1721 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E1726 " --> pdb=" O SER E1722 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 Processing helix chain 'E' and resid 1803 through 1824 removed outlier: 3.665A pdb=" N LEU E1807 " --> pdb=" O PRO E1803 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET E1814 " --> pdb=" O LYS E1810 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY E1816 " --> pdb=" O LEU E1812 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E1824 " --> pdb=" O ARG E1820 " (cutoff:3.500A) Processing helix chain 'E' and resid 1833 through 1838 Processing helix chain 'E' and resid 1840 through 1851 removed outlier: 3.578A 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 1982 removed outlier: 3.612A pdb=" N LEU E1937 " --> pdb=" O GLU E1933 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN E1938 " --> pdb=" O SER E1934 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR E1945 " --> pdb=" O ASN E1941 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E1946 " --> pdb=" O LEU E1942 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP E1948 " --> pdb=" O GLU E1944 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU E1963 " --> pdb=" O ALA E1959 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E1973 " --> pdb=" O LEU E1969 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E1978 " --> pdb=" O ARG E1974 " (cutoff:3.500A) Processing helix chain 'E' and resid 1989 through 1994 removed outlier: 3.613A 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 2011 removed outlier: 3.623A pdb=" N ILE E2006 " --> pdb=" O PRO E2002 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN E2007 " --> pdb=" O GLN E2003 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS E2011 " --> pdb=" O ASN E2007 " (cutoff:3.500A) Processing helix chain 'E' and resid 2029 through 2042 Processing helix chain 'E' and resid 2094 through 2108 removed outlier: 3.796A pdb=" N VAL E2103 " --> pdb=" O SER E2099 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2129 removed outlier: 3.512A pdb=" N VAL E2117 " --> pdb=" O SER E2113 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E2126 " --> pdb=" O SER E2122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR E2128 " --> pdb=" O LEU E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2137 Processing helix chain 'E' and resid 2148 through 2165 removed outlier: 3.901A pdb=" N CYS E2158 " --> pdb=" O SER E2154 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN E2161 " --> pdb=" O GLU E2157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E2165 " --> pdb=" O GLN E2161 " (cutoff:3.500A) Processing helix chain 'E' and resid 2171 through 2186 removed outlier: 3.692A pdb=" N LEU E2177 " --> pdb=" O GLN E2173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E2185 " --> pdb=" O SER E2181 " (cutoff:3.500A) Processing helix chain 'E' and resid 2189 through 2194 Processing helix chain 'E' and resid 2194 through 2201 removed outlier: 4.016A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.974A pdb=" N ASN E2213 " --> pdb=" O GLU E2209 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E2214 " --> pdb=" O VAL E2210 " (cutoff:3.500A) Processing helix chain 'E' and resid 2228 through 2242 removed outlier: 3.641A pdb=" N CYS E2233 " --> pdb=" O VAL E2229 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS E2237 " --> pdb=" O CYS E2233 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR E2238 " --> pdb=" O ARG E2234 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2252 removed outlier: 3.582A pdb=" N ASP E2252 " --> pdb=" O ARG E2248 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2262 removed outlier: 4.074A pdb=" N ASN E2260 " --> pdb=" O TYR E2256 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY E2262 " --> pdb=" O LEU E2258 " (cutoff:3.500A) Processing helix chain 'E' and resid 2271 through 2279 Processing helix chain 'E' and resid 2294 through 2306 removed outlier: 3.543A pdb=" N VAL E2299 " --> pdb=" O LEU E2295 " (cutoff:3.500A) Processing helix chain 'E' and resid 2310 through 2315 removed outlier: 4.307A pdb=" N ALA E2315 " --> pdb=" O PRO E2311 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2331 removed outlier: 3.588A pdb=" N TYR E2331 " --> pdb=" O GLY E2327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2335 through 2339 removed outlier: 4.052A pdb=" N ALA E2338 " --> pdb=" O LEU E2335 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2349 Processing helix chain 'E' and resid 2350 through 2358 removed outlier: 3.589A 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 2375 through 2388 removed outlier: 3.505A pdb=" N ARG E2385 " --> pdb=" O GLU E2381 " (cutoff:3.500A) Processing helix chain 'E' and resid 2389 through 2393 removed outlier: 3.500A pdb=" N ARG E2392 " --> pdb=" O ASP E2389 " (cutoff:3.500A) Processing helix chain 'E' and resid 2417 through 2436 removed outlier: 4.108A pdb=" N ALA E2421 " --> pdb=" O HIS E2417 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E2422 " --> pdb=" O LEU E2418 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET E2423 " --> pdb=" O GLY E2419 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E2425 " --> pdb=" O ALA E2421 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E2428 " --> pdb=" O SER E2424 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E2433 " --> pdb=" O LEU E2429 " (cutoff:3.500A) Processing helix chain 'E' and resid 2440 through 2445 removed outlier: 3.737A pdb=" N ALA E2445 " --> pdb=" O HIS E2441 " (cutoff:3.500A) Processing helix chain 'E' and resid 2448 through 2461 removed outlier: 3.859A pdb=" N ILE E2453 " --> pdb=" O GLU E2449 " (cutoff:3.500A) Processing helix chain 'E' and resid 2466 through 2471 Processing helix chain 'E' and resid 2500 through 2507 removed outlier: 3.517A pdb=" N UNK E2504 " --> pdb=" O UNK E2500 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N UNK E2505 " --> pdb=" O UNK E2501 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK E2506 " --> pdb=" O UNK E2502 " (cutoff:3.500A) Processing helix chain 'E' and resid 2516 through 2522 Processing helix chain 'E' and resid 2525 through 2530 Processing helix chain 'E' and resid 2542 through 2548 removed outlier: 3.679A pdb=" N UNK E2546 " --> pdb=" O UNK E2542 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2557 removed outlier: 3.766A pdb=" N UNK E2555 " --> pdb=" O UNK E2551 " (cutoff:3.500A) Processing helix chain 'E' and resid 2567 through 2581 removed outlier: 3.514A pdb=" N UNK E2578 " --> pdb=" O UNK E2574 " (cutoff:3.500A) Processing helix chain 'E' and resid 2587 through 2602 removed outlier: 3.625A pdb=" N UNK E2597 " --> pdb=" O UNK E2593 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N UNK E2602 " --> pdb=" O UNK E2598 " (cutoff:3.500A) Processing helix chain 'E' and resid 2610 through 2618 removed outlier: 3.767A pdb=" N UNK E2618 " --> pdb=" O UNK E2614 " (cutoff:3.500A) Processing helix chain 'E' and resid 2626 through 2640 removed outlier: 3.892A pdb=" N UNK E2630 " --> pdb=" O UNK E2626 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N UNK E2631 " --> pdb=" O UNK E2627 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N UNK E2634 " --> pdb=" O UNK E2630 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N UNK E2635 " --> pdb=" O UNK E2631 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK E2639 " --> pdb=" O UNK E2635 " (cutoff:3.500A) Processing helix chain 'E' and resid 2641 through 2643 No H-bonds generated for 'chain 'E' and resid 2641 through 2643' Processing helix chain 'E' and resid 2650 through 2666 Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 3.632A pdb=" N ASP E2752 " --> pdb=" O PRO E2748 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE E2768 " --> pdb=" O GLU E2764 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E2769 " --> pdb=" O LYS E2765 " (cutoff:3.500A) Processing helix chain 'E' and resid 2793 through 2797 removed outlier: 3.769A pdb=" N PHE E2797 " --> pdb=" O TYR E2794 " (cutoff:3.500A) Processing helix chain 'E' and resid 2800 through 2804 Processing helix chain 'E' and resid 2809 through 2820 removed outlier: 4.202A pdb=" N ALA E2815 " --> pdb=" O GLU E2811 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET E2816 " --> pdb=" O SER E2812 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E2817 " --> pdb=" O LEU E2813 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2895 removed outlier: 3.968A pdb=" N MET E2874 " --> pdb=" O GLU E2870 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP E2886 " --> pdb=" O TYR E2882 " (cutoff:3.500A) Processing helix chain 'E' and resid 2907 through 2911 Processing helix chain 'E' and resid 2914 through 2932 removed outlier: 3.545A pdb=" N ARG E2918 " --> pdb=" O LYS E2914 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG E2920 " --> pdb=" O LYS E2916 " (cutoff:3.500A) Processing helix chain 'E' and resid 2950 through 2976 removed outlier: 4.250A pdb=" N UNK E2956 " --> pdb=" O UNK E2952 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N UNK E2968 " --> pdb=" O UNK E2964 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N UNK E2969 " --> pdb=" O UNK E2965 " (cutoff:3.500A) Processing helix chain 'E' and resid 2999 through 3015 removed outlier: 3.519A pdb=" N UNK E3004 " --> pdb=" O UNK E3000 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N UNK E3006 " --> pdb=" O UNK E3002 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N UNK E3009 " --> pdb=" O UNK E3005 " (cutoff:3.500A) removed outlier: 3.815A 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 3025 through 3040 removed outlier: 4.260A pdb=" N UNK E3032 " --> pdb=" O UNK E3028 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N UNK E3040 " --> pdb=" O UNK E3036 " (cutoff:3.500A) Processing helix chain 'E' and resid 3052 through 3063 removed outlier: 4.336A pdb=" N UNK E3056 " --> pdb=" O UNK E3052 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNK E3057 " --> pdb=" O UNK E3053 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N UNK E3061 " --> pdb=" O UNK E3057 " (cutoff:3.500A) removed outlier: 4.127A 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 3162 removed outlier: 4.079A pdb=" N UNK E3154 " --> pdb=" O UNK E3150 " (cutoff:3.500A) Processing helix chain 'E' and resid 3175 through 3186 removed outlier: 3.735A 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: 3.908A pdb=" N UNK E3228 " --> pdb=" O UNK E3224 " (cutoff:3.500A) Processing helix chain 'E' and resid 3249 through 3254 Processing helix chain 'E' and resid 3271 through 3285 removed outlier: 3.588A pdb=" N UNK E3281 " --> pdb=" O UNK E3277 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N UNK E3282 " --> pdb=" O UNK E3278 " (cutoff:3.500A) removed outlier: 3.952A 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 3321 removed outlier: 3.633A pdb=" N UNK E3321 " --> pdb=" O UNK E3317 " (cutoff:3.500A) Processing helix chain 'E' and resid 3321 through 3330 removed outlier: 3.568A pdb=" N UNK E3330 " --> pdb=" O UNK E3326 " (cutoff:3.500A) Processing helix chain 'E' and resid 3344 through 3349 removed outlier: 3.564A 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 3399 through 3407 removed outlier: 3.598A pdb=" N UNK E3403 " --> pdb=" O UNK E3399 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK E3404 " --> pdb=" O UNK E3400 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N UNK E3405 " --> pdb=" O UNK E3401 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N UNK E3407 " --> pdb=" O UNK E3403 " (cutoff:3.500A) Processing helix chain 'E' and resid 3410 through 3425 removed outlier: 4.099A pdb=" N UNK E3416 " --> pdb=" O UNK E3412 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N UNK E3417 " --> pdb=" O UNK E3413 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N UNK E3420 " --> pdb=" O UNK E3416 " (cutoff:3.500A) Processing helix chain 'E' and resid 3437 through 3443 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 removed outlier: 3.540A pdb=" N UNK E3468 " --> pdb=" O UNK E3464 " (cutoff:3.500A) Processing helix chain 'E' and resid 3518 through 3521 removed outlier: 3.711A pdb=" N UNK E3521 " --> pdb=" O UNK E3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3518 through 3521' Processing helix chain 'E' and resid 3522 through 3527 Processing helix chain 'E' and resid 3541 through 3547 removed outlier: 3.638A pdb=" N UNK E3547 " --> pdb=" O UNK E3543 " (cutoff:3.500A) Processing helix chain 'E' and resid 3551 through 3560 Processing helix chain 'E' and resid 3574 through 3579 removed outlier: 3.639A pdb=" N UNK E3579 " --> pdb=" O UNK E3575 " (cutoff:3.500A) Processing helix chain 'E' and resid 3589 through 3608 removed outlier: 4.144A pdb=" N UNK E3595 " --> pdb=" O UNK E3591 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N UNK E3598 " --> pdb=" O UNK E3594 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N UNK E3600 " --> pdb=" O UNK E3596 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK E3601 " --> pdb=" O UNK E3597 " (cutoff:3.500A) Processing helix chain 'E' and resid 3645 through 3656 Processing helix chain 'E' and resid 3657 through 3661 Processing helix chain 'E' and resid 3671 through 3680 removed outlier: 4.091A pdb=" N LEU E3677 " --> pdb=" O MET E3673 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER E3678 " --> pdb=" O ILE E3674 " (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 3738 removed outlier: 4.174A pdb=" N GLU E3736 " --> pdb=" O SER E3732 " (cutoff:3.500A) Processing helix chain 'E' and resid 3752 through 3758 Processing helix chain 'E' and resid 3764 through 3769 Processing helix chain 'E' and resid 3774 through 3784 removed outlier: 4.055A pdb=" N MET E3778 " --> pdb=" O GLY E3774 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL E3779 " --> pdb=" O ALA E3775 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU E3780 " --> pdb=" O ALA E3776 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E3783 " --> pdb=" O VAL E3779 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3805 removed outlier: 3.771A pdb=" N SER E3803 " --> pdb=" O LYS E3799 " (cutoff:3.500A) removed outlier: 3.757A 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: 3.577A 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: 3.696A pdb=" N GLN E3882 " --> pdb=" O ASP E3878 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP E3883 " --> pdb=" O GLU E3879 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE E3885 " --> pdb=" O THR E3881 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS E3892 " --> pdb=" O LEU E3888 " (cutoff:3.500A) Processing helix chain 'E' and resid 3898 through 3905 Processing helix chain 'E' and resid 3914 through 3937 removed outlier: 3.952A pdb=" N CYS E3918 " --> pdb=" O ASN E3914 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E3920 " --> pdb=" O ILE E3916 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP E3921 " --> pdb=" O ILE E3917 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER E3929 " --> pdb=" O ARG E3925 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR E3934 " --> pdb=" O ILE E3930 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP E3935 " --> pdb=" O SER E3931 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR E3936 " --> pdb=" O ASP E3932 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E3937 " --> pdb=" O PHE E3933 " (cutoff:3.500A) Processing helix chain 'E' and resid 3944 through 3968 removed outlier: 3.683A pdb=" N LYS E3953 " --> pdb=" O ARG E3949 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E3959 " --> pdb=" O MET E3955 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN E3960 " --> pdb=" O SER E3956 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E3961 " --> pdb=" O VAL E3957 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E3967 " --> pdb=" O ASN E3963 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3983 removed outlier: 3.757A pdb=" N HIS E3982 " --> pdb=" O GLN E3978 " (cutoff:3.500A) Processing helix chain 'E' and resid 3984 through 4004 removed outlier: 3.597A pdb=" N VAL E3990 " --> pdb=" O TRP E3986 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY E3991 " --> pdb=" O ASP E3987 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU E3993 " --> pdb=" O VAL E3989 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS E3994 " --> pdb=" O VAL E3990 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET E3999 " --> pdb=" O VAL E3995 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E4004 " --> pdb=" O MET E4000 " (cutoff:3.500A) Processing helix chain 'E' and resid 4009 through 4030 removed outlier: 3.907A pdb=" N MET E4026 " --> pdb=" O ASP E4022 " (cutoff:3.500A) Processing helix chain 'E' and resid 4039 through 4051 removed outlier: 3.840A pdb=" N ASP E4046 " --> pdb=" O ARG E4042 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E4048 " --> pdb=" O MET E4044 " (cutoff:3.500A) Processing helix chain 'E' and resid 4051 through 4062 removed outlier: 3.541A pdb=" N PHE E4061 " --> pdb=" O MET E4057 " (cutoff:3.500A) Processing helix chain 'E' and resid 4067 through 4072 Processing helix chain 'E' and resid 4074 through 4079 Processing helix chain 'E' and resid 4090 through 4100 removed outlier: 3.524A pdb=" N MET E4097 " --> pdb=" O PHE E4093 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E4098 " --> pdb=" O GLN E4094 " (cutoff:3.500A) Processing helix chain 'E' and resid 4104 through 4115 Processing helix chain 'E' and resid 4124 through 4154 removed outlier: 4.633A pdb=" N PHE E4132 " --> pdb=" O PHE E4128 " (cutoff:3.500A) Proline residue: E4135 - end of helix removed outlier: 6.011A pdb=" N ASP E4138 " --> pdb=" O GLU E4134 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE E4141 " --> pdb=" O ARG E4137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN E4142 " --> pdb=" O ASP E4138 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E4152 " --> pdb=" O THR E4148 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL E4154 " --> pdb=" O LEU E4150 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4167 removed outlier: 3.502A pdb=" N PHE E4163 " --> pdb=" O ARG E4159 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E4165 " --> pdb=" O ARG E4161 " (cutoff:3.500A) Processing helix chain 'E' and resid 4167 through 4174 removed outlier: 3.539A pdb=" N LEU E4171 " --> pdb=" O ALA E4167 " (cutoff:3.500A) Processing helix chain 'E' and resid 4198 through 4206 removed outlier: 3.641A pdb=" N ARG E4202 " --> pdb=" O SER E4198 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN E4204 " --> pdb=" O THR E4200 " (cutoff:3.500A) Processing helix chain 'E' and resid 4207 through 4224 removed outlier: 3.532A pdb=" N ASP E4220 " --> pdb=" O GLN E4216 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL E4222 " --> pdb=" O ILE E4218 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4250 removed outlier: 3.556A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE E4243 " --> pdb=" O GLU E4239 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E4249 " --> pdb=" O MET E4245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN E4250 " --> pdb=" O GLN E4246 " (cutoff:3.500A) Processing helix chain 'E' and resid 4542 through 4558 removed outlier: 3.701A pdb=" N VAL E4546 " --> pdb=" O GLY E4542 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR E4554 " --> pdb=" O LYS E4550 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN E4558 " --> pdb=" O TYR E4554 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4576 removed outlier: 3.570A pdb=" N LEU E4562 " --> pdb=" O ASN E4558 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E4570 " --> pdb=" O ALA E4566 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE E4571 " --> pdb=" O LEU E4567 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA E4572 " --> pdb=" O PHE E4568 " (cutoff:3.500A) Processing helix chain 'E' and resid 4641 through 4664 removed outlier: 3.697A pdb=" N CYS E4657 " --> pdb=" O VAL E4653 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE E4658 " --> pdb=" O ALA E4654 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE E4659 " --> pdb=" O PHE E4655 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E4664 " --> pdb=" O GLY E4660 " (cutoff:3.500A) Processing helix chain 'E' and resid 4667 through 4683 removed outlier: 3.612A pdb=" N GLU E4676 " --> pdb=" O LYS E4672 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E4678 " --> pdb=" O GLU E4674 " (cutoff:3.500A) Processing helix chain 'E' and resid 4696 through 4702 removed outlier: 3.568A pdb=" N GLN E4700 " --> pdb=" O ASP E4696 " (cutoff:3.500A) Processing helix chain 'E' and resid 4703 through 4705 No H-bonds generated for 'chain 'E' and resid 4703 through 4705' Processing helix chain 'E' and resid 4710 through 4714 removed outlier: 3.549A pdb=" N SER E4713 " --> pdb=" O SER E4710 " (cutoff:3.500A) removed outlier: 4.681A 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 4728 Processing helix chain 'E' and resid 4733 through 4741 Processing helix chain 'E' and resid 4745 through 4753 removed outlier: 4.808A pdb=" N THR E4751 " --> pdb=" O SER E4747 " (cutoff:3.500A) Processing helix chain 'E' and resid 4772 through 4786 removed outlier: 3.527A pdb=" N ASP E4786 " --> pdb=" O VAL E4782 " (cutoff:3.500A) Processing helix chain 'E' and resid 4786 through 4802 removed outlier: 3.578A pdb=" N LEU E4790 " --> pdb=" O ASP E4786 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E4799 " --> pdb=" O TYR E4795 " (cutoff:3.500A) Processing helix chain 'E' and resid 4811 through 4820 removed outlier: 4.000A pdb=" N ASP E4815 " --> pdb=" O ALA E4811 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL E4820 " --> pdb=" O ILE E4816 " (cutoff:3.500A) Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.770A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN E4833 " --> pdb=" O SER E4829 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 removed outlier: 3.970A pdb=" N MET E4839 " --> pdb=" O LYS E4835 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E4846 " --> pdb=" O GLY E4842 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL E4848 " --> pdb=" O LEU E4844 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E4853 " --> pdb=" O TYR E4849 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E4854 " --> pdb=" O LEU E4850 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA E4855 " --> pdb=" O TYR E4851 " (cutoff:3.500A) Processing helix chain 'E' and resid 4859 through 4863 removed outlier: 3.864A pdb=" N PHE E4862 " --> pdb=" O PHE E4859 " (cutoff:3.500A) removed outlier: 3.897A 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 4890 removed outlier: 3.547A pdb=" N TYR E4883 " --> pdb=" O MET E4879 " (cutoff:3.500A) Processing helix chain 'E' and resid 4896 through 4900 removed outlier: 3.875A pdb=" N ASP E4899 " --> pdb=" O GLY E4896 " (cutoff:3.500A) Processing helix chain 'E' and resid 4913 through 4922 removed outlier: 3.773A pdb=" N ASP E4917 " --> pdb=" O ARG E4913 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E4918 " --> pdb=" O VAL E4914 " (cutoff:3.500A) Processing helix chain 'E' and resid 4924 through 4957 removed outlier: 3.952A pdb=" N LEU E4929 " --> pdb=" O ILE E4925 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA E4930 " --> pdb=" O VAL E4926 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E4936 " --> pdb=" O ILE E4932 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E4939 " --> pdb=" O LEU E4935 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E4944 " --> pdb=" O PHE E4940 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E4951 " --> pdb=" O GLN E4947 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP E4953 " --> pdb=" O GLN E4949 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET E4954 " --> pdb=" O VAL E4950 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E4955 " --> pdb=" O LYS E4951 " (cutoff:3.500A) Processing helix chain 'E' and resid 4964 through 4968 removed outlier: 3.934A pdb=" N TYR E4967 " --> pdb=" O GLY E4964 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4982 Processing helix chain 'E' and resid 4986 through 4997 removed outlier: 3.549A pdb=" N ILE E4996 " --> pdb=" O LEU E4992 " (cutoff:3.500A) Processing helix chain 'E' and resid 5006 through 5017 Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 251 through 255 removed outlier: 3.593A pdb=" N THR I 254 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 369 Processing helix chain 'I' and resid 395 through 419 removed outlier: 3.754A pdb=" N GLN I 399 " --> pdb=" O GLN I 395 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET I 403 " --> pdb=" O GLN I 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS I 405 " --> pdb=" O ALA I 401 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU I 410 " --> pdb=" O SER I 406 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN I 413 " --> pdb=" O GLY I 409 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE I 414 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS I 416 " --> pdb=" O ASN I 412 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY I 417 " --> pdb=" O GLN I 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP I 419 " --> pdb=" O ILE I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 452 removed outlier: 3.843A pdb=" N GLY I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 481 removed outlier: 3.520A pdb=" N GLN I 465 " --> pdb=" O HIS I 461 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN I 473 " --> pdb=" O ARG I 469 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN I 479 " --> pdb=" O GLN I 475 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU I 480 " --> pdb=" O SER I 476 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU I 481 " --> pdb=" O LEU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 494 Processing helix chain 'I' and resid 510 through 529 removed outlier: 4.076A pdb=" N LYS I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU I 517 " --> pdb=" O GLU I 513 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR I 523 " --> pdb=" O VAL I 519 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU I 524 " --> pdb=" O ASN I 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER I 528 " --> pdb=" O GLU I 524 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 529 " --> pdb=" O LEU I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 534 through 539 removed outlier: 3.820A pdb=" N LEU I 539 " --> pdb=" O ALA I 535 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 542 No H-bonds generated for 'chain 'I' and resid 540 through 542' Processing helix chain 'I' and resid 543 through 551 removed outlier: 3.827A pdb=" N VAL I 548 " --> pdb=" O LEU I 544 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER I 549 " --> pdb=" O ASP I 545 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 550 " --> pdb=" O TRP I 546 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU I 551 " --> pdb=" O VAL I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 571 removed outlier: 3.713A pdb=" N TYR I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 568 " --> pdb=" O LEU I 564 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU I 570 " --> pdb=" O CYS I 566 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER I 571 " --> pdb=" O VAL I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 576 removed outlier: 3.992A 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: 4.117A pdb=" N LEU I 600 " --> pdb=" O ASN I 596 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 603 " --> pdb=" O VAL I 599 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS I 607 " --> pdb=" O LEU I 603 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL I 608 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 625 removed outlier: 3.986A pdb=" N GLN I 618 " --> pdb=" O VAL I 614 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 619 " --> pdb=" O ARG I 615 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR I 622 " --> pdb=" O GLN I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 890 removed outlier: 3.635A pdb=" N ILE I 870 " --> pdb=" O HIS I 866 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU I 872 " --> pdb=" O GLU I 868 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS I 873 " --> pdb=" O ARG I 869 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS I 879 " --> pdb=" O ALA I 875 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG I 886 " --> pdb=" O TRP I 882 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE I 887 " --> pdb=" O ALA I 883 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 889 " --> pdb=" O THR I 885 " (cutoff:3.500A) Processing helix chain 'I' and resid 914 through 934 removed outlier: 3.672A pdb=" N ASN I 919 " --> pdb=" O GLU I 915 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU I 929 " --> pdb=" O SER I 925 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA I 934 " --> pdb=" O LYS I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 988 removed outlier: 3.733A pdb=" N LEU I 984 " --> pdb=" O ALA I 980 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP I 986 " --> pdb=" O THR I 982 " (cutoff:3.500A) Processing helix chain 'I' and resid 988 through 1001 removed outlier: 3.517A pdb=" N HIS I 993 " --> pdb=" O ALA I 989 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN I 994 " --> pdb=" O GLU I 990 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP I 996 " --> pdb=" O GLY I 992 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG I1000 " --> pdb=" O TRP I 996 " (cutoff:3.500A) Processing helix chain 'I' and resid 1028 through 1041 removed outlier: 3.582A pdb=" N LEU I1039 " --> pdb=" O ASN I1035 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN I1041 " --> pdb=" O ASP I1037 " (cutoff:3.500A) Processing helix chain 'I' and resid 1042 through 1049 removed outlier: 3.582A pdb=" N LEU I1046 " --> pdb=" O ALA I1042 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU I1047 " --> pdb=" O VAL I1043 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY I1048 " --> pdb=" O ARG I1044 " (cutoff:3.500A) Processing helix chain 'I' and resid 1078 through 1082 Processing helix chain 'I' and resid 1575 through 1579 removed outlier: 3.565A pdb=" N ALA I1578 " --> pdb=" O LEU I1575 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET I1579 " --> pdb=" O SER I1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1575 through 1579' Processing helix chain 'I' and resid 1652 through 1657 removed outlier: 3.505A pdb=" N LEU I1657 " --> pdb=" O LEU I1653 " (cutoff:3.500A) Processing helix chain 'I' and resid 1658 through 1674 removed outlier: 3.810A pdb=" N HIS I1665 " --> pdb=" O ARG I1661 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR I1670 " --> pdb=" O THR I1666 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG I1671 " --> pdb=" O LEU I1667 " (cutoff:3.500A) Processing helix chain 'I' and resid 1678 through 1686 removed outlier: 3.654A pdb=" N ALA I1684 " --> pdb=" O ARG I1680 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYS I1686 " --> pdb=" O ALA I1682 " (cutoff:3.500A) Processing helix chain 'I' and resid 1692 through 1700 removed outlier: 4.201A pdb=" N LEU I1698 " --> pdb=" O LEU I1694 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU I1699 " --> pdb=" O LEU I1695 " (cutoff:3.500A) Processing helix chain 'I' and resid 1710 through 1714 removed outlier: 3.805A pdb=" N ASP I1713 " --> pdb=" O GLY I1710 " (cutoff:3.500A) Processing helix chain 'I' and resid 1715 through 1720 Processing helix chain 'I' and resid 1720 through 1730 removed outlier: 3.929A pdb=" N ARG I1725 " --> pdb=" O GLU I1721 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER I1726 " --> pdb=" O SER I1722 " (cutoff:3.500A) Processing helix chain 'I' and resid 1739 through 1744 Processing helix chain 'I' and resid 1803 through 1824 removed outlier: 3.667A pdb=" N LEU I1807 " --> pdb=" O PRO I1803 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET I1814 " --> pdb=" O LYS I1810 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY I1816 " --> pdb=" O LEU I1812 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN I1824 " --> pdb=" O ARG I1820 " (cutoff:3.500A) Processing helix chain 'I' and resid 1833 through 1838 Processing helix chain 'I' and resid 1840 through 1851 removed outlier: 3.579A 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 1982 removed outlier: 3.612A pdb=" N LEU I1937 " --> pdb=" O GLU I1933 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN I1938 " --> pdb=" O SER I1934 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR I1945 " --> pdb=" O ASN I1941 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE I1946 " --> pdb=" O LEU I1942 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP I1948 " --> pdb=" O GLU I1944 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU I1963 " --> pdb=" O ALA I1959 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG I1964 " --> pdb=" O ALA I1960 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL I1966 " --> pdb=" O ALA I1962 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS I1968 " --> pdb=" O ARG I1964 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN I1973 " --> pdb=" O LEU I1969 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA I1978 " --> pdb=" O ARG I1974 " (cutoff:3.500A) Processing helix chain 'I' and resid 1989 through 1994 removed outlier: 3.614A 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 2011 removed outlier: 3.623A pdb=" N ILE I2006 " --> pdb=" O PRO I2002 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN I2007 " --> pdb=" O GLN I2003 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS I2011 " --> pdb=" O ASN I2007 " (cutoff:3.500A) Processing helix chain 'I' and resid 2029 through 2042 Processing helix chain 'I' and resid 2094 through 2108 removed outlier: 3.795A pdb=" N VAL I2103 " --> pdb=" O SER I2099 " (cutoff:3.500A) Processing helix chain 'I' and resid 2113 through 2129 removed outlier: 3.512A pdb=" N VAL I2117 " --> pdb=" O SER I2113 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG I2126 " --> pdb=" O SER I2122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR I2128 " --> pdb=" O LEU I2124 " (cutoff:3.500A) Processing helix chain 'I' and resid 2129 through 2137 Processing helix chain 'I' and resid 2148 through 2165 removed outlier: 3.901A pdb=" N CYS I2158 " --> pdb=" O SER I2154 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I2161 " --> pdb=" O GLU I2157 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I2165 " --> pdb=" O GLN I2161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2171 through 2186 removed outlier: 3.692A pdb=" N LEU I2177 " --> pdb=" O GLN I2173 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE I2185 " --> pdb=" O SER I2181 " (cutoff:3.500A) Processing helix chain 'I' and resid 2189 through 2194 Processing helix chain 'I' and resid 2194 through 2201 removed outlier: 4.016A pdb=" N MET I2198 " --> pdb=" O HIS I2194 " (cutoff:3.500A) Processing helix chain 'I' and resid 2202 through 2216 removed outlier: 3.975A pdb=" N ASN I2213 " --> pdb=" O GLU I2209 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I2214 " --> pdb=" O VAL I2210 " (cutoff:3.500A) Processing helix chain 'I' and resid 2228 through 2242 removed outlier: 3.641A pdb=" N CYS I2233 " --> pdb=" O VAL I2229 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS I2237 " --> pdb=" O CYS I2233 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR I2238 " --> pdb=" O ARG I2234 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2252 removed outlier: 3.582A pdb=" N ASP I2252 " --> pdb=" O ARG I2248 " (cutoff:3.500A) Processing helix chain 'I' and resid 2253 through 2262 removed outlier: 4.074A pdb=" N ASN I2260 " --> pdb=" O TYR I2256 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY I2262 " --> pdb=" O LEU I2258 " (cutoff:3.500A) Processing helix chain 'I' and resid 2271 through 2279 Processing helix chain 'I' and resid 2294 through 2306 removed outlier: 3.544A pdb=" N VAL I2299 " --> pdb=" O LEU I2295 " (cutoff:3.500A) Processing helix chain 'I' and resid 2310 through 2315 removed outlier: 4.307A pdb=" N ALA I2315 " --> pdb=" O PRO I2311 " (cutoff:3.500A) Processing helix chain 'I' and resid 2326 through 2331 removed outlier: 3.588A pdb=" N TYR I2331 " --> pdb=" O GLY I2327 " (cutoff:3.500A) Processing helix chain 'I' and resid 2335 through 2339 removed outlier: 4.051A pdb=" N ALA I2338 " --> pdb=" O LEU I2335 " (cutoff:3.500A) Processing helix chain 'I' and resid 2346 through 2349 Processing helix chain 'I' and resid 2350 through 2358 removed outlier: 3.591A 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 2375 through 2388 removed outlier: 3.505A pdb=" N ARG I2385 " --> pdb=" O GLU I2381 " (cutoff:3.500A) Processing helix chain 'I' and resid 2389 through 2393 Processing helix chain 'I' and resid 2417 through 2436 removed outlier: 4.109A pdb=" N ALA I2421 " --> pdb=" O HIS I2417 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE I2422 " --> pdb=" O LEU I2418 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET I2423 " --> pdb=" O GLY I2419 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE I2425 " --> pdb=" O ALA I2421 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA I2428 " --> pdb=" O SER I2424 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU I2433 " --> pdb=" O LEU I2429 " (cutoff:3.500A) Processing helix chain 'I' and resid 2440 through 2445 removed outlier: 3.737A pdb=" N ALA I2445 " --> pdb=" O HIS I2441 " (cutoff:3.500A) Processing helix chain 'I' and resid 2448 through 2461 removed outlier: 3.860A pdb=" N ILE I2453 " --> pdb=" O GLU I2449 " (cutoff:3.500A) Processing helix chain 'I' and resid 2466 through 2471 Processing helix chain 'I' and resid 2499 through 2507 removed outlier: 3.643A pdb=" N UNK I2503 " --> pdb=" O UNK I2499 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK I2504 " --> pdb=" O UNK I2500 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N UNK I2505 " --> pdb=" O UNK I2501 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK I2506 " --> pdb=" O UNK I2502 " (cutoff:3.500A) Processing helix chain 'I' and resid 2516 through 2522 Processing helix chain 'I' and resid 2525 through 2530 removed outlier: 3.526A pdb=" N UNK I2530 " --> pdb=" O UNK I2526 " (cutoff:3.500A) Processing helix chain 'I' and resid 2542 through 2548 removed outlier: 3.683A pdb=" N UNK I2546 " --> pdb=" O UNK I2542 " (cutoff:3.500A) Processing helix chain 'I' and resid 2551 through 2557 removed outlier: 3.744A pdb=" N UNK I2555 " --> pdb=" O UNK I2551 " (cutoff:3.500A) Processing helix chain 'I' and resid 2567 through 2581 removed outlier: 3.517A pdb=" N UNK I2578 " --> pdb=" O UNK I2574 " (cutoff:3.500A) Processing helix chain 'I' and resid 2587 through 2602 removed outlier: 3.636A pdb=" N UNK I2597 " --> pdb=" O UNK I2593 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK I2602 " --> pdb=" O UNK I2598 " (cutoff:3.500A) Processing helix chain 'I' and resid 2610 through 2618 removed outlier: 3.753A pdb=" N UNK I2618 " --> pdb=" O UNK I2614 " (cutoff:3.500A) Processing helix chain 'I' and resid 2626 through 2640 removed outlier: 3.908A pdb=" N UNK I2630 " --> pdb=" O UNK I2626 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N UNK I2631 " --> pdb=" O UNK I2627 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK I2634 " --> pdb=" O UNK I2630 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK I2635 " --> pdb=" O UNK I2631 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK I2639 " --> pdb=" O UNK I2635 " (cutoff:3.500A) Processing helix chain 'I' and resid 2641 through 2643 No H-bonds generated for 'chain 'I' and resid 2641 through 2643' Processing helix chain 'I' and resid 2650 through 2666 Processing helix chain 'I' and resid 2748 through 2773 removed outlier: 3.633A pdb=" N ASP I2752 " --> pdb=" O PRO I2748 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER I2753 " --> pdb=" O GLU I2749 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE I2754 " --> pdb=" O LYS I2750 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE I2768 " --> pdb=" O GLU I2764 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP I2769 " --> pdb=" O LYS I2765 " (cutoff:3.500A) Processing helix chain 'I' and resid 2793 through 2797 removed outlier: 3.770A pdb=" N PHE I2797 " --> pdb=" O TYR I2794 " (cutoff:3.500A) Processing helix chain 'I' and resid 2800 through 2804 Processing helix chain 'I' and resid 2809 through 2820 removed outlier: 4.201A pdb=" N ALA I2815 " --> pdb=" O GLU I2811 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET I2816 " --> pdb=" O SER I2812 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE I2817 " --> pdb=" O LEU I2813 " (cutoff:3.500A) Processing helix chain 'I' and resid 2868 through 2895 removed outlier: 3.967A pdb=" N MET I2874 " --> pdb=" O GLU I2870 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP I2886 " --> pdb=" O TYR I2882 " (cutoff:3.500A) Processing helix chain 'I' and resid 2907 through 2911 Processing helix chain 'I' and resid 2914 through 2932 removed outlier: 3.546A pdb=" N ARG I2918 " --> pdb=" O LYS I2914 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP I2919 " --> pdb=" O GLU I2915 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG I2920 " --> pdb=" O LYS I2916 " (cutoff:3.500A) Processing helix chain 'I' and resid 2950 through 2976 removed outlier: 4.262A pdb=" N UNK I2956 " --> pdb=" O UNK I2952 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK I2968 " --> pdb=" O UNK I2964 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK I2969 " --> pdb=" O UNK I2965 " (cutoff:3.500A) Processing helix chain 'I' and resid 2999 through 3015 removed outlier: 3.550A pdb=" N UNK I3004 " --> pdb=" O UNK I3000 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N UNK I3006 " --> pdb=" O UNK I3002 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK I3009 " --> pdb=" O UNK I3005 " (cutoff:3.500A) removed outlier: 3.813A 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 3025 through 3040 removed outlier: 4.254A pdb=" N UNK I3032 " --> pdb=" O UNK I3028 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N UNK I3040 " --> pdb=" O UNK I3036 " (cutoff:3.500A) Processing helix chain 'I' and resid 3052 through 3063 removed outlier: 4.342A pdb=" N UNK I3056 " --> pdb=" O UNK I3052 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N UNK I3057 " --> pdb=" O UNK I3053 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N UNK I3061 " --> pdb=" O UNK I3057 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N UNK I3062 " --> pdb=" O UNK I3058 " (cutoff:3.500A) Processing helix chain 'I' and resid 3141 through 3146 Processing helix chain 'I' and resid 3146 through 3162 removed outlier: 4.085A pdb=" N UNK I3154 " --> pdb=" O UNK I3150 " (cutoff:3.500A) Processing helix chain 'I' and resid 3175 through 3186 removed outlier: 3.732A pdb=" N UNK I3182 " --> pdb=" O UNK I3178 " (cutoff:3.500A) Processing helix chain 'I' and resid 3198 through 3212 Processing helix chain 'I' and resid 3224 through 3230 removed outlier: 3.893A pdb=" N UNK I3228 " --> pdb=" O UNK I3224 " (cutoff:3.500A) Processing helix chain 'I' and resid 3249 through 3254 Processing helix chain 'I' and resid 3271 through 3285 removed outlier: 3.593A pdb=" N UNK I3281 " --> pdb=" O UNK I3277 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N UNK I3282 " --> pdb=" O UNK I3278 " (cutoff:3.500A) removed outlier: 3.947A 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 3321 removed outlier: 3.635A pdb=" N UNK I3321 " --> pdb=" O UNK I3317 " (cutoff:3.500A) Processing helix chain 'I' and resid 3321 through 3330 removed outlier: 3.565A pdb=" N UNK I3330 " --> pdb=" O UNK I3326 " (cutoff:3.500A) Processing helix chain 'I' and resid 3344 through 3349 removed outlier: 3.588A 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 3407 removed outlier: 3.594A pdb=" N UNK I3403 " --> pdb=" O UNK I3399 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N UNK I3404 " --> pdb=" O UNK I3400 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N UNK I3405 " --> pdb=" O UNK I3401 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK I3407 " --> pdb=" O UNK I3403 " (cutoff:3.500A) Processing helix chain 'I' and resid 3410 through 3425 removed outlier: 4.100A pdb=" N UNK I3416 " --> pdb=" O UNK I3412 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK I3417 " --> pdb=" O UNK I3413 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N UNK I3420 " --> pdb=" O UNK I3416 " (cutoff:3.500A) Processing helix chain 'I' and resid 3437 through 3443 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 removed outlier: 3.538A pdb=" N UNK I3468 " --> pdb=" O UNK I3464 " (cutoff:3.500A) Processing helix chain 'I' and resid 3522 through 3527 Processing helix chain 'I' and resid 3541 through 3547 removed outlier: 3.663A pdb=" N UNK I3547 " --> pdb=" O UNK I3543 " (cutoff:3.500A) Processing helix chain 'I' and resid 3551 through 3560 Processing helix chain 'I' and resid 3574 through 3579 removed outlier: 3.627A pdb=" N UNK I3579 " --> pdb=" O UNK I3575 " (cutoff:3.500A) Processing helix chain 'I' and resid 3589 through 3608 removed outlier: 4.138A pdb=" N UNK I3595 " --> pdb=" O UNK I3591 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNK I3600 " --> pdb=" O UNK I3596 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK I3601 " --> pdb=" O UNK I3597 " (cutoff:3.500A) Processing helix chain 'I' and resid 3645 through 3656 Processing helix chain 'I' and resid 3657 through 3661 Processing helix chain 'I' and resid 3671 through 3680 removed outlier: 4.091A pdb=" N LEU I3677 " --> pdb=" O MET I3673 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER I3678 " --> pdb=" O ILE I3674 " (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 3738 removed outlier: 4.174A pdb=" N GLU I3736 " --> pdb=" O SER I3732 " (cutoff:3.500A) Processing helix chain 'I' and resid 3752 through 3758 Processing helix chain 'I' and resid 3764 through 3769 Processing helix chain 'I' and resid 3774 through 3784 removed outlier: 4.055A pdb=" N MET I3778 " --> pdb=" O GLY I3774 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL I3779 " --> pdb=" O ALA I3775 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU I3780 " --> pdb=" O ALA I3776 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE I3783 " --> pdb=" O VAL I3779 " (cutoff:3.500A) Processing helix chain 'I' and resid 3791 through 3805 removed outlier: 3.772A pdb=" N SER I3803 " --> pdb=" O LYS I3799 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.577A 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: 3.696A pdb=" N GLN I3882 " --> pdb=" O ASP I3878 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP I3883 " --> pdb=" O GLU I3879 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE I3885 " --> pdb=" O THR I3881 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS I3892 " --> pdb=" O LEU I3888 " (cutoff:3.500A) Processing helix chain 'I' and resid 3898 through 3905 Processing helix chain 'I' and resid 3914 through 3937 removed outlier: 3.953A pdb=" N CYS I3918 " --> pdb=" O ASN I3914 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I3920 " --> pdb=" O ILE I3916 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP I3921 " --> pdb=" O ILE I3917 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER I3929 " --> pdb=" O ARG I3925 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR I3934 " --> pdb=" O ILE I3930 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP I3935 " --> pdb=" O SER I3931 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR I3936 " --> pdb=" O ASP I3932 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR I3937 " --> pdb=" O PHE I3933 " (cutoff:3.500A) Processing helix chain 'I' and resid 3944 through 3968 removed outlier: 3.682A pdb=" N LYS I3953 " --> pdb=" O ARG I3949 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA I3954 " --> pdb=" O ASN I3950 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS I3959 " --> pdb=" O MET I3955 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN I3960 " --> pdb=" O SER I3956 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL I3961 " --> pdb=" O VAL I3957 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU I3967 " --> pdb=" O ASN I3963 " (cutoff:3.500A) Processing helix chain 'I' and resid 3973 through 3983 removed outlier: 3.757A pdb=" N HIS I3982 " --> pdb=" O GLN I3978 " (cutoff:3.500A) Processing helix chain 'I' and resid 3984 through 4004 removed outlier: 3.596A pdb=" N VAL I3990 " --> pdb=" O TRP I3986 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY I3991 " --> pdb=" O ASP I3987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE I3992 " --> pdb=" O ALA I3988 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU I3993 " --> pdb=" O VAL I3989 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS I3994 " --> pdb=" O VAL I3990 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS I3998 " --> pdb=" O HIS I3994 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET I3999 " --> pdb=" O VAL I3995 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET I4000 " --> pdb=" O PHE I3996 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA I4004 " --> pdb=" O MET I4000 " (cutoff:3.500A) Processing helix chain 'I' and resid 4009 through 4030 removed outlier: 3.906A pdb=" N MET I4026 " --> pdb=" O ASP I4022 " (cutoff:3.500A) Processing helix chain 'I' and resid 4039 through 4051 removed outlier: 3.839A pdb=" N ASP I4046 " --> pdb=" O ARG I4042 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU I4048 " --> pdb=" O MET I4044 " (cutoff:3.500A) Processing helix chain 'I' and resid 4051 through 4062 removed outlier: 3.542A pdb=" N PHE I4061 " --> pdb=" O MET I4057 " (cutoff:3.500A) Processing helix chain 'I' and resid 4067 through 4072 Processing helix chain 'I' and resid 4074 through 4079 Processing helix chain 'I' and resid 4090 through 4100 removed outlier: 3.523A pdb=" N MET I4097 " --> pdb=" O PHE I4093 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP I4098 " --> pdb=" O GLN I4094 " (cutoff:3.500A) Processing helix chain 'I' and resid 4104 through 4115 Processing helix chain 'I' and resid 4124 through 4154 removed outlier: 4.632A pdb=" N PHE I4132 " --> pdb=" O PHE I4128 " (cutoff:3.500A) Proline residue: I4135 - end of helix removed outlier: 6.010A pdb=" N ASP I4138 " --> pdb=" O GLU I4134 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE I4141 " --> pdb=" O ARG I4137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN I4142 " --> pdb=" O ASP I4138 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU I4152 " --> pdb=" O THR I4148 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL I4154 " --> pdb=" O LEU I4150 " (cutoff:3.500A) Processing helix chain 'I' and resid 4157 through 4167 removed outlier: 3.501A pdb=" N PHE I4163 " --> pdb=" O ARG I4159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I4165 " --> pdb=" O ARG I4161 " (cutoff:3.500A) Processing helix chain 'I' and resid 4167 through 4174 removed outlier: 3.540A pdb=" N LEU I4171 " --> pdb=" O ALA I4167 " (cutoff:3.500A) Processing helix chain 'I' and resid 4198 through 4206 removed outlier: 3.640A pdb=" N ARG I4202 " --> pdb=" O SER I4198 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN I4204 " --> pdb=" O THR I4200 " (cutoff:3.500A) Processing helix chain 'I' and resid 4207 through 4224 removed outlier: 3.532A pdb=" N ASP I4220 " --> pdb=" O GLN I4216 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL I4222 " --> pdb=" O ILE I4218 " (cutoff:3.500A) Processing helix chain 'I' and resid 4228 through 4250 removed outlier: 3.556A pdb=" N PHE I4234 " --> pdb=" O LYS I4230 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE I4243 " --> pdb=" O GLU I4239 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA I4249 " --> pdb=" O MET I4245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN I4250 " --> pdb=" O GLN I4246 " (cutoff:3.500A) Processing helix chain 'I' and resid 4542 through 4558 removed outlier: 3.700A pdb=" N VAL I4546 " --> pdb=" O GLY I4542 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR I4554 " --> pdb=" O LYS I4550 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN I4558 " --> pdb=" O TYR I4554 " (cutoff:3.500A) Processing helix chain 'I' and resid 4558 through 4576 removed outlier: 3.570A pdb=" N LEU I4562 " --> pdb=" O ASN I4558 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA I4570 " --> pdb=" O ALA I4566 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE I4571 " --> pdb=" O LEU I4567 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA I4572 " --> pdb=" O PHE I4568 " (cutoff:3.500A) Processing helix chain 'I' and resid 4641 through 4664 removed outlier: 3.698A pdb=" N CYS I4657 " --> pdb=" O VAL I4653 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE I4658 " --> pdb=" O ALA I4654 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE I4659 " --> pdb=" O PHE I4655 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I4664 " --> pdb=" O GLY I4660 " (cutoff:3.500A) Processing helix chain 'I' and resid 4667 through 4683 removed outlier: 3.613A pdb=" N GLU I4676 " --> pdb=" O LYS I4672 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA I4678 " --> pdb=" O GLU I4674 " (cutoff:3.500A) Processing helix chain 'I' and resid 4696 through 4702 removed outlier: 3.568A pdb=" N GLN I4700 " --> pdb=" O ASP I4696 " (cutoff:3.500A) Processing helix chain 'I' and resid 4703 through 4705 No H-bonds generated for 'chain 'I' and resid 4703 through 4705' Processing helix chain 'I' and resid 4710 through 4714 removed outlier: 3.549A pdb=" N SER I4713 " --> pdb=" O SER I4710 " (cutoff:3.500A) removed outlier: 4.682A 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 4728 Processing helix chain 'I' and resid 4733 through 4741 Processing helix chain 'I' and resid 4745 through 4753 removed outlier: 4.808A pdb=" N THR I4751 " --> pdb=" O SER I4747 " (cutoff:3.500A) Processing helix chain 'I' and resid 4772 through 4786 removed outlier: 3.525A pdb=" N ASP I4786 " --> pdb=" O VAL I4782 " (cutoff:3.500A) Processing helix chain 'I' and resid 4786 through 4802 removed outlier: 3.578A pdb=" N LEU I4790 " --> pdb=" O ASP I4786 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER I4799 " --> pdb=" O TYR I4795 " (cutoff:3.500A) Processing helix chain 'I' and resid 4811 through 4820 removed outlier: 3.999A pdb=" N ASP I4815 " --> pdb=" O ALA I4811 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL I4820 " --> pdb=" O ILE I4816 " (cutoff:3.500A) Processing helix chain 'I' and resid 4820 through 4833 removed outlier: 3.770A pdb=" N ILE I4826 " --> pdb=" O THR I4822 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN I4833 " --> pdb=" O SER I4829 " (cutoff:3.500A) Processing helix chain 'I' and resid 4833 through 4858 removed outlier: 3.970A pdb=" N MET I4839 " --> pdb=" O LYS I4835 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL I4846 " --> pdb=" O GLY I4842 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL I4848 " --> pdb=" O LEU I4844 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL I4853 " --> pdb=" O TYR I4849 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL I4854 " --> pdb=" O LEU I4850 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA I4855 " --> pdb=" O TYR I4851 " (cutoff:3.500A) Processing helix chain 'I' and resid 4859 through 4863 removed outlier: 3.864A pdb=" N PHE I4862 " --> pdb=" O PHE I4859 " (cutoff:3.500A) removed outlier: 3.897A 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 4890 removed outlier: 3.546A pdb=" N TYR I4883 " --> pdb=" O MET I4879 " (cutoff:3.500A) Processing helix chain 'I' and resid 4896 through 4900 removed outlier: 3.876A pdb=" N ASP I4899 " --> pdb=" O GLY I4896 " (cutoff:3.500A) Processing helix chain 'I' and resid 4913 through 4922 removed outlier: 3.774A pdb=" N ASP I4917 " --> pdb=" O ARG I4913 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE I4918 " --> pdb=" O VAL I4914 " (cutoff:3.500A) Processing helix chain 'I' and resid 4924 through 4957 removed outlier: 3.952A pdb=" N LEU I4929 " --> pdb=" O ILE I4925 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA I4930 " --> pdb=" O VAL I4926 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE I4936 " --> pdb=" O ILE I4932 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA I4939 " --> pdb=" O LEU I4935 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG I4944 " --> pdb=" O PHE I4940 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS I4951 " --> pdb=" O GLN I4947 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP I4953 " --> pdb=" O GLN I4949 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET I4954 " --> pdb=" O VAL I4950 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU I4955 " --> pdb=" O LYS I4951 " (cutoff:3.500A) Processing helix chain 'I' and resid 4964 through 4968 removed outlier: 3.935A pdb=" N TYR I4967 " --> pdb=" O GLY I4964 " (cutoff:3.500A) Processing helix chain 'I' and resid 4973 through 4982 Processing helix chain 'I' and resid 4986 through 4997 removed outlier: 3.551A pdb=" N ILE I4996 " --> pdb=" O LEU I4992 " (cutoff:3.500A) Processing helix chain 'I' and resid 5006 through 5017 Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 251 through 255 removed outlier: 3.593A pdb=" N THR G 254 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 369 Processing helix chain 'G' and resid 395 through 419 removed outlier: 3.752A pdb=" N GLN G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET G 403 " --> pdb=" O GLN G 399 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 410 " --> pdb=" O SER G 406 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN G 413 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS G 416 " --> pdb=" O ASN G 412 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY G 417 " --> pdb=" O GLN G 413 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP G 419 " --> pdb=" O ILE G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 452 removed outlier: 3.843A pdb=" N GLY G 450 " --> pdb=" O GLN G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 481 removed outlier: 3.521A pdb=" N GLN G 465 " --> pdb=" O HIS G 461 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN G 473 " --> pdb=" O ARG G 469 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE G 478 " --> pdb=" O ARG G 474 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU G 481 " --> pdb=" O LEU G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 Processing helix chain 'G' and resid 510 through 529 removed outlier: 4.076A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR G 523 " --> pdb=" O VAL G 519 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 524 " --> pdb=" O ASN G 520 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER G 528 " --> pdb=" O GLU G 524 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 529 " --> pdb=" O LEU G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 539 removed outlier: 3.820A pdb=" N LEU G 539 " --> pdb=" O ALA G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 542 No H-bonds generated for 'chain 'G' and resid 540 through 542' Processing helix chain 'G' and resid 543 through 551 removed outlier: 3.826A pdb=" N VAL G 548 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER G 549 " --> pdb=" O ASP G 545 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS G 550 " --> pdb=" O TRP G 546 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU G 551 " --> pdb=" O VAL G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 571 removed outlier: 3.714A pdb=" N TYR G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 568 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU G 570 " --> pdb=" O CYS G 566 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER G 571 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 576 removed outlier: 3.992A 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: 4.117A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 603 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 625 removed outlier: 3.987A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 619 " --> pdb=" O ARG G 615 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR G 622 " --> pdb=" O GLN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 890 removed outlier: 3.636A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS G 873 " --> pdb=" O ARG G 869 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS G 879 " --> pdb=" O ALA G 875 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE G 887 " --> pdb=" O ALA G 883 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN G 889 " --> pdb=" O THR G 885 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 934 removed outlier: 3.672A pdb=" N ASN G 919 " --> pdb=" O GLU G 915 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU G 929 " --> pdb=" O SER G 925 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 934 " --> pdb=" O LYS G 930 " (cutoff:3.500A) Processing helix chain 'G' and resid 980 through 988 removed outlier: 3.733A pdb=" N LEU G 984 " --> pdb=" O ALA G 980 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP G 986 " --> pdb=" O THR G 982 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 1001 removed outlier: 3.519A pdb=" N HIS G 993 " --> pdb=" O ALA G 989 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN G 994 " --> pdb=" O GLU G 990 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP G 996 " --> pdb=" O GLY G 992 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G1000 " --> pdb=" O TRP G 996 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1041 removed outlier: 3.582A pdb=" N LEU G1039 " --> pdb=" O ASN G1035 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN G1041 " --> pdb=" O ASP G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1042 through 1049 removed outlier: 3.580A pdb=" N LEU G1046 " --> pdb=" O ALA G1042 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G1047 " --> pdb=" O VAL G1043 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY G1048 " --> pdb=" O ARG G1044 " (cutoff:3.500A) Processing helix chain 'G' and resid 1078 through 1082 Processing helix chain 'G' and resid 1575 through 1579 removed outlier: 3.567A pdb=" N ALA G1578 " --> pdb=" O LEU G1575 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET G1579 " --> pdb=" O SER G1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1575 through 1579' Processing helix chain 'G' and resid 1652 through 1657 removed outlier: 3.505A pdb=" N LEU G1657 " --> pdb=" O LEU G1653 " (cutoff:3.500A) Processing helix chain 'G' and resid 1658 through 1674 removed outlier: 3.807A pdb=" N HIS G1665 " --> pdb=" O ARG G1661 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR G1670 " --> pdb=" O THR G1666 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG G1671 " --> pdb=" O LEU G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1686 removed outlier: 3.653A pdb=" N ALA G1684 " --> pdb=" O ARG G1680 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS G1686 " --> pdb=" O ALA G1682 " (cutoff:3.500A) Processing helix chain 'G' and resid 1692 through 1700 removed outlier: 4.199A pdb=" N LEU G1698 " --> pdb=" O LEU G1694 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU G1699 " --> pdb=" O LEU G1695 " (cutoff:3.500A) Processing helix chain 'G' and resid 1710 through 1714 removed outlier: 3.804A pdb=" N ASP G1713 " --> pdb=" O GLY G1710 " (cutoff:3.500A) Processing helix chain 'G' and resid 1715 through 1720 Processing helix chain 'G' and resid 1720 through 1730 removed outlier: 3.928A pdb=" N ARG G1725 " --> pdb=" O GLU G1721 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER G1726 " --> pdb=" O SER G1722 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 Processing helix chain 'G' and resid 1803 through 1824 removed outlier: 3.666A pdb=" N LEU G1807 " --> pdb=" O PRO G1803 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET G1814 " --> pdb=" O LYS G1810 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY G1816 " --> pdb=" O LEU G1812 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G1824 " --> pdb=" O ARG G1820 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1838 Processing helix chain 'G' and resid 1840 through 1851 removed outlier: 3.578A 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 1982 removed outlier: 3.612A pdb=" N LEU G1937 " --> pdb=" O GLU G1933 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN G1938 " --> pdb=" O SER G1934 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR G1945 " --> pdb=" O ASN G1941 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE G1946 " --> pdb=" O LEU G1942 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP G1948 " --> pdb=" O GLU G1944 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU G1963 " --> pdb=" O ALA G1959 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G1964 " --> pdb=" O ALA G1960 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN G1973 " --> pdb=" O LEU G1969 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA G1978 " --> pdb=" O ARG G1974 " (cutoff:3.500A) Processing helix chain 'G' and resid 1989 through 1994 removed outlier: 3.614A 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 2011 removed outlier: 3.624A pdb=" N ILE G2006 " --> pdb=" O PRO G2002 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN G2007 " --> pdb=" O GLN G2003 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) Processing helix chain 'G' and resid 2029 through 2042 Processing helix chain 'G' and resid 2094 through 2108 removed outlier: 3.795A pdb=" N VAL G2103 " --> pdb=" O SER G2099 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2129 removed outlier: 3.512A pdb=" N VAL G2117 " --> pdb=" O SER G2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G2126 " --> pdb=" O SER G2122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR G2128 " --> pdb=" O LEU G2124 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2137 Processing helix chain 'G' and resid 2148 through 2165 removed outlier: 3.902A pdb=" N CYS G2158 " --> pdb=" O SER G2154 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN G2161 " --> pdb=" O GLU G2157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G2165 " --> pdb=" O GLN G2161 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2186 removed outlier: 3.691A pdb=" N LEU G2177 " --> pdb=" O GLN G2173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G2185 " --> pdb=" O SER G2181 " (cutoff:3.500A) Processing helix chain 'G' and resid 2189 through 2194 Processing helix chain 'G' and resid 2194 through 2201 removed outlier: 4.016A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.975A pdb=" N ASN G2213 " --> pdb=" O GLU G2209 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL G2214 " --> pdb=" O VAL G2210 " (cutoff:3.500A) Processing helix chain 'G' and resid 2228 through 2242 removed outlier: 3.640A pdb=" N CYS G2233 " --> pdb=" O VAL G2229 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS G2237 " --> pdb=" O CYS G2233 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR G2238 " --> pdb=" O ARG G2234 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2252 removed outlier: 3.582A pdb=" N ASP G2252 " --> pdb=" O ARG G2248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2262 removed outlier: 4.074A pdb=" N ASN G2260 " --> pdb=" O TYR G2256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G2262 " --> pdb=" O LEU G2258 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2279 Processing helix chain 'G' and resid 2294 through 2306 removed outlier: 3.544A pdb=" N VAL G2299 " --> pdb=" O LEU G2295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2315 removed outlier: 4.307A pdb=" N ALA G2315 " --> pdb=" O PRO G2311 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2331 removed outlier: 3.588A pdb=" N TYR G2331 " --> pdb=" O GLY G2327 " (cutoff:3.500A) Processing helix chain 'G' and resid 2335 through 2339 removed outlier: 4.051A pdb=" N ALA G2338 " --> pdb=" O LEU G2335 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2349 Processing helix chain 'G' and resid 2350 through 2358 removed outlier: 3.590A 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 2375 through 2388 removed outlier: 3.505A pdb=" N ARG G2385 " --> pdb=" O GLU G2381 " (cutoff:3.500A) Processing helix chain 'G' and resid 2389 through 2393 removed outlier: 3.501A pdb=" N ARG G2392 " --> pdb=" O ASP G2389 " (cutoff:3.500A) Processing helix chain 'G' and resid 2417 through 2436 removed outlier: 4.110A pdb=" N ALA G2421 " --> pdb=" O HIS G2417 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G2422 " --> pdb=" O LEU G2418 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET G2423 " --> pdb=" O GLY G2419 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G2425 " --> pdb=" O ALA G2421 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA G2428 " --> pdb=" O SER G2424 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G2433 " --> pdb=" O LEU G2429 " (cutoff:3.500A) Processing helix chain 'G' and resid 2440 through 2445 removed outlier: 3.737A pdb=" N ALA G2445 " --> pdb=" O HIS G2441 " (cutoff:3.500A) Processing helix chain 'G' and resid 2448 through 2461 removed outlier: 3.860A pdb=" N ILE G2453 " --> pdb=" O GLU G2449 " (cutoff:3.500A) Processing helix chain 'G' and resid 2466 through 2471 Processing helix chain 'G' and resid 2499 through 2507 removed outlier: 3.624A pdb=" N UNK G2503 " --> pdb=" O UNK G2499 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK G2504 " --> pdb=" O UNK G2500 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N UNK G2505 " --> pdb=" O UNK G2501 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N UNK G2506 " --> pdb=" O UNK G2502 " (cutoff:3.500A) Processing helix chain 'G' and resid 2516 through 2521 Processing helix chain 'G' and resid 2525 through 2530 removed outlier: 3.521A pdb=" N UNK G2530 " --> pdb=" O UNK G2526 " (cutoff:3.500A) Processing helix chain 'G' and resid 2542 through 2548 removed outlier: 3.691A pdb=" N UNK G2546 " --> pdb=" O UNK G2542 " (cutoff:3.500A) Processing helix chain 'G' and resid 2551 through 2557 removed outlier: 3.749A pdb=" N UNK G2555 " --> pdb=" O UNK G2551 " (cutoff:3.500A) Processing helix chain 'G' and resid 2567 through 2581 removed outlier: 3.524A pdb=" N UNK G2578 " --> pdb=" O UNK G2574 " (cutoff:3.500A) Processing helix chain 'G' and resid 2587 through 2602 removed outlier: 3.629A pdb=" N UNK G2597 " --> pdb=" O UNK G2593 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N UNK G2602 " --> pdb=" O UNK G2598 " (cutoff:3.500A) Processing helix chain 'G' and resid 2610 through 2618 removed outlier: 3.760A pdb=" N UNK G2618 " --> pdb=" O UNK G2614 " (cutoff:3.500A) Processing helix chain 'G' and resid 2626 through 2640 removed outlier: 3.901A pdb=" N UNK G2630 " --> pdb=" O UNK G2626 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N UNK G2631 " --> pdb=" O UNK G2627 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N UNK G2634 " --> pdb=" O UNK G2630 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK G2635 " --> pdb=" O UNK G2631 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N UNK G2639 " --> pdb=" O UNK G2635 " (cutoff:3.500A) Processing helix chain 'G' and resid 2641 through 2643 No H-bonds generated for 'chain 'G' and resid 2641 through 2643' Processing helix chain 'G' and resid 2650 through 2666 Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 3.631A pdb=" N ASP G2752 " --> pdb=" O PRO G2748 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE G2768 " --> pdb=" O GLU G2764 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP G2769 " --> pdb=" O LYS G2765 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2797 removed outlier: 3.769A pdb=" N PHE G2797 " --> pdb=" O TYR G2794 " (cutoff:3.500A) Processing helix chain 'G' and resid 2800 through 2804 Processing helix chain 'G' and resid 2809 through 2820 removed outlier: 4.202A pdb=" N ALA G2815 " --> pdb=" O GLU G2811 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET G2816 " --> pdb=" O SER G2812 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE G2817 " --> pdb=" O LEU G2813 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2895 removed outlier: 3.966A pdb=" N MET G2874 " --> pdb=" O GLU G2870 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP G2886 " --> pdb=" O TYR G2882 " (cutoff:3.500A) Processing helix chain 'G' and resid 2907 through 2911 Processing helix chain 'G' and resid 2914 through 2932 removed outlier: 3.546A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG G2920 " --> pdb=" O LYS G2916 " (cutoff:3.500A) Processing helix chain 'G' and resid 2950 through 2976 removed outlier: 4.247A pdb=" N UNK G2956 " --> pdb=" O UNK G2952 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N UNK G2968 " --> pdb=" O UNK G2964 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N UNK G2969 " --> pdb=" O UNK G2965 " (cutoff:3.500A) Processing helix chain 'G' and resid 2999 through 3015 removed outlier: 3.536A pdb=" N UNK G3004 " --> pdb=" O UNK G3000 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK G3006 " --> pdb=" O UNK G3002 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNK G3009 " --> pdb=" O UNK G3005 " (cutoff:3.500A) removed outlier: 3.818A 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 3025 through 3040 removed outlier: 4.252A pdb=" N UNK G3032 " --> pdb=" O UNK G3028 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N UNK G3040 " --> pdb=" O UNK G3036 " (cutoff:3.500A) Processing helix chain 'G' and resid 3052 through 3063 removed outlier: 4.340A pdb=" N UNK G3056 " --> pdb=" O UNK G3052 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N UNK G3057 " --> pdb=" O UNK G3053 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N UNK G3061 " --> pdb=" O UNK G3057 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N UNK G3062 " --> pdb=" O UNK G3058 " (cutoff:3.500A) Processing helix chain 'G' and resid 3141 through 3146 Processing helix chain 'G' and resid 3146 through 3162 removed outlier: 4.082A pdb=" N UNK G3154 " --> pdb=" O UNK G3150 " (cutoff:3.500A) Processing helix chain 'G' and resid 3175 through 3186 removed outlier: 3.743A 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: 3.905A pdb=" N UNK G3228 " --> pdb=" O UNK G3224 " (cutoff:3.500A) Processing helix chain 'G' and resid 3249 through 3254 Processing helix chain 'G' and resid 3271 through 3285 removed outlier: 3.588A pdb=" N UNK G3281 " --> pdb=" O UNK G3277 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N UNK G3282 " --> pdb=" O UNK G3278 " (cutoff:3.500A) removed outlier: 3.945A 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 3321 removed outlier: 3.626A pdb=" N UNK G3321 " --> pdb=" O UNK G3317 " (cutoff:3.500A) Processing helix chain 'G' and resid 3321 through 3330 removed outlier: 3.564A pdb=" N UNK G3330 " --> pdb=" O UNK G3326 " (cutoff:3.500A) Processing helix chain 'G' and resid 3344 through 3349 removed outlier: 3.575A 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 3399 through 3407 removed outlier: 3.599A pdb=" N UNK G3403 " --> pdb=" O UNK G3399 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N UNK G3404 " --> pdb=" O UNK G3400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK G3405 " --> pdb=" O UNK G3401 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N UNK G3407 " --> pdb=" O UNK G3403 " (cutoff:3.500A) Processing helix chain 'G' and resid 3410 through 3425 removed outlier: 4.094A pdb=" N UNK G3416 " --> pdb=" O UNK G3412 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK G3417 " --> pdb=" O UNK G3413 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N UNK G3420 " --> pdb=" O UNK G3416 " (cutoff:3.500A) Processing helix chain 'G' and resid 3437 through 3443 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: 3.531A pdb=" N UNK G3468 " --> pdb=" O UNK G3464 " (cutoff:3.500A) Processing helix chain 'G' and resid 3518 through 3521 removed outlier: 3.699A pdb=" N UNK G3521 " --> pdb=" O UNK G3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3518 through 3521' Processing helix chain 'G' and resid 3522 through 3527 Processing helix chain 'G' and resid 3541 through 3547 removed outlier: 3.636A pdb=" N UNK G3547 " --> pdb=" O UNK G3543 " (cutoff:3.500A) Processing helix chain 'G' and resid 3551 through 3560 Processing helix chain 'G' and resid 3574 through 3579 removed outlier: 3.633A pdb=" N UNK G3579 " --> pdb=" O UNK G3575 " (cutoff:3.500A) Processing helix chain 'G' and resid 3589 through 3608 removed outlier: 4.141A pdb=" N UNK G3595 " --> pdb=" O UNK G3591 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N UNK G3600 " --> pdb=" O UNK G3596 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK G3601 " --> pdb=" O UNK G3597 " (cutoff:3.500A) Processing helix chain 'G' and resid 3645 through 3656 Processing helix chain 'G' and resid 3657 through 3661 Processing helix chain 'G' and resid 3671 through 3680 removed outlier: 4.091A pdb=" N LEU G3677 " --> pdb=" O MET G3673 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER G3678 " --> pdb=" O ILE G3674 " (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 3738 removed outlier: 4.174A pdb=" N GLU G3736 " --> pdb=" O SER G3732 " (cutoff:3.500A) Processing helix chain 'G' and resid 3752 through 3758 Processing helix chain 'G' and resid 3764 through 3769 Processing helix chain 'G' and resid 3774 through 3784 removed outlier: 4.054A pdb=" N MET G3778 " --> pdb=" O GLY G3774 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G3779 " --> pdb=" O ALA G3775 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G3783 " --> pdb=" O VAL G3779 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3805 removed outlier: 3.772A pdb=" N SER G3803 " --> pdb=" O LYS G3799 " (cutoff:3.500A) removed outlier: 3.757A 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: 3.576A 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: 3.695A pdb=" N GLN G3882 " --> pdb=" O ASP G3878 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP G3883 " --> pdb=" O GLU G3879 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE G3885 " --> pdb=" O THR G3881 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS G3892 " --> pdb=" O LEU G3888 " (cutoff:3.500A) Processing helix chain 'G' and resid 3898 through 3905 Processing helix chain 'G' and resid 3914 through 3937 removed outlier: 3.952A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G3920 " --> pdb=" O ILE G3916 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP G3921 " --> pdb=" O ILE G3917 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER G3929 " --> pdb=" O ARG G3925 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR G3934 " --> pdb=" O ILE G3930 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP G3935 " --> pdb=" O SER G3931 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3968 removed outlier: 3.683A pdb=" N LYS G3953 " --> pdb=" O ARG G3949 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA G3954 " --> pdb=" O ASN G3950 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS G3959 " --> pdb=" O MET G3955 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN G3960 " --> pdb=" O SER G3956 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G3961 " --> pdb=" O VAL G3957 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU G3967 " --> pdb=" O ASN G3963 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3983 removed outlier: 3.757A pdb=" N HIS G3982 " --> pdb=" O GLN G3978 " (cutoff:3.500A) Processing helix chain 'G' and resid 3984 through 4004 removed outlier: 3.597A pdb=" N VAL G3990 " --> pdb=" O TRP G3986 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU G3993 " --> pdb=" O VAL G3989 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS G3994 " --> pdb=" O VAL G3990 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS G3998 " --> pdb=" O HIS G3994 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET G3999 " --> pdb=" O VAL G3995 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G4004 " --> pdb=" O MET G4000 " (cutoff:3.500A) Processing helix chain 'G' and resid 4009 through 4030 removed outlier: 3.906A pdb=" N MET G4026 " --> pdb=" O ASP G4022 " (cutoff:3.500A) Processing helix chain 'G' and resid 4039 through 4051 removed outlier: 3.840A pdb=" N ASP G4046 " --> pdb=" O ARG G4042 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G4048 " --> pdb=" O MET G4044 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4062 removed outlier: 3.541A pdb=" N PHE G4061 " --> pdb=" O MET G4057 " (cutoff:3.500A) Processing helix chain 'G' and resid 4067 through 4072 Processing helix chain 'G' and resid 4074 through 4079 Processing helix chain 'G' and resid 4090 through 4100 removed outlier: 3.524A pdb=" N MET G4097 " --> pdb=" O PHE G4093 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP G4098 " --> pdb=" O GLN G4094 " (cutoff:3.500A) Processing helix chain 'G' and resid 4104 through 4115 Processing helix chain 'G' and resid 4124 through 4154 removed outlier: 4.633A pdb=" N PHE G4132 " --> pdb=" O PHE G4128 " (cutoff:3.500A) Proline residue: G4135 - end of helix removed outlier: 6.010A pdb=" N ASP G4138 " --> pdb=" O GLU G4134 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE G4141 " --> pdb=" O ARG G4137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN G4142 " --> pdb=" O ASP G4138 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU G4152 " --> pdb=" O THR G4148 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL G4154 " --> pdb=" O LEU G4150 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4167 removed outlier: 3.502A pdb=" N PHE G4163 " --> pdb=" O ARG G4159 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G4165 " --> pdb=" O ARG G4161 " (cutoff:3.500A) Processing helix chain 'G' and resid 4167 through 4174 removed outlier: 3.539A pdb=" N LEU G4171 " --> pdb=" O ALA G4167 " (cutoff:3.500A) Processing helix chain 'G' and resid 4198 through 4206 removed outlier: 3.641A pdb=" N ARG G4202 " --> pdb=" O SER G4198 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN G4204 " --> pdb=" O THR G4200 " (cutoff:3.500A) Processing helix chain 'G' and resid 4207 through 4224 removed outlier: 3.532A pdb=" N ASP G4220 " --> pdb=" O GLN G4216 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G4222 " --> pdb=" O ILE G4218 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4250 removed outlier: 3.557A pdb=" N PHE G4234 " --> pdb=" O LYS G4230 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE G4243 " --> pdb=" O GLU G4239 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA G4249 " --> pdb=" O MET G4245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN G4250 " --> pdb=" O GLN G4246 " (cutoff:3.500A) Processing helix chain 'G' and resid 4542 through 4558 removed outlier: 3.701A pdb=" N VAL G4546 " --> pdb=" O GLY G4542 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR G4554 " --> pdb=" O LYS G4550 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN G4558 " --> pdb=" O TYR G4554 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4576 removed outlier: 3.570A pdb=" N LEU G4562 " --> pdb=" O ASN G4558 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G4570 " --> pdb=" O ALA G4566 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE G4571 " --> pdb=" O LEU G4567 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA G4572 " --> pdb=" O PHE G4568 " (cutoff:3.500A) Processing helix chain 'G' and resid 4641 through 4664 removed outlier: 3.698A pdb=" N CYS G4657 " --> pdb=" O VAL G4653 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G4658 " --> pdb=" O ALA G4654 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G4664 " --> pdb=" O GLY G4660 " (cutoff:3.500A) Processing helix chain 'G' and resid 4667 through 4683 removed outlier: 3.611A pdb=" N GLU G4676 " --> pdb=" O LYS G4672 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA G4678 " --> pdb=" O GLU G4674 " (cutoff:3.500A) Processing helix chain 'G' and resid 4696 through 4702 removed outlier: 3.568A pdb=" N GLN G4700 " --> pdb=" O ASP G4696 " (cutoff:3.500A) Processing helix chain 'G' and resid 4703 through 4705 No H-bonds generated for 'chain 'G' and resid 4703 through 4705' Processing helix chain 'G' and resid 4710 through 4714 removed outlier: 3.548A pdb=" N SER G4713 " --> pdb=" O SER G4710 " (cutoff:3.500A) removed outlier: 4.682A 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 4728 Processing helix chain 'G' and resid 4733 through 4741 Processing helix chain 'G' and resid 4745 through 4753 removed outlier: 4.807A pdb=" N THR G4751 " --> pdb=" O SER G4747 " (cutoff:3.500A) Processing helix chain 'G' and resid 4772 through 4786 removed outlier: 3.526A pdb=" N ASP G4786 " --> pdb=" O VAL G4782 " (cutoff:3.500A) Processing helix chain 'G' and resid 4786 through 4802 removed outlier: 3.578A pdb=" N LEU G4790 " --> pdb=" O ASP G4786 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) Processing helix chain 'G' and resid 4811 through 4820 removed outlier: 3.999A pdb=" N ASP G4815 " --> pdb=" O ALA G4811 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL G4820 " --> pdb=" O ILE G4816 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.769A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 3.970A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G4846 " --> pdb=" O GLY G4842 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL G4848 " --> pdb=" O LEU G4844 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL G4853 " --> pdb=" O TYR G4849 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL G4854 " --> pdb=" O LEU G4850 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G4855 " --> pdb=" O TYR G4851 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4863 removed outlier: 3.864A pdb=" N PHE G4862 " --> pdb=" O PHE G4859 " (cutoff:3.500A) removed outlier: 3.897A 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 4890 removed outlier: 3.547A pdb=" N TYR G4883 " --> pdb=" O MET G4879 " (cutoff:3.500A) Processing helix chain 'G' and resid 4896 through 4900 removed outlier: 3.874A pdb=" N ASP G4899 " --> pdb=" O GLY G4896 " (cutoff:3.500A) Processing helix chain 'G' and resid 4913 through 4922 removed outlier: 3.774A pdb=" N ASP G4917 " --> pdb=" O ARG G4913 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G4918 " --> pdb=" O VAL G4914 " (cutoff:3.500A) Processing helix chain 'G' and resid 4924 through 4957 removed outlier: 3.953A pdb=" N LEU G4929 " --> pdb=" O ILE G4925 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA G4930 " --> pdb=" O VAL G4926 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G4936 " --> pdb=" O ILE G4932 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA G4939 " --> pdb=" O LEU G4935 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG G4944 " --> pdb=" O PHE G4940 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G4951 " --> pdb=" O GLN G4947 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP G4953 " --> pdb=" O GLN G4949 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET G4954 " --> pdb=" O VAL G4950 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU G4955 " --> pdb=" O LYS G4951 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4968 removed outlier: 3.934A pdb=" N TYR G4967 " --> pdb=" O GLY G4964 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4982 Processing helix chain 'G' and resid 4986 through 4997 removed outlier: 3.549A pdb=" N ILE G4996 " --> pdb=" O LEU G4992 " (cutoff:3.500A) Processing helix chain 'G' and resid 5006 through 5017 Processing helix chain 'F' and resid 38 through 43 removed outlier: 3.907A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 4.067A pdb=" N GLY F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.779A pdb=" N VAL F 80 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.907A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 removed outlier: 4.067A pdb=" N GLY A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.779A pdb=" N VAL A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.908A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 4.066A pdb=" N GLY H 62 " --> pdb=" O GLY H 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.780A pdb=" N VAL H 80 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 43 removed outlier: 3.907A pdb=" N ARG J 42 " --> pdb=" O SER J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 4.067A pdb=" N GLY J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.780A pdb=" N VAL J 80 " --> pdb=" O THR J 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.733A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.733A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 21 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN B 23 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET B 202 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER B 25 " --> pdb=" O TRP B 200 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP B 200 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP B 200 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA4, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AA5, first strand: chain 'B' and resid 280 through 284 removed outlier: 3.552A pdb=" N PHE B 389 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 230 through 233 removed outlier: 5.673A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 376 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 374 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.522A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) 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 634 through 639 removed outlier: 4.041A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 644 through 646 Processing sheet with id=AB2, first strand: chain 'B' and resid 661 through 663 removed outlier: 3.512A pdb=" N TRP B 662 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 742 through 744 removed outlier: 3.547A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 713 through 714 Processing sheet with id=AB5, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AB6, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AB7, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.267A pdb=" N THR B 892 " --> pdb=" O HIS B 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 938 through 941 Processing sheet with id=AB9, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 5.475A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1255 through 1259 removed outlier: 3.546A pdb=" N GLU B1256 " --> pdb=" O ALA B1273 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1459 through 1462 removed outlier: 3.771A pdb=" N UNK B1287 " --> pdb=" O UNK B1460 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N UNK B1462 " --> pdb=" O UNK B1285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1293 through 1294 Processing sheet with id=AC4, first strand: chain 'B' and resid 1515 through 1516 Processing sheet with id=AC5, first strand: chain 'B' and resid 1734 through 1736 Processing sheet with id=AC6, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AC7, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AC8, first strand: chain 'E' and resid 48 through 51 removed outlier: 5.734A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 48 through 51 removed outlier: 5.734A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 21 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN E 23 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET E 202 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER E 25 " --> pdb=" O TRP E 200 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP E 200 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP E 200 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AD2, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AD3, first strand: chain 'E' and resid 280 through 284 removed outlier: 3.553A pdb=" N PHE E 389 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 230 through 233 removed outlier: 5.675A pdb=" N VAL E 245 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA E 376 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E 374 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 290 through 292 removed outlier: 3.523A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AD7, first strand: chain 'E' and resid 634 through 639 removed outlier: 4.043A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E1646 " --> pdb=" O ILE E1641 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 644 through 646 Processing sheet with id=AD9, first strand: chain 'E' and resid 661 through 663 removed outlier: 3.512A pdb=" N TRP E 662 " --> pdb=" O LEU E 748 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 742 through 744 removed outlier: 3.547A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 666 " --> pdb=" O VAL E 744 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 713 through 714 Processing sheet with id=AE3, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AE4, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AE5, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.267A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 938 through 941 Processing sheet with id=AE7, first strand: chain 'E' and resid 1136 through 1138 removed outlier: 5.475A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 1255 through 1259 removed outlier: 3.545A pdb=" N GLU E1256 " --> pdb=" O ALA E1273 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 1459 through 1462 removed outlier: 3.821A pdb=" N UNK E1287 " --> pdb=" O UNK E1460 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N UNK E1462 " --> pdb=" O UNK E1285 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 1293 through 1294 Processing sheet with id=AF2, first strand: chain 'E' and resid 1515 through 1516 Processing sheet with id=AF3, first strand: chain 'E' and resid 1734 through 1736 Processing sheet with id=AF4, first strand: chain 'E' and resid 4178 through 4184 Processing sheet with id=AF5, first strand: chain 'E' and resid 4580 through 4583 Processing sheet with id=AF6, first strand: chain 'I' and resid 48 through 51 removed outlier: 5.734A pdb=" N LEU I 22 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 48 through 51 removed outlier: 5.734A pdb=" N LEU I 22 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 21 " --> pdb=" O PRO I 204 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN I 23 " --> pdb=" O MET I 202 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET I 202 " --> pdb=" O GLN I 23 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER I 25 " --> pdb=" O TRP I 200 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP I 200 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP I 200 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AF9, first strand: chain 'I' and resid 181 through 184 Processing sheet with id=AG1, first strand: chain 'I' and resid 280 through 284 removed outlier: 3.552A pdb=" N PHE I 389 " --> pdb=" O PHE I 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 230 through 233 removed outlier: 5.674A pdb=" N VAL I 245 " --> pdb=" O ALA I 376 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 376 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS I 374 " --> pdb=" O TYR I 247 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 290 through 292 removed outlier: 3.523A pdb=" N VAL I 300 " --> pdb=" O ALA I 292 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 314 through 317 Processing sheet with id=AG5, first strand: chain 'I' and resid 634 through 639 removed outlier: 4.042A pdb=" N GLN I 634 " --> pdb=" O HIS I1640 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG I1646 " --> pdb=" O ILE I1641 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 644 through 646 Processing sheet with id=AG7, first strand: chain 'I' and resid 661 through 663 removed outlier: 3.511A pdb=" N TRP I 662 " --> pdb=" O LEU I 748 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 742 through 744 removed outlier: 3.547A pdb=" N ASP I 742 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL I 666 " --> pdb=" O VAL I 744 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 713 through 714 Processing sheet with id=AH1, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AH2, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AH3, first strand: chain 'I' and resid 892 through 893 removed outlier: 6.267A pdb=" N THR I 892 " --> pdb=" O HIS I 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 938 through 941 Processing sheet with id=AH5, first strand: chain 'I' and resid 1136 through 1138 removed outlier: 5.475A pdb=" N ILE I1074 " --> pdb=" O SER I1239 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 1255 through 1259 removed outlier: 3.543A pdb=" N GLU I1256 " --> pdb=" O ALA I1273 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 1459 through 1462 removed outlier: 3.880A pdb=" N UNK I1287 " --> pdb=" O UNK I1460 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK I1462 " --> pdb=" O UNK I1285 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 1293 through 1294 Processing sheet with id=AH9, first strand: chain 'I' and resid 1515 through 1516 Processing sheet with id=AI1, first strand: chain 'I' and resid 1734 through 1736 Processing sheet with id=AI2, first strand: chain 'I' and resid 4178 through 4184 Processing sheet with id=AI3, first strand: chain 'I' and resid 4580 through 4583 Processing sheet with id=AI4, first strand: chain 'G' and resid 48 through 51 removed outlier: 5.734A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 48 through 51 removed outlier: 5.734A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL G 21 " --> pdb=" O PRO G 204 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN G 23 " --> pdb=" O MET G 202 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET G 202 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N SER G 25 " --> pdb=" O TRP G 200 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP G 200 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP G 200 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 110 through 111 Processing sheet with id=AI7, first strand: chain 'G' and resid 181 through 184 Processing sheet with id=AI8, first strand: chain 'G' and resid 280 through 284 removed outlier: 3.552A pdb=" N PHE G 389 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 230 through 233 removed outlier: 5.674A pdb=" N VAL G 245 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA G 376 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS G 374 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 290 through 292 removed outlier: 3.523A pdb=" N VAL G 300 " --> pdb=" O ALA G 292 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 314 through 317 Processing sheet with id=AJ3, first strand: chain 'G' and resid 634 through 639 removed outlier: 4.042A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG G1646 " --> pdb=" O ILE G1641 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 644 through 646 Processing sheet with id=AJ5, first strand: chain 'G' and resid 661 through 663 removed outlier: 3.511A pdb=" N TRP G 662 " --> pdb=" O LEU G 748 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 742 through 744 removed outlier: 3.547A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL G 666 " --> pdb=" O VAL G 744 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 713 through 714 Processing sheet with id=AJ8, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AJ9, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AK1, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.268A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'G' and resid 938 through 941 Processing sheet with id=AK3, first strand: chain 'G' and resid 1136 through 1138 removed outlier: 5.475A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 1255 through 1259 removed outlier: 3.545A pdb=" N GLU G1256 " --> pdb=" O ALA G1273 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 1459 through 1462 removed outlier: 3.802A pdb=" N UNK G1287 " --> pdb=" O UNK G1460 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 1293 through 1294 Processing sheet with id=AK7, first strand: chain 'G' and resid 1734 through 1736 Processing sheet with id=AK8, first strand: chain 'G' and resid 4178 through 4184 Processing sheet with id=AK9, first strand: chain 'G' and resid 4580 through 4583 Processing sheet with id=AL1, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AL2, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AL3, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AL4, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AL5, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AL6, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AL7, first strand: chain 'J' and resid 21 through 23 Processing sheet with id=AL8, first strand: chain 'J' and resid 28 through 30 4996 hydrogen bonds defined for protein. 14349 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: 101.99 Time building geometry restraints manager: 37.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 25704 1.33 - 1.45: 27433 1.45 - 1.57: 68855 1.57 - 1.70: 0 1.70 - 1.82: 1020 Bond restraints: 123012 Sorted by residual: bond pdb=" C ARG E4175 " pdb=" N PRO E4176 " ideal model delta sigma weight residual 1.336 1.375 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" C ARG I4175 " pdb=" N PRO I4176 " ideal model delta sigma weight residual 1.336 1.375 -0.040 1.23e-02 6.61e+03 1.03e+01 bond pdb=" C ARG B4175 " pdb=" N PRO B4176 " ideal model delta sigma weight residual 1.336 1.374 -0.038 1.23e-02 6.61e+03 9.65e+00 bond pdb=" C ARG G4175 " pdb=" N PRO G4176 " ideal model delta sigma weight residual 1.336 1.374 -0.038 1.23e-02 6.61e+03 9.59e+00 bond pdb=" C PRO E4872 " pdb=" O PRO E4872 " ideal model delta sigma weight residual 1.237 1.205 0.033 1.26e-02 6.30e+03 6.74e+00 ... (remaining 123007 not shown) Histogram of bond angle deviations from ideal: 97.37 - 105.64: 2666 105.64 - 113.90: 70415 113.90 - 122.16: 70504 122.16 - 130.43: 23558 130.43 - 138.69: 577 Bond angle restraints: 167720 Sorted by residual: angle pdb=" N PRO I4872 " pdb=" CA PRO I4872 " pdb=" C PRO I4872 " ideal model delta sigma weight residual 113.53 103.63 9.90 1.39e+00 5.18e-01 5.08e+01 angle pdb=" N PRO G4872 " pdb=" CA PRO G4872 " pdb=" C PRO G4872 " ideal model delta sigma weight residual 113.53 103.78 9.75 1.39e+00 5.18e-01 4.92e+01 angle pdb=" N PRO E4872 " pdb=" CA PRO E4872 " pdb=" C PRO E4872 " ideal model delta sigma weight residual 113.53 104.05 9.48 1.39e+00 5.18e-01 4.65e+01 angle pdb=" N PRO B4872 " pdb=" CA PRO B4872 " pdb=" C PRO B4872 " ideal model delta sigma weight residual 113.53 104.18 9.35 1.39e+00 5.18e-01 4.52e+01 angle pdb=" C GLN B 579 " pdb=" N GLU B 580 " pdb=" CA GLU B 580 " ideal model delta sigma weight residual 121.54 132.22 -10.68 1.91e+00 2.74e-01 3.13e+01 ... (remaining 167715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 70222 15.29 - 30.57: 2302 30.57 - 45.86: 748 45.86 - 61.15: 60 61.15 - 76.43: 92 Dihedral angle restraints: 73424 sinusoidal: 23656 harmonic: 49768 Sorted by residual: 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 -120.72 -59.28 0 5.00e+00 4.00e-02 1.41e+02 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 -120.77 -59.23 0 5.00e+00 4.00e-02 1.40e+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 -120.78 -59.22 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 73421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 17007 0.069 - 0.138: 2326 0.138 - 0.206: 204 0.206 - 0.275: 51 0.275 - 0.344: 12 Chirality restraints: 19600 Sorted by residual: chirality pdb=" CB THR B 978 " pdb=" CA THR B 978 " pdb=" OG1 THR B 978 " pdb=" CG2 THR B 978 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB THR I 978 " pdb=" CA THR I 978 " pdb=" OG1 THR I 978 " pdb=" CG2 THR I 978 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB THR G 978 " pdb=" CA THR G 978 " pdb=" OG1 THR G 978 " pdb=" CG2 THR G 978 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 19597 not shown) Planarity restraints: 22092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP I2807 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO I2808 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO I2808 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO I2808 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E2807 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO E2808 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO E2808 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E2808 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G2807 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO G2808 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO G2808 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO G2808 " -0.054 5.00e-02 4.00e+02 ... (remaining 22089 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 12 2.08 - 2.78: 30629 2.78 - 3.49: 159895 3.49 - 4.19: 277939 4.19 - 4.90: 457391 Nonbonded interactions: 925866 Sorted by model distance: nonbonded pdb=" O UNK G1487 " pdb=" CB UNK G1551 " model vdw 1.373 3.440 nonbonded pdb=" O UNK I1487 " pdb=" CB UNK I1551 " model vdw 1.373 3.440 nonbonded pdb=" O UNK I3557 " pdb=" CB UNK I3561 " model vdw 1.374 3.440 nonbonded pdb=" O UNK E1487 " pdb=" CB UNK E1551 " model vdw 1.374 3.440 nonbonded pdb=" CB UNK I1297 " pdb=" O UNK I1452 " model vdw 1.374 3.440 ... (remaining 925861 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: 2.950 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: 17.500 Check model and map are aligned: 1.390 Set scattering table: 0.900 Process input model: 312.820 Find NCS groups from input model: 6.500 Set up NCS constraints: 0.670 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.040 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3588 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 : 0.005 0.068 123012 Z= 0.318 Angle : 0.928 14.565 167720 Z= 0.504 Chirality : 0.047 0.344 19600 Planarity : 0.007 0.100 22092 Dihedral : 9.821 76.433 41064 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.31 % Favored : 89.57 % Rotamer: Outliers : 0.27 % Allowed : 2.65 % Favored : 97.07 % 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: -4.77 (0.06), residues: 13356 helix: -3.47 (0.04), residues: 5332 sheet: -2.52 (0.15), residues: 1104 loop : -3.04 (0.06), residues: 6920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP G5019 HIS 0.012 0.002 HIS E1665 PHE 0.031 0.003 PHE G4065 TYR 0.031 0.002 TYR B4863 ARG 0.018 0.001 ARG I 683 *********************** 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 : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.4112 time to fit residues: 3.8939 Evaluate side-chains 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.078 Evaluate side-chains 451 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 444 time to evaluate : 2.343 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: symmetry clash revert: symmetry clash REVERT: B 348 VAL cc_start: 0.5329 (t) cc_final: 0.5086 (t) REVERT: B 498 THR cc_start: 0.5384 (p) cc_final: 0.5119 (p) REVERT: B 3835 LEU cc_start: 0.7897 (mt) cc_final: 0.7393 (mt) REVERT: B 4769 MET cc_start: 0.4827 (ptm) cc_final: 0.3634 (pmm) outliers start: 7 outliers final: 2 residues processed: 451 average time/residue: 0.3671 time to fit residues: 252.3621 Evaluate side-chains 256 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 30.0000 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 105 HIS B 111 HIS B 113 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS B 383 HIS B 395 GLN B 413 GLN B 446 GLN B 465 GLN B 479 GLN B 797 HIS ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 ASN B1598 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 HIS B1691 GLN B1972 ASN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN B3761 GLN B3771 HIS ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3946 GLN B3950 ASN ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 ASN B4109 GLN B4553 ASN ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3654 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 123012 Z= 0.202 Angle : 0.712 13.693 167720 Z= 0.361 Chirality : 0.040 0.254 19600 Planarity : 0.006 0.161 22092 Dihedral : 5.772 55.011 18056 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.83 % Favored : 91.08 % Rotamer: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % 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: -3.59 (0.06), residues: 13356 helix: -2.01 (0.06), residues: 5732 sheet: -2.08 (0.15), residues: 1060 loop : -2.79 (0.07), residues: 6564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B3935 HIS 0.008 0.001 HIS I4886 PHE 0.062 0.002 PHE E2340 TYR 0.030 0.002 TYR E5009 ARG 0.022 0.001 ARG I2336 *********************** 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 6 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.3776 time to fit residues: 2.4334 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.077 Evaluate side-chains 335 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 333 time to evaluate : 2.312 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 357 LEU cc_start: 0.3626 (mt) cc_final: 0.3422 (mt) REVERT: B 924 MET cc_start: -0.1650 (ptt) cc_final: -0.2231 (ptt) REVERT: B 2228 MET cc_start: 0.6468 (ptp) cc_final: 0.6014 (ptp) REVERT: B 4000 MET cc_start: 0.5398 (ttt) cc_final: 0.5115 (ttp) REVERT: B 4723 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7541 (mtmm) REVERT: B 4730 ASP cc_start: 0.6237 (p0) cc_final: 0.5903 (p0) REVERT: B 4769 MET cc_start: 0.5636 (ptm) cc_final: 0.4253 (pmm) REVERT: B 4816 ILE cc_start: 0.7216 (mt) cc_final: 0.6321 (mt) outliers start: 2 outliers final: 1 residues processed: 334 average time/residue: 0.3538 time to fit residues: 184.3192 Evaluate side-chains 228 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 2.300 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 0.0970 chunk 32 optimal weight: 0.0030 chunk 12 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 1.2228 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1719 HIS B1775 HIS B1972 ASN B2011 HIS B2036 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2291 GLN B2931 GLN B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3813 GLN ** B3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3978 GLN B4109 GLN B4553 ASN B4691 GLN B4886 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3678 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 123012 Z= 0.163 Angle : 0.653 12.122 167720 Z= 0.330 Chirality : 0.039 0.273 19600 Planarity : 0.005 0.098 22092 Dihedral : 5.393 53.856 18056 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.92 % Favored : 90.93 % Rotamer: Outliers : 0.19 % Allowed : 3.18 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.13 % 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: -2.87 (0.07), residues: 13356 helix: -1.20 (0.06), residues: 5772 sheet: -1.83 (0.15), residues: 1084 loop : -2.60 (0.07), residues: 6500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G3935 HIS 0.022 0.001 HIS B 113 PHE 0.046 0.001 PHE G 67 TYR 0.034 0.001 TYR I5009 ARG 0.009 0.001 ARG B3886 *********************** 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 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3275 time to fit residues: 1.7836 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.067 Evaluate side-chains 314 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 309 time to evaluate : 2.075 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: B 348 VAL cc_start: 0.5026 (t) cc_final: 0.4797 (t) REVERT: B 924 MET cc_start: -0.1604 (ptt) cc_final: -0.2131 (ptt) REVERT: B 2423 MET cc_start: 0.4507 (ppp) cc_final: 0.3044 (ptp) REVERT: B 3720 TYR cc_start: 0.5021 (p90) cc_final: 0.4692 (p90) REVERT: B 3920 VAL cc_start: 0.7682 (t) cc_final: 0.7386 (t) REVERT: B 4691 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.6148 (tm-30) REVERT: B 4730 ASP cc_start: 0.6276 (p0) cc_final: 0.5990 (p0) REVERT: B 4769 MET cc_start: 0.5424 (ptm) cc_final: 0.4091 (pmm) REVERT: B 4816 ILE cc_start: 0.6717 (mt) cc_final: 0.5897 (mt) outliers start: 5 outliers final: 0 residues processed: 312 average time/residue: 0.3237 time to fit residues: 160.4421 Evaluate side-chains 222 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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: 7.9990 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.0040 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 0.3450 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 446 GLN B 838 HIS B 877 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN B2005 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4142 ASN B4553 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3657 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 123012 Z= 0.148 Angle : 0.626 11.852 167720 Z= 0.316 Chirality : 0.039 0.290 19600 Planarity : 0.005 0.075 22092 Dihedral : 5.170 52.760 18056 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.54 % Favored : 91.37 % Rotamer: Outliers : 0.04 % Allowed : 2.05 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.13 % 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: -2.46 (0.07), residues: 13356 helix: -0.79 (0.06), residues: 5800 sheet: -1.61 (0.15), residues: 1068 loop : -2.46 (0.07), residues: 6488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G3986 HIS 0.017 0.001 HIS E 113 PHE 0.047 0.001 PHE B 67 TYR 0.030 0.002 TYR G 117 ARG 0.012 0.000 ARG I 317 *********************** 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 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3774 time to fit residues: 2.0583 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.077 Evaluate side-chains 303 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 3.871 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 473 ASN cc_start: 0.5335 (t0) cc_final: 0.5119 (t0) REVERT: B 924 MET cc_start: -0.1087 (ptt) cc_final: -0.1916 (ptt) REVERT: B 3720 TYR cc_start: 0.4948 (p90) cc_final: 0.4535 (p90) REVERT: B 4769 MET cc_start: 0.5506 (ptm) cc_final: 0.4215 (pmm) REVERT: B 4816 ILE cc_start: 0.6492 (mt) cc_final: 0.6158 (mt) REVERT: B 4841 VAL cc_start: 0.8602 (m) cc_final: 0.8251 (p) REVERT: B 4999 ASP cc_start: 0.3772 (p0) cc_final: 0.3183 (p0) REVERT: B 5001 THR cc_start: 0.7471 (p) cc_final: 0.6756 (p) REVERT: B 5026 ASP cc_start: 0.3339 (t0) cc_final: 0.2970 (t0) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.3429 time to fit residues: 168.5603 Evaluate side-chains 218 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 0.0670 chunk 32 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 0.0060 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.2892 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 201 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 446 GLN B 765 GLN B 838 HIS B 877 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1660 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN B2127 GLN ** B4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4153 HIS ** B4216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4553 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3643 moved from start: 0.3884 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= 0.145 Angle : 0.615 11.951 167720 Z= 0.309 Chirality : 0.038 0.239 19600 Planarity : 0.005 0.075 22092 Dihedral : 4.963 50.538 18056 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.86 % Favored : 91.11 % Rotamer: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.13 % 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: -2.13 (0.07), residues: 13356 helix: -0.44 (0.07), residues: 5736 sheet: -1.52 (0.16), residues: 1072 loop : -2.33 (0.08), residues: 6548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I3935 HIS 0.019 0.001 HIS E 113 PHE 0.044 0.001 PHE I 67 TYR 0.028 0.001 TYR E 117 ARG 0.017 0.000 ARG G 317 *********************** 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 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3737 time to fit residues: 2.0391 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.078 Evaluate side-chains 297 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 2.326 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 924 MET cc_start: -0.0481 (ptt) cc_final: -0.1506 (ptt) REVERT: B 3838 THR cc_start: 0.7368 (p) cc_final: 0.7011 (p) REVERT: B 4730 ASP cc_start: 0.6390 (p0) cc_final: 0.6127 (p0) REVERT: B 4769 MET cc_start: 0.5425 (ptm) cc_final: 0.4061 (pmm) REVERT: B 4816 ILE cc_start: 0.6426 (mt) cc_final: 0.6142 (mt) REVERT: B 4841 VAL cc_start: 0.8780 (m) cc_final: 0.7997 (p) REVERT: B 4919 THR cc_start: 0.5167 (p) cc_final: 0.4911 (p) REVERT: B 5026 ASP cc_start: 0.3044 (t0) cc_final: 0.2535 (t0) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.3259 time to fit residues: 156.0014 Evaluate side-chains 219 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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: 0.9980 chunk 38 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 overall best weight: 1.0680 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 446 GLN ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN B3781 GLN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4553 ASN ** B4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3662 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 123012 Z= 0.146 Angle : 0.622 15.193 167720 Z= 0.309 Chirality : 0.039 0.296 19600 Planarity : 0.005 0.203 22092 Dihedral : 4.868 49.591 18056 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.60 % Favored : 91.34 % Rotamer: Outliers : 0.04 % Allowed : 1.67 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.06 % 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: -1.95 (0.07), residues: 13356 helix: -0.26 (0.07), residues: 5784 sheet: -1.48 (0.16), residues: 1076 loop : -2.27 (0.08), residues: 6496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E3935 HIS 0.017 0.001 HIS I 113 PHE 0.037 0.001 PHE I 67 TYR 0.028 0.001 TYR G5009 ARG 0.012 0.000 ARG G 317 *********************** 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 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 revert: symmetry clash REVERT: A 66 MET cc_start: 0.2133 (tpt) cc_final: 0.1510 (tpp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.3682 time to fit residues: 1.6451 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 Evaluate side-chains 279 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 2.561 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: B 924 MET cc_start: -0.0482 (ptt) cc_final: -0.1578 (ptt) REVERT: B 1100 MET cc_start: 0.1002 (mpp) cc_final: 0.0461 (mpp) REVERT: B 2423 MET cc_start: 0.4595 (ppp) cc_final: 0.3081 (ptp) REVERT: B 3790 THR cc_start: 0.7091 (p) cc_final: 0.6820 (p) REVERT: B 3838 THR cc_start: 0.7349 (p) cc_final: 0.7011 (p) REVERT: B 4730 ASP cc_start: 0.6547 (p0) cc_final: 0.6138 (p0) REVERT: B 4769 MET cc_start: 0.5328 (ptm) cc_final: 0.4012 (pmm) REVERT: B 4839 MET cc_start: 0.4874 (ttt) cc_final: 0.4553 (ttt) REVERT: B 4841 VAL cc_start: 0.8556 (m) cc_final: 0.8169 (p) REVERT: B 5026 ASP cc_start: 0.3605 (t0) cc_final: 0.3260 (t0) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.3651 time to fit residues: 169.5476 Evaluate side-chains 214 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 0.0030 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 11 optimal weight: 0.0050 chunk 7 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 overall best weight: 0.2182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 151 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 446 GLN B 495 ASN B 877 ASN ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4946 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3635 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 123012 Z= 0.140 Angle : 0.616 13.341 167720 Z= 0.304 Chirality : 0.039 0.336 19600 Planarity : 0.004 0.075 22092 Dihedral : 4.716 48.173 18056 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.81 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.06 % 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: -1.85 (0.07), residues: 13356 helix: -0.16 (0.07), residues: 5792 sheet: -1.41 (0.15), residues: 1116 loop : -2.24 (0.08), residues: 6448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G3935 HIS 0.019 0.001 HIS E 113 PHE 0.039 0.001 PHE B 67 TYR 0.027 0.001 TYR B 117 ARG 0.012 0.000 ARG I3672 *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.078 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.3794 time to fit residues: 1.6860 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.079 Evaluate side-chains 292 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 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: symmetry clash REVERT: B 924 MET cc_start: 0.0019 (ptt) cc_final: -0.1199 (ptt) REVERT: B 961 MET cc_start: 0.0405 (mmp) cc_final: -0.0680 (mtt) REVERT: B 1100 MET cc_start: 0.1560 (mpp) cc_final: 0.0958 (mpp) REVERT: B 3790 THR cc_start: 0.6967 (p) cc_final: 0.6680 (t) REVERT: B 3838 THR cc_start: 0.7235 (p) cc_final: 0.6823 (p) REVERT: B 3920 VAL cc_start: 0.7592 (t) cc_final: 0.7388 (t) REVERT: B 4170 ILE cc_start: 0.6547 (mp) cc_final: 0.6321 (tp) REVERT: B 4730 ASP cc_start: 0.6501 (p0) cc_final: 0.6138 (p0) REVERT: B 4769 MET cc_start: 0.5246 (ptm) cc_final: 0.3851 (pmm) REVERT: B 4841 VAL cc_start: 0.8563 (m) cc_final: 0.8276 (p) REVERT: B 5026 ASP cc_start: 0.3324 (t0) cc_final: 0.2854 (t0) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.3252 time to fit residues: 154.1385 Evaluate side-chains 215 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 68.5272 > 50: distance: 0 - 2: 3.981 distance: 4 - 5: 8.204 distance: 5 - 6: 24.298 distance: 5 - 8: 5.823 distance: 6 - 7: 35.493 distance: 6 - 10: 32.353 distance: 8 - 9: 9.886 distance: 10 - 11: 50.320 distance: 11 - 12: 50.447 distance: 11 - 14: 21.012 distance: 12 - 13: 62.714 distance: 12 - 16: 54.873 distance: 14 - 15: 18.411 distance: 16 - 17: 34.600 distance: 17 - 18: 30.116 distance: 17 - 20: 21.424 distance: 18 - 19: 28.714 distance: 18 - 27: 28.491 distance: 20 - 21: 5.975 distance: 21 - 22: 17.366 distance: 21 - 23: 10.722 distance: 22 - 24: 6.498 distance: 24 - 26: 5.065 distance: 27 - 28: 10.818 distance: 28 - 29: 17.696 distance: 28 - 31: 4.634 distance: 29 - 30: 3.707 distance: 29 - 34: 22.721 distance: 31 - 32: 8.651 distance: 31 - 33: 8.765 distance: 34 - 35: 22.456 distance: 35 - 36: 36.391 distance: 35 - 38: 45.682 distance: 36 - 37: 44.244 distance: 36 - 42: 29.016 distance: 38 - 39: 32.426 distance: 39 - 40: 43.239 distance: 39 - 41: 21.325 distance: 42 - 43: 31.550 distance: 43 - 44: 54.769 distance: 43 - 46: 45.072 distance: 44 - 45: 61.836 distance: 44 - 51: 35.952 distance: 46 - 47: 27.591 distance: 47 - 48: 13.197 distance: 48 - 49: 6.897 distance: 48 - 50: 7.308 distance: 51 - 52: 12.229 distance: 52 - 53: 57.449 distance: 52 - 55: 39.097 distance: 53 - 54: 42.618 distance: 53 - 60: 3.157 distance: 55 - 56: 22.150 distance: 56 - 57: 19.050 distance: 57 - 58: 4.145 distance: 57 - 59: 4.813 distance: 60 - 61: 17.393 distance: 61 - 62: 33.829 distance: 61 - 64: 30.679 distance: 62 - 63: 36.473 distance: 62 - 66: 4.634 distance: 64 - 65: 8.279 distance: 66 - 67: 20.954 distance: 67 - 68: 25.334 distance: 67 - 70: 30.806 distance: 68 - 69: 29.452 distance: 68 - 74: 23.881 distance: 70 - 71: 24.625 distance: 71 - 72: 11.521 distance: 71 - 73: 8.574 distance: 74 - 75: 22.979 distance: 75 - 76: 9.644 distance: 76 - 77: 5.759