Starting phenix.real_space_refine on Thu Mar 14 11:07:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmh_22394/03_2024/7jmh_22394_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmh_22394/03_2024/7jmh_22394.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/7jmh_22394/03_2024/7jmh_22394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmh_22394/03_2024/7jmh_22394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmh_22394/03_2024/7jmh_22394_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmh_22394/03_2024/7jmh_22394_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= 0.027 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 PHE 3669": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 4063": "OD1" <-> "OD2" Residue "B PHE 4132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4137": "NH1" <-> "NH2" Residue "B ARG 4159": "NH1" <-> "NH2" Residue "B ARG 4175": "NH1" <-> "NH2" Residue "B ARG 4192": "NH1" <-> "NH2" Residue "B ARG 4548": "NH1" <-> "NH2" Residue "B ARG 4557": "NH1" <-> "NH2" Residue "B ARG 4563": "NH1" <-> "NH2" Residue "B ARG 4673": "NH1" <-> "NH2" Residue "B ARG 4703": "NH1" <-> "NH2" Residue "B ARG 4722": "NH1" <-> "NH2" Residue "B ARG 4734": "NH1" <-> "NH2" Residue "B ARG 4736": "NH1" <-> "NH2" Residue "B PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4824": "NH1" <-> "NH2" Residue "B ARG 4860": "NH1" <-> "NH2" Residue "B PHE 4862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4892": "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 PHE 3669": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 4063": "OD1" <-> "OD2" Residue "E PHE 4132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4137": "NH1" <-> "NH2" Residue "E ARG 4159": "NH1" <-> "NH2" Residue "E ARG 4175": "NH1" <-> "NH2" Residue "E ARG 4192": "NH1" <-> "NH2" Residue "E ARG 4548": "NH1" <-> "NH2" Residue "E ARG 4557": "NH1" <-> "NH2" Residue "E ARG 4563": "NH1" <-> "NH2" Residue "E ARG 4673": "NH1" <-> "NH2" Residue "E ARG 4703": "NH1" <-> "NH2" Residue "E ARG 4722": "NH1" <-> "NH2" Residue "E ARG 4734": "NH1" <-> "NH2" Residue "E ARG 4736": "NH1" <-> "NH2" Residue "E PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4824": "NH1" <-> "NH2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E ARG 5017": "NH1" <-> "NH2" Residue "E 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 PHE 3669": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 4063": "OD1" <-> "OD2" Residue "G PHE 4132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4137": "NH1" <-> "NH2" Residue "G ARG 4159": "NH1" <-> "NH2" Residue "G ARG 4175": "NH1" <-> "NH2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4548": "NH1" <-> "NH2" Residue "G ARG 4557": "NH1" <-> "NH2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G ARG 4673": "NH1" <-> "NH2" Residue "G ARG 4703": "NH1" <-> "NH2" Residue "G ARG 4722": "NH1" <-> "NH2" Residue "G ARG 4734": "NH1" <-> "NH2" Residue "G ARG 4736": "NH1" <-> "NH2" Residue "G PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4824": "NH1" <-> "NH2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G ARG 5017": "NH1" <-> "NH2" Residue "G 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 PHE 3669": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 4063": "OD1" <-> "OD2" Residue "I PHE 4132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4137": "NH1" <-> "NH2" Residue "I ARG 4159": "NH1" <-> "NH2" Residue "I ARG 4175": "NH1" <-> "NH2" Residue "I ARG 4192": "NH1" <-> "NH2" Residue "I ARG 4548": "NH1" <-> "NH2" Residue "I ARG 4557": "NH1" <-> "NH2" Residue "I ARG 4563": "NH1" <-> "NH2" Residue "I ARG 4673": "NH1" <-> "NH2" Residue "I ARG 4703": "NH1" <-> "NH2" Residue "I ARG 4722": "NH1" <-> "NH2" Residue "I ARG 4734": "NH1" <-> "NH2" Residue "I ARG 4736": "NH1" <-> "NH2" Residue "I PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4824": "NH1" <-> "NH2" Residue "I ARG 4860": "NH1" <-> "NH2" Residue "I PHE 4862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4892": "NH1" <-> "NH2" Residue "I ARG 5017": "NH1" <-> "NH2" Residue "I ARG 5029": "NH1" <-> "NH2" Time to flip residues: 0.24s 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: "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: "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: "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: "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: "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: "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: "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: "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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29516 SG CYS B4958 176.757 204.964 87.877 1.00 1.02 S ATOM 29541 SG CYS B4961 179.173 203.401 91.233 1.00 1.48 S ATOM 58885 SG CYS E4958 204.499 208.083 87.588 1.00 1.58 S ATOM 58910 SG CYS E4961 202.992 205.685 90.982 1.00 1.51 S ATOM 89072 SG CYS G4958 207.667 180.442 87.471 1.00 2.11 S ATOM 89097 SG CYS G4961 205.316 181.970 90.888 1.00 2.17 S ATOM A0EUZ SG CYS I4958 179.861 177.250 87.707 1.00 1.46 S ATOM A0EVO SG CYS I4961 181.436 179.613 91.095 1.00 2.05 S Time building chain proxies: 45.85, per 1000 atoms: 0.38 Number of scatterers: 120756 At special positions: 0 Unit cell: (386.54, 386.54, 209.585, 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: 36.25 Conformation dependent library (CDL) restraints added in 13.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" ND1 HIS E4983 " pdb="ZN ZN E5101 " - pdb=" NE2 HIS E4978 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4961 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4958 " pdb=" ZN G5101 " pdb="ZN ZN G5101 " - pdb=" ND1 HIS G4983 " pdb="ZN ZN G5101 " - pdb=" NE2 HIS G4978 " 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=" NE2 HIS I4978 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4961 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4958 " Number of angles added : 8 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32360 Finding SS restraints... Secondary structure from input PDB file: 678 helices and 98 sheets defined 59.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.13 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.865A pdb=" N GLY A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.794A pdb=" N VAL A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 395 through 412 removed outlier: 3.929A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.576A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 removed outlier: 3.612A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 512 through 531 removed outlier: 4.304A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.644A pdb=" N SER B 541 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.736A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 568 removed outlier: 3.894A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 removed outlier: 3.784A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 596 through 608 removed outlier: 4.035A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.965A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 621 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 622 " --> pdb=" O GLN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 888 removed outlier: 3.973A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 879 " --> pdb=" O ALA B 875 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 932 removed outlier: 3.672A pdb=" N ASN B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 932 " --> pdb=" O THR B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 936 removed outlier: 3.972A pdb=" N GLY B 936 " --> pdb=" O LEU B 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 933 through 936' Processing helix chain 'B' and resid 980 through 988 removed outlier: 3.720A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1001 removed outlier: 3.808A pdb=" N ASN B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1041 removed outlier: 4.381A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.654A pdb=" N LEU B1046 " --> pdb=" O ALA B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1082 Processing helix chain 'B' and resid 1652 through 1657 Processing helix chain 'B' and resid 1658 through 1674 removed outlier: 3.735A pdb=" N TYR B1670 " --> pdb=" O THR B1666 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG B1671 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1686 removed outlier: 3.718A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) Processing helix chain 'B' and resid 1692 through 1700 removed outlier: 3.843A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) Processing helix chain 'B' and resid 1709 through 1712 removed outlier: 3.650A pdb=" N TYR B1712 " --> pdb=" O ALA B1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1709 through 1712' Processing helix chain 'B' and resid 1713 through 1718 Processing helix chain 'B' and resid 1723 through 1730 removed outlier: 3.605A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1753 through 1758 removed outlier: 4.070A pdb=" N ALA B1757 " --> pdb=" O LYS B1753 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1823 removed outlier: 3.516A pdb=" N GLY B1816 " --> pdb=" O LEU B1812 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B1823 " --> pdb=" O VAL B1819 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1838 Processing helix chain 'B' and resid 1840 through 1852 Processing helix chain 'B' and resid 1855 through 1863 Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1925 through 1929 removed outlier: 3.627A pdb=" N GLN B1928 " --> pdb=" O GLY B1925 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B1929 " --> pdb=" O LEU B1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1925 through 1929' Processing helix chain 'B' and resid 1933 through 1982 removed outlier: 3.794A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B1947 " --> pdb=" O LEU B1943 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B1965 " --> pdb=" O PHE B1961 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B1966 " --> pdb=" O ALA B1962 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B1978 " --> pdb=" O ARG B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1994 removed outlier: 3.819A pdb=" N ARG B1993 " --> pdb=" O ALA B1989 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1989 through 1994' Processing helix chain 'B' and resid 1995 through 1998 Processing helix chain 'B' and resid 2001 through 2011 removed outlier: 3.687A pdb=" N ILE B2006 " --> pdb=" O PRO B2002 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) Processing helix chain 'B' and resid 2028 through 2042 removed outlier: 3.696A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2108 removed outlier: 3.803A pdb=" N HIS B2100 " --> pdb=" O GLU B2096 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B2105 " --> pdb=" O MET B2101 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2129 removed outlier: 3.612A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B2123 " --> pdb=" O ALA B2119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2138 Processing helix chain 'B' and resid 2148 through 2165 removed outlier: 3.737A pdb=" N CYS B2158 " --> pdb=" O SER B2154 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2187 removed outlier: 3.672A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.546A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2216 removed outlier: 3.859A pdb=" N VAL B2210 " --> pdb=" O THR B2206 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2242 removed outlier: 3.642A pdb=" N CYS B2233 " --> pdb=" O VAL B2229 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2253 removed outlier: 3.620A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2262 removed outlier: 4.110A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 removed outlier: 3.520A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2306 removed outlier: 3.518A pdb=" N VAL B2298 " --> pdb=" O ASP B2294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 4.085A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2331 removed outlier: 3.534A pdb=" N TYR B2331 " --> pdb=" O GLY B2327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2355 removed outlier: 3.897A pdb=" N ALA B2350 " --> pdb=" O VAL B2346 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B2353 " --> pdb=" O ASN B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2360 through 2364 Processing helix chain 'B' and resid 2375 through 2388 Processing helix chain 'B' and resid 2389 through 2393 Processing helix chain 'B' and resid 2418 through 2436 removed outlier: 3.810A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B2428 " --> pdb=" O SER B2424 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B2435 " --> pdb=" O ASP B2431 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2445 Processing helix chain 'B' and resid 2448 through 2461 removed outlier: 3.708A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2471 removed outlier: 3.645A pdb=" N ILE B2470 " --> pdb=" O LEU B2466 " (cutoff:3.500A) Processing helix chain 'B' and resid 2502 through 2507 removed outlier: 3.860A pdb=" N UNK B2506 " --> pdb=" O UNK B2502 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2522 Processing helix chain 'B' and resid 2525 through 2530 removed outlier: 3.557A pdb=" N UNK B2530 " --> pdb=" O UNK B2526 " (cutoff:3.500A) Processing helix chain 'B' and resid 2542 through 2548 removed outlier: 3.685A pdb=" N UNK B2546 " --> pdb=" O UNK B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2557 removed outlier: 3.754A pdb=" N UNK B2555 " --> pdb=" O UNK B2551 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2581 removed outlier: 3.603A pdb=" N UNK B2578 " --> pdb=" O UNK B2574 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2602 removed outlier: 3.561A pdb=" N UNK B2597 " --> pdb=" O UNK B2593 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N UNK B2602 " --> pdb=" O UNK B2598 " (cutoff:3.500A) Processing helix chain 'B' and resid 2610 through 2618 removed outlier: 3.622A pdb=" N UNK B2617 " --> pdb=" O UNK B2613 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNK B2618 " --> pdb=" O UNK B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2626 through 2641 removed outlier: 3.920A pdb=" N UNK B2630 " --> pdb=" O UNK B2626 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N UNK B2631 " --> pdb=" O UNK B2627 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK B2634 " --> pdb=" O UNK B2630 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK B2635 " --> pdb=" O UNK B2631 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N UNK B2639 " --> pdb=" O UNK B2635 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK B2641 " --> pdb=" O UNK B2637 " (cutoff:3.500A) Processing helix chain 'B' and resid 2650 through 2666 Processing helix chain 'B' and resid 2677 through 2683 removed outlier: 3.904A pdb=" N UNK B2681 " --> pdb=" O UNK B2677 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N UNK B2683 " --> pdb=" O UNK B2679 " (cutoff:3.500A) Processing helix chain 'B' and resid 2684 through 2687 removed outlier: 4.012A pdb=" N UNK B2687 " --> pdb=" O UNK B2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2684 through 2687' Processing helix chain 'B' and resid 2751 through 2773 removed outlier: 3.887A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.503A pdb=" N THR B2796 " --> pdb=" O PRO B2793 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B2797 " --> pdb=" O TYR B2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2793 through 2797' Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 3.842A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B2816 " --> pdb=" O SER B2812 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.045A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B2875 " --> pdb=" O LEU B2871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B2876 " --> pdb=" O GLN B2872 " (cutoff:3.500A) removed outlier: 4.119A 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: 4.005A pdb=" N ARG B2920 " --> pdb=" O LYS B2916 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B2921 " --> pdb=" O ALA B2917 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B2926 " --> pdb=" O LYS B2922 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2976 removed outlier: 3.501A pdb=" N UNK B2955 " --> pdb=" O UNK B2951 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N UNK B2956 " --> pdb=" O UNK B2952 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK B2968 " --> pdb=" O UNK B2964 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N UNK B2969 " --> pdb=" O UNK B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2999 through 3016 removed outlier: 3.604A pdb=" N UNK B3004 " --> pdb=" O UNK B3000 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N UNK B3006 " --> pdb=" O UNK B3002 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N UNK B3013 " --> pdb=" O UNK B3009 " (cutoff:3.500A) Processing helix chain 'B' and resid 3017 through 3022 Processing helix chain 'B' and resid 3029 through 3040 removed outlier: 3.594A pdb=" N UNK B3037 " --> pdb=" O UNK B3033 " (cutoff:3.500A) Processing helix chain 'B' and resid 3052 through 3058 removed outlier: 4.108A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) Processing helix chain 'B' and resid 3058 through 3063 removed outlier: 4.201A 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 3151 Processing helix chain 'B' and resid 3151 through 3162 Processing helix chain 'B' and resid 3175 through 3186 removed outlier: 3.631A pdb=" N UNK B3182 " --> pdb=" O UNK B3178 " (cutoff:3.500A) Processing helix chain 'B' and resid 3198 through 3212 removed outlier: 3.545A pdb=" N UNK B3205 " --> pdb=" O UNK B3201 " (cutoff:3.500A) Processing helix chain 'B' and resid 3224 through 3230 removed outlier: 3.779A pdb=" N UNK B3228 " --> pdb=" O UNK B3224 " (cutoff:3.500A) Processing helix chain 'B' and resid 3248 through 3254 removed outlier: 3.534A pdb=" N UNK B3252 " --> pdb=" O UNK B3248 " (cutoff:3.500A) Processing helix chain 'B' and resid 3271 through 3280 Processing helix chain 'B' and resid 3280 through 3285 removed outlier: 4.046A pdb=" N UNK B3284 " --> pdb=" O UNK B3280 " (cutoff:3.500A) Processing helix chain 'B' and resid 3305 through 3310 Processing helix chain 'B' and resid 3316 through 3331 removed outlier: 3.874A pdb=" N UNK B3323 " --> pdb=" O UNK B3319 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N UNK B3324 " --> pdb=" O UNK B3320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N UNK B3330 " --> pdb=" O UNK B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3349 removed outlier: 3.546A pdb=" N UNK B3348 " --> pdb=" O UNK B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3361 through 3388 Processing helix chain 'B' and resid 3399 through 3409 removed outlier: 3.783A pdb=" N UNK B3405 " --> pdb=" O UNK B3401 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N UNK B3407 " --> pdb=" O UNK B3403 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N UNK B3409 " --> pdb=" O UNK B3405 " (cutoff:3.500A) Processing helix chain 'B' and resid 3410 through 3425 removed outlier: 3.993A pdb=" N UNK B3416 " --> pdb=" O UNK B3412 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N UNK B3420 " --> pdb=" O UNK B3416 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK B3421 " --> pdb=" O UNK B3417 " (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: 3.533A pdb=" N UNK B3468 " --> pdb=" O UNK B3464 " (cutoff:3.500A) Processing helix chain 'B' and resid 3518 through 3521 removed outlier: 3.513A 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 3529 removed outlier: 3.674A pdb=" N UNK B3529 " --> pdb=" O UNK B3525 " (cutoff:3.500A) Processing helix chain 'B' and resid 3541 through 3547 removed outlier: 3.559A 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: 3.608A pdb=" N UNK B3579 " --> pdb=" O UNK B3575 " (cutoff:3.500A) Processing helix chain 'B' and resid 3589 through 3611 removed outlier: 4.012A pdb=" N UNK B3595 " --> pdb=" O UNK B3591 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK B3598 " --> pdb=" O UNK B3594 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N UNK B3600 " --> pdb=" O UNK B3596 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N UNK B3601 " --> pdb=" O UNK B3597 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N UNK B3610 " --> pdb=" O UNK B3606 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N UNK B3611 " --> pdb=" O UNK B3607 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 removed outlier: 3.801A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) Processing helix chain 'B' and resid 3657 through 3661 Processing helix chain 'B' and resid 3671 through 3680 removed outlier: 3.562A pdb=" N ASP B3676 " --> pdb=" O ARG B3672 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 removed outlier: 3.584A pdb=" N ALA B3709 " --> pdb=" O PHE B3705 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR B3711 " --> pdb=" O ARG B3707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3738 removed outlier: 3.607A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) Processing helix chain 'B' and resid 3754 through 3770 removed outlier: 4.155A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B3762 " --> pdb=" O MET B3758 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B3763 " --> pdb=" O GLU B3759 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN B3767 " --> pdb=" O LEU B3763 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B3768 " --> pdb=" O LEU B3764 " (cutoff:3.500A) Processing helix chain 'B' and resid 3771 through 3784 removed outlier: 4.279A pdb=" N GLU B3777 " --> pdb=" O ARG B3773 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B3779 " --> pdb=" O ALA B3775 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3803 removed outlier: 3.897A pdb=" N LYS B3799 " --> pdb=" O SER B3795 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3828 through 3838 removed outlier: 3.649A pdb=" N ILE B3832 " --> pdb=" O PHE B3828 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3856 removed outlier: 3.553A pdb=" N LYS B3852 " --> pdb=" O GLU B3848 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3891 removed outlier: 4.484A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B3886 " --> pdb=" O GLN B3882 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B3887 " --> pdb=" O ASP B3883 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3903 Processing helix chain 'B' and resid 3914 through 3937 removed outlier: 4.116A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B3934 " --> pdb=" O ILE B3930 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3967 removed outlier: 3.641A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET B3955 " --> pdb=" O PHE B3951 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4005 removed outlier: 3.739A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B3992 " --> pdb=" O ALA B3988 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU B3993 " --> pdb=" O VAL B3989 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS B3994 " --> pdb=" O VAL B3990 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B3999 " --> pdb=" O VAL B3995 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B4004 " --> pdb=" O MET B4000 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4006 through 4008 No H-bonds generated for 'chain 'B' and resid 4006 through 4008' Processing helix chain 'B' and resid 4009 through 4030 removed outlier: 4.114A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4051 Processing helix chain 'B' and resid 4051 through 4063 Processing helix chain 'B' and resid 4067 through 4072 Processing helix chain 'B' and resid 4074 through 4081 removed outlier: 4.536A pdb=" N TYR B4080 " --> pdb=" O ALA B4076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) Processing helix chain 'B' and resid 4090 through 4100 removed outlier: 3.763A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4114 Processing helix chain 'B' and resid 4124 through 4128 Processing helix chain 'B' and resid 4132 through 4154 removed outlier: 3.542A pdb=" N ALA B4136 " --> pdb=" O PHE B4132 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B4141 " --> pdb=" O ARG B4137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B4146 " --> pdb=" O ASN B4142 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B4152 " --> pdb=" O THR B4148 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B4154 " --> pdb=" O LEU B4150 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 Processing helix chain 'B' and resid 4167 through 4175 removed outlier: 3.736A pdb=" N LEU B4171 " --> pdb=" O ALA B4167 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B4174 " --> pdb=" O ILE B4170 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4206 Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 4.095A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4251 removed outlier: 4.084A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B4250 " --> pdb=" O GLN B4246 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B4251 " --> pdb=" O ILE B4247 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4558 removed outlier: 3.996A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4576 removed outlier: 3.683A pdb=" N ALA B4570 " --> pdb=" O ALA B4566 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) Processing helix chain 'B' and resid 4641 through 4665 removed outlier: 3.605A pdb=" N ALA B4654 " --> pdb=" O HIS B4650 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B4655 " --> pdb=" O THR B4651 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B4660 " --> pdb=" O LEU B4656 " (cutoff:3.500A) Processing helix chain 'B' and resid 4667 through 4683 removed outlier: 3.865A pdb=" N ALA B4678 " --> pdb=" O GLU B4674 " (cutoff:3.500A) Processing helix chain 'B' and resid 4697 through 4702 Processing helix chain 'B' and resid 4703 through 4708 removed outlier: 3.707A pdb=" N LEU B4706 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN B4707 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4728 Processing helix chain 'B' and resid 4733 through 4741 Processing helix chain 'B' and resid 4748 through 4753 Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.794A pdb=" N PHE B4780 " --> pdb=" O GLN B4776 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B4781 " --> pdb=" O ILE B4777 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4802 removed outlier: 3.598A pdb=" N TRP B4794 " --> pdb=" O LEU B4790 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B4797 " --> pdb=" O GLY B4793 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET B4798 " --> pdb=" O TRP B4794 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B4799 " --> pdb=" O TYR B4795 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B4800 " --> pdb=" O MET B4796 " (cutoff:3.500A) Processing helix chain 'B' and resid 4812 through 4819 removed outlier: 3.580A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4832 removed outlier: 3.980A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 removed outlier: 4.258A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B4845 " --> pdb=" O VAL B4841 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B4848 " --> pdb=" O LEU B4844 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B4853 " --> pdb=" O TYR B4849 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA B4855 " --> pdb=" O TYR B4851 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4889 removed outlier: 3.754A pdb=" N PHE B4885 " --> pdb=" O THR B4881 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B4886 " --> pdb=" O CYS B4882 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4922 removed outlier: 3.729A pdb=" N ARG B4913 " --> pdb=" O TYR B4909 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B4918 " --> pdb=" O VAL B4914 " (cutoff:3.500A) Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 3.775A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B4944 " --> pdb=" O PHE B4940 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B4952 " --> pdb=" O GLU B4948 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B4953 " --> pdb=" O GLN B4949 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET B4954 " --> pdb=" O VAL B4950 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B4955 " --> pdb=" O LYS B4951 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B4957 " --> pdb=" O ASP B4953 " (cutoff:3.500A) Processing helix chain 'B' and resid 4965 through 4970 removed outlier: 3.577A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4986 through 4997 removed outlier: 3.578A pdb=" N PHE B4990 " --> pdb=" O ALA B4986 " (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 Processing helix chain 'E' and resid 395 through 412 removed outlier: 3.928A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 438 through 452 removed outlier: 3.576A pdb=" N GLY E 450 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 478 removed outlier: 3.613A pdb=" N GLN E 465 " --> pdb=" O HIS E 461 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE E 478 " --> pdb=" O ARG E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 512 through 531 removed outlier: 4.304A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU E 524 " --> pdb=" O ASN E 520 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER E 528 " --> pdb=" O GLU E 524 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU E 529 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.644A pdb=" N SER E 541 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 542' Processing helix chain 'E' and resid 543 through 548 removed outlier: 3.737A pdb=" N VAL E 548 " --> pdb=" O LEU E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 568 removed outlier: 3.894A pdb=" N TYR E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 577 removed outlier: 3.785A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 593 Processing helix chain 'E' and resid 596 through 608 removed outlier: 4.036A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 625 removed outlier: 3.966A pdb=" N GLN E 618 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP E 619 " --> pdb=" O ARG E 615 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 621 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 622 " --> pdb=" O GLN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 888 removed outlier: 3.972A pdb=" N GLU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS E 873 " --> pdb=" O ARG E 869 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS E 879 " --> pdb=" O ALA E 875 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 887 " --> pdb=" O ALA E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 932 removed outlier: 3.672A pdb=" N ASN E 919 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 923 " --> pdb=" O ASN E 919 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 932 " --> pdb=" O THR E 928 " (cutoff:3.500A) Processing helix chain 'E' and resid 933 through 936 removed outlier: 3.971A pdb=" N GLY E 936 " --> pdb=" O LEU E 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 933 through 936' Processing helix chain 'E' and resid 980 through 988 removed outlier: 3.719A pdb=" N LEU E 984 " --> pdb=" O ALA E 980 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 986 " --> pdb=" O THR E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 1001 removed outlier: 3.807A pdb=" N ASN E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1041 removed outlier: 4.382A pdb=" N GLN E1041 " --> pdb=" O ASP E1037 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1049 removed outlier: 3.654A pdb=" N LEU E1046 " --> pdb=" O ALA E1042 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1082 Processing helix chain 'E' and resid 1652 through 1657 Processing helix chain 'E' and resid 1658 through 1674 removed outlier: 3.735A pdb=" N TYR E1670 " --> pdb=" O THR E1666 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG E1671 " --> pdb=" O LEU E1667 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1686 removed outlier: 3.718A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS E1686 " --> pdb=" O ALA E1682 " (cutoff:3.500A) Processing helix chain 'E' and resid 1692 through 1700 removed outlier: 3.842A pdb=" N LEU E1698 " --> pdb=" O LEU E1694 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU E1699 " --> pdb=" O LEU E1695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP E1700 " --> pdb=" O HIS E1696 " (cutoff:3.500A) Processing helix chain 'E' and resid 1709 through 1712 removed outlier: 3.649A pdb=" N TYR E1712 " --> pdb=" O ALA E1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1709 through 1712' Processing helix chain 'E' and resid 1713 through 1718 Processing helix chain 'E' and resid 1723 through 1730 removed outlier: 3.605A pdb=" N MET E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 Processing helix chain 'E' and resid 1753 through 1758 removed outlier: 4.070A pdb=" N ALA E1757 " --> pdb=" O LYS E1753 " (cutoff:3.500A) Processing helix chain 'E' and resid 1804 through 1823 removed outlier: 3.515A pdb=" N GLY E1816 " --> pdb=" O LEU E1812 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E1823 " --> pdb=" O VAL E1819 " (cutoff:3.500A) Processing helix chain 'E' and resid 1833 through 1838 Processing helix chain 'E' and resid 1840 through 1852 Processing helix chain 'E' and resid 1855 through 1863 Processing helix chain 'E' and resid 1866 through 1871 Processing helix chain 'E' and resid 1925 through 1929 removed outlier: 3.628A pdb=" N GLN E1928 " --> pdb=" O GLY E1925 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET E1929 " --> pdb=" O LEU E1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1925 through 1929' Processing helix chain 'E' and resid 1933 through 1982 removed outlier: 3.793A pdb=" N TYR E1945 " --> pdb=" O ASN E1941 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE E1946 " --> pdb=" O LEU E1942 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS E1947 " --> pdb=" O LEU E1943 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E1963 " --> pdb=" O ALA E1959 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR E1965 " --> pdb=" O PHE E1961 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E1967 " --> pdb=" O GLU E1963 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA E1978 " --> pdb=" O ARG E1974 " (cutoff:3.500A) Processing helix chain 'E' and resid 1989 through 1994 removed outlier: 3.818A pdb=" N ARG E1993 " --> pdb=" O ALA E1989 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E1994 " --> pdb=" O GLU E1990 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1989 through 1994' Processing helix chain 'E' and resid 1995 through 1998 Processing helix chain 'E' and resid 2001 through 2011 removed outlier: 3.687A pdb=" N ILE E2006 " --> pdb=" O PRO E2002 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN E2007 " --> pdb=" O GLN E2003 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS E2011 " --> pdb=" O ASN E2007 " (cutoff:3.500A) Processing helix chain 'E' and resid 2028 through 2042 removed outlier: 3.696A pdb=" N GLN E2032 " --> pdb=" O ARG E2028 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2108 removed outlier: 3.803A pdb=" N HIS E2100 " --> pdb=" O GLU E2096 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E2103 " --> pdb=" O SER E2099 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP E2105 " --> pdb=" O MET E2101 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2129 removed outlier: 3.613A pdb=" N VAL E2117 " --> pdb=" O SER E2113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E2123 " --> pdb=" O ALA E2119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR E2128 " --> pdb=" O LEU E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2138 Processing helix chain 'E' and resid 2148 through 2165 removed outlier: 3.736A pdb=" N CYS E2158 " --> pdb=" O SER E2154 " (cutoff:3.500A) Processing helix chain 'E' and resid 2171 through 2187 removed outlier: 3.672A pdb=" N LEU E2177 " --> pdb=" O GLN E2173 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.546A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.859A pdb=" N VAL E2210 " --> pdb=" O THR E2206 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E2213 " --> pdb=" O GLU E2209 " (cutoff:3.500A) Processing helix chain 'E' and resid 2227 through 2242 removed outlier: 3.641A pdb=" N CYS E2233 " --> pdb=" O VAL E2229 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2253 removed outlier: 3.621A pdb=" N ASP E2252 " --> pdb=" O ARG E2248 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS E2253 " --> pdb=" O SER E2249 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2262 removed outlier: 4.110A pdb=" N ASN E2260 " --> pdb=" O TYR E2256 " (cutoff:3.500A) Processing helix chain 'E' and resid 2271 through 2279 removed outlier: 3.519A pdb=" N ALA E2276 " --> pdb=" O PRO E2272 " (cutoff:3.500A) Processing helix chain 'E' and resid 2294 through 2306 removed outlier: 3.518A pdb=" N VAL E2298 " --> pdb=" O ASP E2294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E2299 " --> pdb=" O LEU E2295 " (cutoff:3.500A) Processing helix chain 'E' and resid 2310 through 2315 removed outlier: 4.083A pdb=" N ALA E2315 " --> pdb=" O PRO E2311 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2331 removed outlier: 3.535A pdb=" N TYR E2331 " --> pdb=" O GLY E2327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2355 removed outlier: 3.899A pdb=" N ALA E2350 " --> pdb=" O VAL E2346 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E2353 " --> pdb=" O ASN E2349 " (cutoff:3.500A) Processing helix chain 'E' and resid 2360 through 2364 Processing helix chain 'E' and resid 2375 through 2388 Processing helix chain 'E' and resid 2389 through 2393 Processing helix chain 'E' and resid 2418 through 2436 removed outlier: 3.808A pdb=" N MET E2423 " --> pdb=" O GLY E2419 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E2428 " --> pdb=" O SER E2424 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E2435 " --> pdb=" O ASP E2431 " (cutoff:3.500A) Processing helix chain 'E' and resid 2440 through 2445 Processing helix chain 'E' and resid 2448 through 2461 removed outlier: 3.707A pdb=" N ILE E2453 " --> pdb=" O GLU E2449 " (cutoff:3.500A) Processing helix chain 'E' and resid 2466 through 2471 removed outlier: 3.645A pdb=" N ILE E2470 " --> pdb=" O LEU E2466 " (cutoff:3.500A) Processing helix chain 'E' and resid 2502 through 2507 removed outlier: 3.894A 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 removed outlier: 3.530A pdb=" N UNK E2530 " --> pdb=" O UNK E2526 " (cutoff:3.500A) Processing helix chain 'E' and resid 2542 through 2548 removed outlier: 3.660A pdb=" N UNK E2546 " --> pdb=" O UNK E2542 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2557 removed outlier: 3.765A pdb=" N UNK E2555 " --> pdb=" O UNK E2551 " (cutoff:3.500A) Processing helix chain 'E' and resid 2567 through 2581 removed outlier: 3.565A pdb=" N UNK E2578 " --> pdb=" O UNK E2574 " (cutoff:3.500A) Processing helix chain 'E' and resid 2587 through 2602 removed outlier: 3.537A pdb=" N UNK E2597 " --> pdb=" O UNK E2593 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK E2602 " --> pdb=" O UNK E2598 " (cutoff:3.500A) Processing helix chain 'E' and resid 2610 through 2618 removed outlier: 3.612A pdb=" N UNK E2617 " --> pdb=" O UNK E2613 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N UNK E2618 " --> pdb=" O UNK E2614 " (cutoff:3.500A) Processing helix chain 'E' and resid 2626 through 2641 removed outlier: 3.935A pdb=" N UNK E2630 " --> pdb=" O UNK E2626 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N UNK E2631 " --> pdb=" O UNK E2627 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N UNK E2634 " --> pdb=" O UNK E2630 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N UNK E2635 " --> pdb=" O UNK E2631 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N UNK E2639 " --> pdb=" O UNK E2635 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N UNK E2641 " --> pdb=" O UNK E2637 " (cutoff:3.500A) Processing helix chain 'E' and resid 2650 through 2666 Processing helix chain 'E' and resid 2677 through 2683 removed outlier: 3.921A pdb=" N UNK E2681 " --> pdb=" O UNK E2677 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N UNK E2683 " --> pdb=" O UNK E2679 " (cutoff:3.500A) Processing helix chain 'E' and resid 2751 through 2773 removed outlier: 3.888A pdb=" N PHE E2768 " --> pdb=" O GLU E2764 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP E2769 " --> pdb=" O LYS E2765 " (cutoff:3.500A) Processing helix chain 'E' and resid 2793 through 2797 removed outlier: 3.504A pdb=" N THR E2796 " --> pdb=" O PRO E2793 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E2797 " --> pdb=" O TYR E2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2793 through 2797' Processing helix chain 'E' and resid 2809 through 2820 removed outlier: 3.841A pdb=" N ALA E2815 " --> pdb=" O GLU E2811 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET E2816 " --> pdb=" O SER E2812 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2895 removed outlier: 4.045A pdb=" N MET E2874 " --> pdb=" O GLU E2870 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E2875 " --> pdb=" O LEU E2871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E2876 " --> pdb=" O GLN E2872 " (cutoff:3.500A) removed outlier: 4.119A 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: 4.005A pdb=" N ARG E2920 " --> pdb=" O LYS E2916 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E2921 " --> pdb=" O ALA E2917 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E2926 " --> pdb=" O LYS E2922 " (cutoff:3.500A) Processing helix chain 'E' and resid 2950 through 2976 removed outlier: 3.507A pdb=" N UNK E2955 " --> pdb=" O UNK E2951 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N UNK E2956 " --> pdb=" O UNK E2952 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N UNK E2968 " --> pdb=" O UNK E2964 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N UNK E2969 " --> pdb=" O UNK E2965 " (cutoff:3.500A) Processing helix chain 'E' and resid 2999 through 3016 removed outlier: 3.568A pdb=" N UNK E3004 " --> pdb=" O UNK E3000 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N UNK E3006 " --> pdb=" O UNK E3002 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N UNK E3009 " --> pdb=" O UNK E3005 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK E3010 " --> pdb=" O UNK E3006 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N UNK E3013 " --> pdb=" O UNK E3009 " (cutoff:3.500A) Processing helix chain 'E' and resid 3017 through 3022 Processing helix chain 'E' and resid 3029 through 3040 removed outlier: 3.624A pdb=" N UNK E3037 " --> pdb=" O UNK E3033 " (cutoff:3.500A) Processing helix chain 'E' and resid 3052 through 3063 removed outlier: 4.079A pdb=" N UNK E3056 " --> pdb=" O UNK E3052 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N UNK E3061 " --> pdb=" O UNK E3057 " (cutoff:3.500A) removed outlier: 4.206A 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 3151 Processing helix chain 'E' and resid 3151 through 3162 Processing helix chain 'E' and resid 3175 through 3186 removed outlier: 3.614A pdb=" N UNK E3182 " --> pdb=" O UNK E3178 " (cutoff:3.500A) Processing helix chain 'E' and resid 3198 through 3212 removed outlier: 3.585A pdb=" N UNK E3205 " --> pdb=" O UNK E3201 " (cutoff:3.500A) Processing helix chain 'E' and resid 3224 through 3230 removed outlier: 3.780A pdb=" N UNK E3228 " --> pdb=" O UNK E3224 " (cutoff:3.500A) Processing helix chain 'E' and resid 3248 through 3254 removed outlier: 3.535A pdb=" N UNK E3252 " --> pdb=" O UNK E3248 " (cutoff:3.500A) Processing helix chain 'E' and resid 3271 through 3280 Processing helix chain 'E' and resid 3280 through 3285 removed outlier: 4.016A pdb=" N UNK E3284 " --> pdb=" O UNK E3280 " (cutoff:3.500A) Processing helix chain 'E' and resid 3296 through 3301 removed outlier: 3.820A pdb=" N UNK E3301 " --> pdb=" O UNK E3297 " (cutoff:3.500A) Processing helix chain 'E' and resid 3305 through 3310 Processing helix chain 'E' and resid 3316 through 3331 removed outlier: 3.876A pdb=" N UNK E3323 " --> pdb=" O UNK E3319 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N UNK E3324 " --> pdb=" O UNK E3320 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK E3330 " --> pdb=" O UNK E3326 " (cutoff:3.500A) Processing helix chain 'E' and resid 3344 through 3349 removed outlier: 3.527A 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 3409 removed outlier: 3.761A pdb=" N UNK E3405 " --> pdb=" O UNK E3401 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNK E3407 " --> pdb=" O UNK E3403 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N UNK E3409 " --> pdb=" O UNK E3405 " (cutoff:3.500A) Processing helix chain 'E' and resid 3410 through 3425 removed outlier: 4.030A pdb=" N UNK E3416 " --> pdb=" O UNK E3412 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N UNK E3420 " --> pdb=" O UNK E3416 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N UNK E3421 " --> pdb=" O UNK E3417 " (cutoff:3.500A) Processing helix chain 'E' and resid 3434 through 3443 removed outlier: 4.009A pdb=" N UNK E3439 " --> pdb=" O UNK E3435 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N UNK E3440 " --> pdb=" O UNK E3436 " (cutoff:3.500A) Processing helix chain 'E' and resid 3445 through 3450 Processing helix chain 'E' and resid 3461 through 3468 removed outlier: 3.575A pdb=" N UNK E3468 " --> pdb=" O UNK E3464 " (cutoff:3.500A) Processing helix chain 'E' and resid 3518 through 3521 Processing helix chain 'E' and resid 3522 through 3529 removed outlier: 3.693A pdb=" N UNK E3529 " --> pdb=" O UNK E3525 " (cutoff:3.500A) Processing helix chain 'E' and resid 3541 through 3547 removed outlier: 3.568A 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: 3.576A pdb=" N UNK E3579 " --> pdb=" O UNK E3575 " (cutoff:3.500A) Processing helix chain 'E' and resid 3589 through 3611 removed outlier: 4.035A pdb=" N UNK E3595 " --> pdb=" O UNK E3591 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK E3598 " --> pdb=" O UNK E3594 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N UNK E3600 " --> pdb=" O UNK E3596 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N UNK E3601 " --> pdb=" O UNK E3597 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N UNK E3610 " --> pdb=" O UNK E3606 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N UNK E3611 " --> pdb=" O UNK E3607 " (cutoff:3.500A) Processing helix chain 'E' and resid 3645 through 3656 removed outlier: 3.801A pdb=" N GLU E3655 " --> pdb=" O ASN E3651 " (cutoff:3.500A) Processing helix chain 'E' and resid 3657 through 3661 Processing helix chain 'E' and resid 3671 through 3680 removed outlier: 3.562A pdb=" N ASP E3676 " --> pdb=" O ARG E3672 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E3677 " --> pdb=" O MET E3673 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E3678 " --> pdb=" O ILE E3674 " (cutoff:3.500A) Processing helix chain 'E' and resid 3696 through 3711 removed outlier: 3.584A pdb=" N ALA E3709 " --> pdb=" O PHE E3705 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR E3711 " --> pdb=" O ARG E3707 " (cutoff:3.500A) Processing helix chain 'E' and resid 3719 through 3738 removed outlier: 3.606A pdb=" N GLU E3736 " --> pdb=" O SER E3732 " (cutoff:3.500A) Processing helix chain 'E' and resid 3754 through 3770 removed outlier: 4.157A pdb=" N LYS E3760 " --> pdb=" O LYS E3756 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG E3762 " --> pdb=" O MET E3758 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E3763 " --> pdb=" O GLU E3759 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN E3767 " --> pdb=" O LEU E3763 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER E3768 " --> pdb=" O LEU E3764 " (cutoff:3.500A) Processing helix chain 'E' and resid 3771 through 3784 removed outlier: 4.279A pdb=" N GLU E3777 " --> pdb=" O ARG E3773 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET E3778 " --> pdb=" O GLY E3774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E3779 " --> pdb=" O ALA E3775 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU E3780 " --> pdb=" O ALA E3776 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3803 removed outlier: 3.898A pdb=" N LYS E3799 " --> pdb=" O SER E3795 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3824 Processing helix chain 'E' and resid 3828 through 3838 removed outlier: 3.650A pdb=" N ILE E3832 " --> pdb=" O PHE E3828 " (cutoff:3.500A) Processing helix chain 'E' and resid 3843 through 3856 removed outlier: 3.553A pdb=" N LYS E3852 " --> pdb=" O GLU E3848 " (cutoff:3.500A) Processing helix chain 'E' and resid 3877 through 3891 removed outlier: 4.484A pdb=" N ASP E3883 " --> pdb=" O GLU E3879 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG E3886 " --> pdb=" O GLN E3882 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E3887 " --> pdb=" O ASP E3883 " (cutoff:3.500A) Processing helix chain 'E' and resid 3898 through 3903 Processing helix chain 'E' and resid 3914 through 3932 removed outlier: 4.117A pdb=" N CYS E3918 " --> pdb=" O ASN E3914 " (cutoff:3.500A) Processing helix chain 'E' and resid 3932 through 3937 removed outlier: 3.876A pdb=" N TYR E3936 " --> pdb=" O ASP E3932 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR E3937 " --> pdb=" O PHE E3933 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3932 through 3937' Processing helix chain 'E' and resid 3944 through 3967 removed outlier: 3.639A pdb=" N LYS E3953 " --> pdb=" O ARG E3949 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET E3955 " --> pdb=" O PHE E3951 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN E3960 " --> pdb=" O SER E3956 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E3967 " --> pdb=" O ASN E3963 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3983 Processing helix chain 'E' and resid 3984 through 4005 removed outlier: 3.739A pdb=" N ALA E3988 " --> pdb=" O ARG E3984 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY E3991 " --> pdb=" O ASP E3987 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU E3993 " --> pdb=" O VAL E3989 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS E3994 " --> pdb=" O VAL E3990 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E3999 " --> pdb=" O VAL E3995 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E4004 " --> pdb=" O MET E4000 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN E4005 " --> pdb=" O MET E4001 " (cutoff:3.500A) Processing helix chain 'E' and resid 4006 through 4008 No H-bonds generated for 'chain 'E' and resid 4006 through 4008' Processing helix chain 'E' and resid 4009 through 4030 removed outlier: 4.114A pdb=" N MET E4026 " --> pdb=" O ASP E4022 " (cutoff:3.500A) Processing helix chain 'E' and resid 4039 through 4051 Processing helix chain 'E' and resid 4051 through 4063 Processing helix chain 'E' and resid 4067 through 4072 Processing helix chain 'E' and resid 4074 through 4081 removed outlier: 4.535A pdb=" N TYR E4080 " --> pdb=" O ALA E4076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL E4081 " --> pdb=" O PHE E4077 " (cutoff:3.500A) Processing helix chain 'E' and resid 4090 through 4100 removed outlier: 3.763A pdb=" N ASP E4098 " --> pdb=" O GLN E4094 " (cutoff:3.500A) Processing helix chain 'E' and resid 4104 through 4114 Processing helix chain 'E' and resid 4124 through 4128 Processing helix chain 'E' and resid 4132 through 4154 removed outlier: 3.544A pdb=" N ALA E4136 " --> pdb=" O PHE E4132 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP E4138 " --> pdb=" O GLU E4134 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE E4139 " --> pdb=" O PRO E4135 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE E4141 " --> pdb=" O ARG E4137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E4146 " --> pdb=" O ASN E4142 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E4152 " --> pdb=" O THR E4148 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL E4154 " --> pdb=" O LEU E4150 " (cutoff:3.500A) Processing helix chain 'E' and resid 4157 through 4167 Processing helix chain 'E' and resid 4167 through 4175 removed outlier: 3.736A pdb=" N LEU E4171 " --> pdb=" O ALA E4167 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E4174 " --> pdb=" O ILE E4170 " (cutoff:3.500A) Processing helix chain 'E' and resid 4198 through 4206 Processing helix chain 'E' and resid 4207 through 4224 removed outlier: 4.096A pdb=" N VAL E4222 " --> pdb=" O ILE E4218 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4251 removed outlier: 4.084A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E4243 " --> pdb=" O GLU E4239 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN E4250 " --> pdb=" O GLN E4246 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE E4251 " --> pdb=" O ILE E4247 " (cutoff:3.500A) Processing helix chain 'E' and resid 4542 through 4558 removed outlier: 3.996A pdb=" N TYR E4554 " --> pdb=" O LYS E4550 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E4558 " --> pdb=" O TYR E4554 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4576 removed outlier: 3.682A pdb=" N ALA E4570 " --> pdb=" O ALA E4566 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE E4571 " --> pdb=" O LEU E4567 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA E4572 " --> pdb=" O PHE E4568 " (cutoff:3.500A) Processing helix chain 'E' and resid 4641 through 4665 removed outlier: 3.606A pdb=" N ALA E4654 " --> pdb=" O HIS E4650 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E4655 " --> pdb=" O THR E4651 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE E4659 " --> pdb=" O PHE E4655 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY E4660 " --> pdb=" O LEU E4656 " (cutoff:3.500A) Processing helix chain 'E' and resid 4667 through 4683 removed outlier: 3.865A pdb=" N ALA E4678 " --> pdb=" O GLU E4674 " (cutoff:3.500A) Processing helix chain 'E' and resid 4697 through 4702 Processing helix chain 'E' and resid 4703 through 4708 removed outlier: 3.707A pdb=" N LEU E4706 " --> pdb=" O ARG E4703 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN E4707 " --> pdb=" O LEU E4704 " (cutoff:3.500A) Processing helix chain 'E' and resid 4719 through 4732 removed outlier: 4.725A pdb=" N ASP E4730 " --> pdb=" O ASP E4726 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE E4731 " --> pdb=" O LYS E4727 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E4732 " --> pdb=" O HIS E4728 " (cutoff:3.500A) Processing helix chain 'E' and resid 4733 through 4741 Processing helix chain 'E' and resid 4748 through 4753 Processing helix chain 'E' and resid 4772 through 4786 removed outlier: 3.794A pdb=" N PHE E4780 " --> pdb=" O GLN E4776 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY E4781 " --> pdb=" O ILE E4777 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP E4786 " --> pdb=" O VAL E4782 " (cutoff:3.500A) Processing helix chain 'E' and resid 4786 through 4802 removed outlier: 3.599A pdb=" N TRP E4794 " --> pdb=" O LEU E4790 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E4797 " --> pdb=" O GLY E4793 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET E4798 " --> pdb=" O TRP E4794 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER E4799 " --> pdb=" O TYR E4795 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E4800 " --> pdb=" O MET E4796 " (cutoff:3.500A) Processing helix chain 'E' and resid 4812 through 4819 removed outlier: 3.579A pdb=" N ILE E4816 " --> pdb=" O HIS E4812 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E4817 " --> pdb=" O LEU E4813 " (cutoff:3.500A) Processing helix chain 'E' and resid 4820 through 4832 removed outlier: 3.980A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E4830 " --> pdb=" O ILE E4826 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 removed outlier: 4.257A pdb=" N MET E4839 " --> pdb=" O LYS E4835 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E4845 " --> pdb=" O VAL E4841 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E4848 " --> pdb=" O LEU E4844 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E4853 " --> pdb=" O TYR E4849 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E4854 " --> pdb=" O LEU E4850 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA E4855 " --> pdb=" O TYR E4851 " (cutoff:3.500A) Processing helix chain 'E' and resid 4878 through 4889 removed outlier: 3.754A pdb=" N PHE E4885 " --> pdb=" O THR E4881 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS E4886 " --> pdb=" O CYS E4882 " (cutoff:3.500A) Processing helix chain 'E' and resid 4909 through 4922 removed outlier: 3.729A pdb=" N ARG E4913 " --> pdb=" O TYR E4909 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E4914 " --> pdb=" O GLU E4910 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL E4915 " --> pdb=" O LEU E4911 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE E4918 " --> pdb=" O VAL E4914 " (cutoff:3.500A) Processing helix chain 'E' and resid 4926 through 4957 removed outlier: 3.773A pdb=" N ILE E4936 " --> pdb=" O ILE E4932 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E4944 " --> pdb=" O PHE E4940 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS E4951 " --> pdb=" O GLN E4947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E4952 " --> pdb=" O GLU E4948 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP E4953 " --> pdb=" O GLN E4949 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET E4954 " --> pdb=" O VAL E4950 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU E4955 " --> pdb=" O LYS E4951 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E4957 " --> pdb=" O ASP E4953 " (cutoff:3.500A) Processing helix chain 'E' and resid 4965 through 4970 removed outlier: 3.577A pdb=" N THR E4970 " --> pdb=" O ASP E4966 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4981 Processing helix chain 'E' and resid 4986 through 4997 removed outlier: 3.577A pdb=" N PHE E4990 " --> pdb=" O ALA E4986 " (cutoff:3.500A) Processing helix chain 'E' and resid 5006 through 5017 Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.864A pdb=" N GLY F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 63 " --> pdb=" O PHE F 59 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.793A pdb=" N VAL F 80 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 395 through 412 removed outlier: 3.929A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET G 403 " --> pdb=" O GLN G 399 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 410 " --> pdb=" O SER G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 419 Processing helix chain 'G' and resid 438 through 452 removed outlier: 3.576A pdb=" N GLY G 450 " --> pdb=" O GLN G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 478 removed outlier: 3.612A pdb=" N GLN G 465 " --> pdb=" O HIS G 461 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 478 " --> pdb=" O ARG G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 Processing helix chain 'G' and resid 512 through 531 removed outlier: 4.305A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR G 523 " --> pdb=" O VAL G 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU G 524 " --> pdb=" O ASN G 520 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER G 528 " --> pdb=" O GLU G 524 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU G 529 " --> pdb=" O LEU G 525 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE G 530 " --> pdb=" O LEU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 removed outlier: 3.644A pdb=" N SER G 541 " --> pdb=" O ALA G 538 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR G 542 " --> pdb=" O LEU G 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 538 through 542' Processing helix chain 'G' and resid 543 through 548 removed outlier: 3.736A pdb=" N VAL G 548 " --> pdb=" O LEU G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 568 removed outlier: 3.894A pdb=" N TYR G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 577 removed outlier: 3.785A pdb=" N LEU G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 593 Processing helix chain 'G' and resid 596 through 608 removed outlier: 4.036A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 625 removed outlier: 3.966A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP G 619 " --> pdb=" O ARG G 615 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE G 621 " --> pdb=" O ASN G 617 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 622 " --> pdb=" O GLN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 888 removed outlier: 3.973A pdb=" N GLU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS G 873 " --> pdb=" O ARG G 869 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS G 879 " --> pdb=" O ALA G 875 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE G 887 " --> pdb=" O ALA G 883 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 932 removed outlier: 3.672A pdb=" N ASN G 919 " --> pdb=" O GLU G 915 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN G 923 " --> pdb=" O ASN G 919 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 932 " --> pdb=" O THR G 928 " (cutoff:3.500A) Processing helix chain 'G' and resid 933 through 936 removed outlier: 3.969A pdb=" N GLY G 936 " --> pdb=" O LEU G 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 933 through 936' Processing helix chain 'G' and resid 980 through 988 removed outlier: 3.720A pdb=" N LEU G 984 " --> pdb=" O ALA G 980 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP G 986 " --> pdb=" O THR G 982 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 1001 removed outlier: 3.806A pdb=" N ASN G 994 " --> pdb=" O GLU G 990 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1041 removed outlier: 4.382A pdb=" N GLN G1041 " --> pdb=" O ASP G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1042 through 1049 removed outlier: 3.654A pdb=" N LEU G1046 " --> pdb=" O ALA G1042 " (cutoff:3.500A) Processing helix chain 'G' and resid 1078 through 1082 Processing helix chain 'G' and resid 1652 through 1657 Processing helix chain 'G' and resid 1658 through 1674 removed outlier: 3.735A pdb=" N TYR G1670 " --> pdb=" O THR G1666 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG G1671 " --> pdb=" O LEU G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1686 removed outlier: 3.719A pdb=" N ALA G1684 " --> pdb=" O ARG G1680 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS G1686 " --> pdb=" O ALA G1682 " (cutoff:3.500A) Processing helix chain 'G' and resid 1692 through 1700 removed outlier: 3.842A pdb=" N LEU G1698 " --> pdb=" O LEU G1694 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU G1699 " --> pdb=" O LEU G1695 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP G1700 " --> pdb=" O HIS G1696 " (cutoff:3.500A) Processing helix chain 'G' and resid 1709 through 1712 removed outlier: 3.650A pdb=" N TYR G1712 " --> pdb=" O ALA G1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1709 through 1712' Processing helix chain 'G' and resid 1713 through 1718 Processing helix chain 'G' and resid 1723 through 1730 removed outlier: 3.605A pdb=" N MET G1730 " --> pdb=" O SER G1726 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 Processing helix chain 'G' and resid 1753 through 1758 removed outlier: 4.069A pdb=" N ALA G1757 " --> pdb=" O LYS G1753 " (cutoff:3.500A) Processing helix chain 'G' and resid 1804 through 1823 removed outlier: 3.516A pdb=" N GLY G1816 " --> pdb=" O LEU G1812 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G1823 " --> pdb=" O VAL G1819 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1838 Processing helix chain 'G' and resid 1840 through 1852 Processing helix chain 'G' and resid 1855 through 1863 Processing helix chain 'G' and resid 1866 through 1871 Processing helix chain 'G' and resid 1925 through 1929 removed outlier: 3.627A pdb=" N GLN G1928 " --> pdb=" O GLY G1925 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET G1929 " --> pdb=" O LEU G1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1925 through 1929' Processing helix chain 'G' and resid 1933 through 1982 removed outlier: 3.795A pdb=" N TYR G1945 " --> pdb=" O ASN G1941 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G1946 " --> pdb=" O LEU G1942 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS G1947 " --> pdb=" O LEU G1943 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU G1963 " --> pdb=" O ALA G1959 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG G1964 " --> pdb=" O ALA G1960 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR G1965 " --> pdb=" O PHE G1961 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP G1967 " --> pdb=" O GLU G1963 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA G1978 " --> pdb=" O ARG G1974 " (cutoff:3.500A) Processing helix chain 'G' and resid 1989 through 1994 removed outlier: 3.818A pdb=" N ARG G1993 " --> pdb=" O ALA G1989 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG G1994 " --> pdb=" O GLU G1990 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1989 through 1994' Processing helix chain 'G' and resid 1995 through 1998 Processing helix chain 'G' and resid 2001 through 2011 removed outlier: 3.686A pdb=" N ILE G2006 " --> pdb=" O PRO G2002 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN G2007 " --> pdb=" O GLN G2003 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) Processing helix chain 'G' and resid 2028 through 2042 removed outlier: 3.696A pdb=" N GLN G2032 " --> pdb=" O ARG G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2094 through 2108 removed outlier: 3.803A pdb=" N HIS G2100 " --> pdb=" O GLU G2096 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL G2103 " --> pdb=" O SER G2099 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP G2105 " --> pdb=" O MET G2101 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2129 removed outlier: 3.613A pdb=" N VAL G2117 " --> pdb=" O SER G2113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G2123 " --> pdb=" O ALA G2119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR G2128 " --> pdb=" O LEU G2124 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2138 Processing helix chain 'G' and resid 2148 through 2165 removed outlier: 3.737A pdb=" N CYS G2158 " --> pdb=" O SER G2154 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2187 removed outlier: 3.672A pdb=" N LEU G2177 " --> pdb=" O GLN G2173 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.546A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.860A pdb=" N VAL G2210 " --> pdb=" O THR G2206 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G2213 " --> pdb=" O GLU G2209 " (cutoff:3.500A) Processing helix chain 'G' and resid 2227 through 2242 removed outlier: 3.642A pdb=" N CYS G2233 " --> pdb=" O VAL G2229 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2253 removed outlier: 3.620A pdb=" N ASP G2252 " --> pdb=" O ARG G2248 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS G2253 " --> pdb=" O SER G2249 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2262 removed outlier: 4.111A pdb=" N ASN G2260 " --> pdb=" O TYR G2256 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2279 removed outlier: 3.520A pdb=" N ALA G2276 " --> pdb=" O PRO G2272 " (cutoff:3.500A) Processing helix chain 'G' and resid 2294 through 2306 removed outlier: 3.519A pdb=" N VAL G2298 " --> pdb=" O ASP G2294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G2299 " --> pdb=" O LEU G2295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2315 removed outlier: 4.084A pdb=" N ALA G2315 " --> pdb=" O PRO G2311 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2331 removed outlier: 3.534A pdb=" N TYR G2331 " --> pdb=" O GLY G2327 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2355 removed outlier: 3.900A pdb=" N ALA G2350 " --> pdb=" O VAL G2346 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL G2353 " --> pdb=" O ASN G2349 " (cutoff:3.500A) Processing helix chain 'G' and resid 2360 through 2364 Processing helix chain 'G' and resid 2375 through 2388 Processing helix chain 'G' and resid 2389 through 2393 Processing helix chain 'G' and resid 2418 through 2436 removed outlier: 3.809A pdb=" N MET G2423 " --> pdb=" O GLY G2419 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G2428 " --> pdb=" O SER G2424 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G2435 " --> pdb=" O ASP G2431 " (cutoff:3.500A) Processing helix chain 'G' and resid 2440 through 2445 Processing helix chain 'G' and resid 2448 through 2461 removed outlier: 3.708A pdb=" N ILE G2453 " --> pdb=" O GLU G2449 " (cutoff:3.500A) Processing helix chain 'G' and resid 2466 through 2471 removed outlier: 3.645A pdb=" N ILE G2470 " --> pdb=" O LEU G2466 " (cutoff:3.500A) Processing helix chain 'G' and resid 2502 through 2507 removed outlier: 3.885A pdb=" N UNK G2506 " --> pdb=" O UNK G2502 " (cutoff:3.500A) Processing helix chain 'G' and resid 2516 through 2525 removed outlier: 3.808A pdb=" N UNK G2523 " --> pdb=" O UNK G2519 " (cutoff:3.500A) Processing helix chain 'G' and resid 2525 through 2530 removed outlier: 3.540A pdb=" N UNK G2530 " --> pdb=" O UNK G2526 " (cutoff:3.500A) Processing helix chain 'G' and resid 2542 through 2548 removed outlier: 3.640A pdb=" N UNK G2546 " --> pdb=" O UNK G2542 " (cutoff:3.500A) Processing helix chain 'G' and resid 2551 through 2557 removed outlier: 3.748A pdb=" N UNK G2555 " --> pdb=" O UNK G2551 " (cutoff:3.500A) Processing helix chain 'G' and resid 2567 through 2581 removed outlier: 3.544A pdb=" N UNK G2578 " --> pdb=" O UNK G2574 " (cutoff:3.500A) Processing helix chain 'G' and resid 2587 through 2602 removed outlier: 3.560A pdb=" N UNK G2597 " --> pdb=" O UNK G2593 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N UNK G2602 " --> pdb=" O UNK G2598 " (cutoff:3.500A) Processing helix chain 'G' and resid 2610 through 2618 removed outlier: 3.589A pdb=" N UNK G2617 " --> pdb=" O UNK G2613 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK G2618 " --> pdb=" O UNK G2614 " (cutoff:3.500A) Processing helix chain 'G' and resid 2626 through 2641 removed outlier: 3.912A pdb=" N UNK G2630 " --> pdb=" O UNK G2626 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N UNK G2631 " --> pdb=" O UNK G2627 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK G2634 " --> pdb=" O UNK G2630 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK G2635 " --> pdb=" O UNK G2631 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N UNK G2639 " --> pdb=" O UNK G2635 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK G2641 " --> pdb=" O UNK G2637 " (cutoff:3.500A) Processing helix chain 'G' and resid 2650 through 2666 Processing helix chain 'G' and resid 2677 through 2683 removed outlier: 3.988A pdb=" N UNK G2681 " --> pdb=" O UNK G2677 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N UNK G2683 " --> pdb=" O UNK G2679 " (cutoff:3.500A) Processing helix chain 'G' and resid 2751 through 2773 removed outlier: 3.888A pdb=" N PHE G2768 " --> pdb=" O GLU G2764 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP G2769 " --> pdb=" O LYS G2765 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2797 removed outlier: 3.503A pdb=" N THR G2796 " --> pdb=" O PRO G2793 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE G2797 " --> pdb=" O TYR G2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2793 through 2797' Processing helix chain 'G' and resid 2800 through 2804 Processing helix chain 'G' and resid 2809 through 2820 removed outlier: 3.842A pdb=" N ALA G2815 " --> pdb=" O GLU G2811 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET G2816 " --> pdb=" O SER G2812 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2895 removed outlier: 4.046A pdb=" N MET G2874 " --> pdb=" O GLU G2870 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G2875 " --> pdb=" O LEU G2871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU G2876 " --> pdb=" O GLN G2872 " (cutoff:3.500A) removed outlier: 4.119A 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: 4.005A pdb=" N ARG G2920 " --> pdb=" O LYS G2916 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU G2921 " --> pdb=" O ALA G2917 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU G2926 " --> pdb=" O LYS G2922 " (cutoff:3.500A) Processing helix chain 'G' and resid 2950 through 2976 removed outlier: 4.116A pdb=" N UNK G2956 " --> pdb=" O UNK G2952 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N UNK G2968 " --> pdb=" O UNK G2964 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N UNK G2969 " --> pdb=" O UNK G2965 " (cutoff:3.500A) Processing helix chain 'G' and resid 2999 through 3016 removed outlier: 3.564A pdb=" N UNK G3004 " --> pdb=" O UNK G3000 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N UNK G3006 " --> pdb=" O UNK G3002 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK G3009 " --> pdb=" O UNK G3005 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK G3010 " --> pdb=" O UNK G3006 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N UNK G3013 " --> pdb=" O UNK G3009 " (cutoff:3.500A) Processing helix chain 'G' and resid 3017 through 3022 Processing helix chain 'G' and resid 3029 through 3040 removed outlier: 3.664A pdb=" N UNK G3037 " --> pdb=" O UNK G3033 " (cutoff:3.500A) Processing helix chain 'G' and resid 3052 through 3063 removed outlier: 4.149A pdb=" N UNK G3056 " --> pdb=" O UNK G3052 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N UNK G3061 " --> pdb=" O UNK G3057 " (cutoff:3.500A) removed outlier: 4.167A 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: 4.039A pdb=" N UNK G3154 " --> pdb=" O UNK G3150 " (cutoff:3.500A) Processing helix chain 'G' and resid 3175 through 3186 removed outlier: 3.670A pdb=" N UNK G3182 " --> pdb=" O UNK G3178 " (cutoff:3.500A) Processing helix chain 'G' and resid 3198 through 3212 removed outlier: 3.597A pdb=" N UNK G3205 " --> pdb=" O UNK G3201 " (cutoff:3.500A) Processing helix chain 'G' and resid 3224 through 3230 removed outlier: 3.783A pdb=" N UNK G3228 " --> pdb=" O UNK G3224 " (cutoff:3.500A) Processing helix chain 'G' and resid 3248 through 3254 removed outlier: 3.539A pdb=" N UNK G3252 " --> pdb=" O UNK G3248 " (cutoff:3.500A) Processing helix chain 'G' and resid 3271 through 3280 Processing helix chain 'G' and resid 3280 through 3285 removed outlier: 3.997A pdb=" N UNK G3284 " --> pdb=" O UNK G3280 " (cutoff:3.500A) Processing helix chain 'G' and resid 3296 through 3301 removed outlier: 3.790A pdb=" N UNK G3301 " --> pdb=" O UNK G3297 " (cutoff:3.500A) Processing helix chain 'G' and resid 3305 through 3310 Processing helix chain 'G' and resid 3316 through 3321 Processing helix chain 'G' and resid 3321 through 3331 removed outlier: 3.551A pdb=" N UNK G3330 " --> pdb=" O UNK G3326 " (cutoff:3.500A) Processing helix chain 'G' and resid 3344 through 3349 Processing helix chain 'G' and resid 3361 through 3388 Processing helix chain 'G' and resid 3399 through 3409 removed outlier: 3.793A pdb=" N UNK G3405 " --> pdb=" O UNK G3401 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNK G3407 " --> pdb=" O UNK G3403 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N UNK G3409 " --> pdb=" O UNK G3405 " (cutoff:3.500A) Processing helix chain 'G' and resid 3410 through 3425 removed outlier: 4.009A pdb=" N UNK G3416 " --> pdb=" O UNK G3412 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N UNK G3420 " --> pdb=" O UNK G3416 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N UNK G3421 " --> pdb=" O UNK G3417 " (cutoff:3.500A) Processing helix chain 'G' and resid 3434 through 3443 removed outlier: 4.028A pdb=" N UNK G3439 " --> pdb=" O UNK G3435 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N UNK G3440 " --> pdb=" O UNK G3436 " (cutoff:3.500A) Processing helix chain 'G' and resid 3445 through 3450 Processing helix chain 'G' and resid 3461 through 3468 removed outlier: 3.535A pdb=" N UNK G3468 " --> pdb=" O UNK G3464 " (cutoff:3.500A) Processing helix chain 'G' and resid 3518 through 3521 Processing helix chain 'G' and resid 3522 through 3529 removed outlier: 3.695A pdb=" N UNK G3529 " --> pdb=" O UNK G3525 " (cutoff:3.500A) Processing helix chain 'G' and resid 3541 through 3547 Processing helix chain 'G' and resid 3551 through 3560 Processing helix chain 'G' and resid 3574 through 3579 removed outlier: 3.585A pdb=" N UNK G3579 " --> pdb=" O UNK G3575 " (cutoff:3.500A) Processing helix chain 'G' and resid 3589 through 3611 removed outlier: 4.033A pdb=" N UNK G3595 " --> pdb=" O UNK G3591 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N UNK G3598 " --> pdb=" O UNK G3594 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N UNK G3600 " --> pdb=" O UNK G3596 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N UNK G3601 " --> pdb=" O UNK G3597 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N UNK G3610 " --> pdb=" O UNK G3606 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N UNK G3611 " --> pdb=" O UNK G3607 " (cutoff:3.500A) Processing helix chain 'G' and resid 3645 through 3656 removed outlier: 3.801A pdb=" N GLU G3655 " --> pdb=" O ASN G3651 " (cutoff:3.500A) Processing helix chain 'G' and resid 3657 through 3661 Processing helix chain 'G' and resid 3671 through 3680 removed outlier: 3.562A pdb=" N ASP G3676 " --> pdb=" O ARG G3672 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU G3677 " --> pdb=" O MET G3673 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER G3678 " --> pdb=" O ILE G3674 " (cutoff:3.500A) Processing helix chain 'G' and resid 3696 through 3711 removed outlier: 3.584A pdb=" N ALA G3709 " --> pdb=" O PHE G3705 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR G3711 " --> pdb=" O ARG G3707 " (cutoff:3.500A) Processing helix chain 'G' and resid 3719 through 3738 removed outlier: 3.605A pdb=" N GLU G3736 " --> pdb=" O SER G3732 " (cutoff:3.500A) Processing helix chain 'G' and resid 3754 through 3770 removed outlier: 4.158A pdb=" N LYS G3760 " --> pdb=" O LYS G3756 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG G3762 " --> pdb=" O MET G3758 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G3763 " --> pdb=" O GLU G3759 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN G3767 " --> pdb=" O LEU G3763 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER G3768 " --> pdb=" O LEU G3764 " (cutoff:3.500A) Processing helix chain 'G' and resid 3771 through 3784 removed outlier: 4.279A pdb=" N GLU G3777 " --> pdb=" O ARG G3773 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET G3778 " --> pdb=" O GLY G3774 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL G3779 " --> pdb=" O ALA G3775 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3803 removed outlier: 3.897A pdb=" N LYS G3799 " --> pdb=" O SER G3795 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3824 Processing helix chain 'G' and resid 3828 through 3838 removed outlier: 3.651A pdb=" N ILE G3832 " --> pdb=" O PHE G3828 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3856 removed outlier: 3.553A pdb=" N LYS G3852 " --> pdb=" O GLU G3848 " (cutoff:3.500A) Processing helix chain 'G' and resid 3877 through 3891 removed outlier: 4.484A pdb=" N ASP G3883 " --> pdb=" O GLU G3879 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG G3886 " --> pdb=" O GLN G3882 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G3887 " --> pdb=" O ASP G3883 " (cutoff:3.500A) Processing helix chain 'G' and resid 3898 through 3903 Processing helix chain 'G' and resid 3914 through 3937 removed outlier: 4.116A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G3934 " --> pdb=" O ILE G3930 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP G3935 " --> pdb=" O SER G3931 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3967 removed outlier: 3.639A pdb=" N LYS G3953 " --> pdb=" O ARG G3949 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA G3954 " --> pdb=" O ASN G3950 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET G3955 " --> pdb=" O PHE G3951 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN G3960 " --> pdb=" O SER G3956 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G3967 " --> pdb=" O ASN G3963 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3983 Processing helix chain 'G' and resid 3984 through 4005 removed outlier: 3.740A pdb=" N ALA G3988 " --> pdb=" O ARG G3984 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU G3993 " --> pdb=" O VAL G3989 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS G3994 " --> pdb=" O VAL G3990 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS G3998 " --> pdb=" O HIS G3994 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET G3999 " --> pdb=" O VAL G3995 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA G4004 " --> pdb=" O MET G4000 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN G4005 " --> pdb=" O MET G4001 " (cutoff:3.500A) Processing helix chain 'G' and resid 4006 through 4008 No H-bonds generated for 'chain 'G' and resid 4006 through 4008' Processing helix chain 'G' and resid 4009 through 4030 removed outlier: 4.114A pdb=" N MET G4026 " --> pdb=" O ASP G4022 " (cutoff:3.500A) Processing helix chain 'G' and resid 4039 through 4051 Processing helix chain 'G' and resid 4051 through 4063 Processing helix chain 'G' and resid 4067 through 4072 Processing helix chain 'G' and resid 4074 through 4081 removed outlier: 4.537A pdb=" N TYR G4080 " --> pdb=" O ALA G4076 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL G4081 " --> pdb=" O PHE G4077 " (cutoff:3.500A) Processing helix chain 'G' and resid 4090 through 4100 removed outlier: 3.763A pdb=" N ASP G4098 " --> pdb=" O GLN G4094 " (cutoff:3.500A) Processing helix chain 'G' and resid 4104 through 4114 Processing helix chain 'G' and resid 4124 through 4128 Processing helix chain 'G' and resid 4132 through 4154 removed outlier: 3.586A pdb=" N ALA G4136 " --> pdb=" O PHE G4132 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP G4138 " --> pdb=" O GLU G4134 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE G4139 " --> pdb=" O PRO G4135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE G4141 " --> pdb=" O ARG G4137 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU G4146 " --> pdb=" O ASN G4142 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G4152 " --> pdb=" O THR G4148 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL G4154 " --> pdb=" O LEU G4150 " (cutoff:3.500A) Processing helix chain 'G' and resid 4157 through 4167 Processing helix chain 'G' and resid 4167 through 4175 removed outlier: 3.736A pdb=" N LEU G4171 " --> pdb=" O ALA G4167 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE G4174 " --> pdb=" O ILE G4170 " (cutoff:3.500A) Processing helix chain 'G' and resid 4198 through 4206 Processing helix chain 'G' and resid 4207 through 4224 removed outlier: 4.096A pdb=" N VAL G4222 " --> pdb=" O ILE G4218 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4251 removed outlier: 4.085A pdb=" N PHE G4234 " --> pdb=" O LYS G4230 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE G4243 " --> pdb=" O GLU G4239 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN G4250 " --> pdb=" O GLN G4246 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE G4251 " --> pdb=" O ILE G4247 " (cutoff:3.500A) Processing helix chain 'G' and resid 4542 through 4558 removed outlier: 3.995A pdb=" N TYR G4554 " --> pdb=" O LYS G4550 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN G4558 " --> pdb=" O TYR G4554 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4576 removed outlier: 3.681A pdb=" N ALA G4570 " --> pdb=" O ALA G4566 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE G4571 " --> pdb=" O LEU G4567 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA G4572 " --> pdb=" O PHE G4568 " (cutoff:3.500A) Processing helix chain 'G' and resid 4641 through 4665 removed outlier: 3.606A pdb=" N ALA G4654 " --> pdb=" O HIS G4650 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE G4655 " --> pdb=" O THR G4651 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY G4660 " --> pdb=" O LEU G4656 " (cutoff:3.500A) Processing helix chain 'G' and resid 4667 through 4683 removed outlier: 3.865A pdb=" N ALA G4678 " --> pdb=" O GLU G4674 " (cutoff:3.500A) Processing helix chain 'G' and resid 4697 through 4702 Processing helix chain 'G' and resid 4703 through 4708 removed outlier: 3.707A pdb=" N LEU G4706 " --> pdb=" O ARG G4703 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN G4707 " --> pdb=" O LEU G4704 " (cutoff:3.500A) Processing helix chain 'G' and resid 4719 through 4728 Processing helix chain 'G' and resid 4733 through 4741 Processing helix chain 'G' and resid 4748 through 4753 Processing helix chain 'G' and resid 4772 through 4786 removed outlier: 3.794A pdb=" N PHE G4780 " --> pdb=" O GLN G4776 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY G4781 " --> pdb=" O ILE G4777 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP G4786 " --> pdb=" O VAL G4782 " (cutoff:3.500A) Processing helix chain 'G' and resid 4786 through 4802 removed outlier: 3.600A pdb=" N TRP G4794 " --> pdb=" O LEU G4790 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL G4797 " --> pdb=" O GLY G4793 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET G4798 " --> pdb=" O TRP G4794 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU G4800 " --> pdb=" O MET G4796 " (cutoff:3.500A) Processing helix chain 'G' and resid 4812 through 4819 removed outlier: 3.580A pdb=" N ILE G4816 " --> pdb=" O HIS G4812 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA G4817 " --> pdb=" O LEU G4813 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4832 removed outlier: 3.979A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 4.258A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA G4845 " --> pdb=" O VAL G4841 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G4848 " --> pdb=" O LEU G4844 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G4853 " --> pdb=" O TYR G4849 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL G4854 " --> pdb=" O LEU G4850 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA G4855 " --> pdb=" O TYR G4851 " (cutoff:3.500A) Processing helix chain 'G' and resid 4878 through 4889 removed outlier: 3.753A pdb=" N PHE G4885 " --> pdb=" O THR G4881 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS G4886 " --> pdb=" O CYS G4882 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4922 removed outlier: 3.724A pdb=" N ARG G4913 " --> pdb=" O TYR G4909 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G4914 " --> pdb=" O GLU G4910 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE G4918 " --> pdb=" O VAL G4914 " (cutoff:3.500A) Processing helix chain 'G' and resid 4926 through 4957 removed outlier: 3.774A pdb=" N ILE G4936 " --> pdb=" O ILE G4932 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG G4944 " --> pdb=" O PHE G4940 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G4951 " --> pdb=" O GLN G4947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G4952 " --> pdb=" O GLU G4948 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP G4953 " --> pdb=" O GLN G4949 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET G4954 " --> pdb=" O VAL G4950 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU G4955 " --> pdb=" O LYS G4951 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS G4957 " --> pdb=" O ASP G4953 " (cutoff:3.500A) Processing helix chain 'G' and resid 4965 through 4970 removed outlier: 3.577A pdb=" N THR G4970 " --> pdb=" O ASP G4966 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4981 Processing helix chain 'G' and resid 4986 through 4997 removed outlier: 3.578A pdb=" N PHE G4990 " --> pdb=" O ALA G4986 " (cutoff:3.500A) Processing helix chain 'G' and resid 5006 through 5017 Processing helix chain 'H' and resid 38 through 43 Processing helix chain 'H' and resid 56 through 65 removed outlier: 3.865A pdb=" N GLY H 62 " --> pdb=" O GLY H 58 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.795A pdb=" N VAL H 80 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 251 through 255 Processing helix chain 'I' and resid 395 through 412 removed outlier: 3.929A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET I 403 " --> pdb=" O GLN I 399 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU I 410 " --> pdb=" O SER I 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 419 Processing helix chain 'I' and resid 438 through 452 removed outlier: 3.575A pdb=" N GLY I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 478 removed outlier: 3.613A pdb=" N GLN I 465 " --> pdb=" O HIS I 461 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 494 Processing helix chain 'I' and resid 512 through 531 removed outlier: 4.304A pdb=" N LYS I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU I 517 " --> pdb=" O GLU I 513 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR I 523 " --> pdb=" O VAL I 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU I 524 " --> pdb=" O ASN I 520 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER I 528 " --> pdb=" O GLU I 524 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU I 529 " --> pdb=" O LEU I 525 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 530 " --> pdb=" O LEU I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 538 through 542 removed outlier: 3.644A pdb=" N SER I 541 " --> pdb=" O ALA I 538 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR I 542 " --> pdb=" O LEU I 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 538 through 542' Processing helix chain 'I' and resid 543 through 548 removed outlier: 3.737A pdb=" N VAL I 548 " --> pdb=" O LEU I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 568 removed outlier: 3.894A pdb=" N TYR I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 577 removed outlier: 3.785A pdb=" N LEU I 575 " --> pdb=" O SER I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 593 Processing helix chain 'I' and resid 596 through 608 removed outlier: 4.036A pdb=" N LEU I 600 " --> pdb=" O ASN I 596 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL I 608 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 625 removed outlier: 3.966A pdb=" N GLN I 618 " --> pdb=" O VAL I 614 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP I 619 " --> pdb=" O ARG I 615 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE I 621 " --> pdb=" O ASN I 617 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR I 622 " --> pdb=" O GLN I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 888 removed outlier: 3.974A pdb=" N GLU I 872 " --> pdb=" O GLU I 868 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS I 873 " --> pdb=" O ARG I 869 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS I 879 " --> pdb=" O ALA I 875 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG I 886 " --> pdb=" O TRP I 882 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE I 887 " --> pdb=" O ALA I 883 " (cutoff:3.500A) Processing helix chain 'I' and resid 914 through 932 removed outlier: 3.673A pdb=" N ASN I 919 " --> pdb=" O GLU I 915 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 923 " --> pdb=" O ASN I 919 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU I 932 " --> pdb=" O THR I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 933 through 936 removed outlier: 3.971A pdb=" N GLY I 936 " --> pdb=" O LEU I 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 933 through 936' Processing helix chain 'I' and resid 980 through 988 removed outlier: 3.719A pdb=" N LEU I 984 " --> pdb=" O ALA I 980 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP I 986 " --> pdb=" O THR I 982 " (cutoff:3.500A) Processing helix chain 'I' and resid 988 through 1001 removed outlier: 3.807A pdb=" N ASN I 994 " --> pdb=" O GLU I 990 " (cutoff:3.500A) Processing helix chain 'I' and resid 1028 through 1041 removed outlier: 4.382A pdb=" N GLN I1041 " --> pdb=" O ASP I1037 " (cutoff:3.500A) Processing helix chain 'I' and resid 1042 through 1049 removed outlier: 3.654A pdb=" N LEU I1046 " --> pdb=" O ALA I1042 " (cutoff:3.500A) Processing helix chain 'I' and resid 1078 through 1082 Processing helix chain 'I' and resid 1652 through 1657 Processing helix chain 'I' and resid 1658 through 1674 removed outlier: 3.735A pdb=" N TYR I1670 " --> pdb=" O THR I1666 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG I1671 " --> pdb=" O LEU I1667 " (cutoff:3.500A) Processing helix chain 'I' and resid 1678 through 1686 removed outlier: 3.719A pdb=" N ALA I1684 " --> pdb=" O ARG I1680 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS I1686 " --> pdb=" O ALA I1682 " (cutoff:3.500A) Processing helix chain 'I' and resid 1692 through 1700 removed outlier: 3.841A pdb=" N LEU I1698 " --> pdb=" O LEU I1694 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU I1699 " --> pdb=" O LEU I1695 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP I1700 " --> pdb=" O HIS I1696 " (cutoff:3.500A) Processing helix chain 'I' and resid 1709 through 1712 removed outlier: 3.650A pdb=" N TYR I1712 " --> pdb=" O ALA I1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1709 through 1712' Processing helix chain 'I' and resid 1713 through 1718 Processing helix chain 'I' and resid 1723 through 1730 removed outlier: 3.605A pdb=" N MET I1730 " --> pdb=" O SER I1726 " (cutoff:3.500A) Processing helix chain 'I' and resid 1739 through 1744 Processing helix chain 'I' and resid 1753 through 1758 removed outlier: 4.071A pdb=" N ALA I1757 " --> pdb=" O LYS I1753 " (cutoff:3.500A) Processing helix chain 'I' and resid 1804 through 1823 removed outlier: 3.516A pdb=" N GLY I1816 " --> pdb=" O LEU I1812 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY I1823 " --> pdb=" O VAL I1819 " (cutoff:3.500A) Processing helix chain 'I' and resid 1833 through 1838 Processing helix chain 'I' and resid 1840 through 1852 Processing helix chain 'I' and resid 1855 through 1863 Processing helix chain 'I' and resid 1866 through 1871 Processing helix chain 'I' and resid 1925 through 1929 removed outlier: 3.628A pdb=" N GLN I1928 " --> pdb=" O GLY I1925 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET I1929 " --> pdb=" O LEU I1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1925 through 1929' Processing helix chain 'I' and resid 1933 through 1982 removed outlier: 3.795A pdb=" N TYR I1945 " --> pdb=" O ASN I1941 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE I1946 " --> pdb=" O LEU I1942 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS I1947 " --> pdb=" O LEU I1943 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU I1963 " --> pdb=" O ALA I1959 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG I1964 " --> pdb=" O ALA I1960 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I1965 " --> pdb=" O PHE I1961 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL I1966 " --> pdb=" O ALA I1962 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP I1967 " --> pdb=" O GLU I1963 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS I1968 " --> pdb=" O ARG I1964 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA I1978 " --> pdb=" O ARG I1974 " (cutoff:3.500A) Processing helix chain 'I' and resid 1989 through 1994 removed outlier: 3.819A pdb=" N ARG I1993 " --> pdb=" O ALA I1989 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG I1994 " --> pdb=" O GLU I1990 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1989 through 1994' Processing helix chain 'I' and resid 1995 through 1998 Processing helix chain 'I' and resid 2001 through 2011 removed outlier: 3.686A pdb=" N ILE I2006 " --> pdb=" O PRO I2002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN I2007 " --> pdb=" O GLN I2003 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N HIS I2011 " --> pdb=" O ASN I2007 " (cutoff:3.500A) Processing helix chain 'I' and resid 2028 through 2042 removed outlier: 3.696A pdb=" N GLN I2032 " --> pdb=" O ARG I2028 " (cutoff:3.500A) Processing helix chain 'I' and resid 2094 through 2108 removed outlier: 3.804A pdb=" N HIS I2100 " --> pdb=" O GLU I2096 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL I2103 " --> pdb=" O SER I2099 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP I2105 " --> pdb=" O MET I2101 " (cutoff:3.500A) Processing helix chain 'I' and resid 2113 through 2129 removed outlier: 3.614A pdb=" N VAL I2117 " --> pdb=" O SER I2113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU I2123 " --> pdb=" O ALA I2119 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR I2128 " --> pdb=" O LEU I2124 " (cutoff:3.500A) Processing helix chain 'I' and resid 2129 through 2138 Processing helix chain 'I' and resid 2148 through 2165 removed outlier: 3.737A pdb=" N CYS I2158 " --> pdb=" O SER I2154 " (cutoff:3.500A) Processing helix chain 'I' and resid 2171 through 2187 removed outlier: 3.672A pdb=" N LEU I2177 " --> pdb=" O GLN I2173 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.545A pdb=" N MET I2198 " --> pdb=" O HIS I2194 " (cutoff:3.500A) Processing helix chain 'I' and resid 2202 through 2216 removed outlier: 3.859A pdb=" N VAL I2210 " --> pdb=" O THR I2206 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN I2213 " --> pdb=" O GLU I2209 " (cutoff:3.500A) Processing helix chain 'I' and resid 2227 through 2242 removed outlier: 3.642A pdb=" N CYS I2233 " --> pdb=" O VAL I2229 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2253 removed outlier: 3.620A pdb=" N ASP I2252 " --> pdb=" O ARG I2248 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS I2253 " --> pdb=" O SER I2249 " (cutoff:3.500A) Processing helix chain 'I' and resid 2253 through 2262 removed outlier: 4.109A pdb=" N ASN I2260 " --> pdb=" O TYR I2256 " (cutoff:3.500A) Processing helix chain 'I' and resid 2271 through 2279 removed outlier: 3.520A pdb=" N ALA I2276 " --> pdb=" O PRO I2272 " (cutoff:3.500A) Processing helix chain 'I' and resid 2294 through 2306 removed outlier: 3.518A pdb=" N VAL I2298 " --> pdb=" O ASP I2294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL I2299 " --> pdb=" O LEU I2295 " (cutoff:3.500A) Processing helix chain 'I' and resid 2310 through 2315 removed outlier: 4.085A pdb=" N ALA I2315 " --> pdb=" O PRO I2311 " (cutoff:3.500A) Processing helix chain 'I' and resid 2326 through 2331 removed outlier: 3.534A pdb=" N TYR I2331 " --> pdb=" O GLY I2327 " (cutoff:3.500A) Processing helix chain 'I' and resid 2346 through 2355 removed outlier: 3.899A pdb=" N ALA I2350 " --> pdb=" O VAL I2346 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I2352 " --> pdb=" O GLU I2348 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL I2353 " --> pdb=" O ASN I2349 " (cutoff:3.500A) Processing helix chain 'I' and resid 2360 through 2364 Processing helix chain 'I' and resid 2375 through 2388 Processing helix chain 'I' and resid 2389 through 2393 Processing helix chain 'I' and resid 2418 through 2436 removed outlier: 3.810A pdb=" N MET I2423 " --> pdb=" O GLY I2419 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA I2428 " --> pdb=" O SER I2424 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG I2435 " --> pdb=" O ASP I2431 " (cutoff:3.500A) Processing helix chain 'I' and resid 2440 through 2445 Processing helix chain 'I' and resid 2448 through 2461 removed outlier: 3.708A pdb=" N ILE I2453 " --> pdb=" O GLU I2449 " (cutoff:3.500A) Processing helix chain 'I' and resid 2466 through 2471 removed outlier: 3.645A pdb=" N ILE I2470 " --> pdb=" O LEU I2466 " (cutoff:3.500A) Processing helix chain 'I' and resid 2502 through 2507 removed outlier: 3.854A 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: 3.560A pdb=" N UNK I2530 " --> pdb=" O UNK I2526 " (cutoff:3.500A) Processing helix chain 'I' and resid 2542 through 2548 removed outlier: 3.639A pdb=" N UNK I2546 " --> pdb=" O UNK I2542 " (cutoff:3.500A) Processing helix chain 'I' and resid 2551 through 2557 removed outlier: 3.760A pdb=" N UNK I2555 " --> pdb=" O UNK I2551 " (cutoff:3.500A) Processing helix chain 'I' and resid 2567 through 2581 removed outlier: 3.547A pdb=" N UNK I2578 " --> pdb=" O UNK I2574 " (cutoff:3.500A) Processing helix chain 'I' and resid 2587 through 2602 removed outlier: 3.544A pdb=" N UNK I2597 " --> pdb=" O UNK I2593 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK I2602 " --> pdb=" O UNK I2598 " (cutoff:3.500A) Processing helix chain 'I' and resid 2610 through 2618 removed outlier: 3.602A pdb=" N UNK I2617 " --> pdb=" O UNK I2613 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N UNK I2618 " --> pdb=" O UNK I2614 " (cutoff:3.500A) Processing helix chain 'I' and resid 2626 through 2641 removed outlier: 3.918A pdb=" N UNK I2630 " --> pdb=" O UNK I2626 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N UNK I2631 " --> pdb=" O UNK I2627 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK I2634 " --> pdb=" O UNK I2630 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N UNK I2635 " --> pdb=" O UNK I2631 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK I2639 " --> pdb=" O UNK I2635 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N UNK I2641 " --> pdb=" O UNK I2637 " (cutoff:3.500A) Processing helix chain 'I' and resid 2650 through 2666 Processing helix chain 'I' and resid 2677 through 2683 removed outlier: 3.971A pdb=" N UNK I2681 " --> pdb=" O UNK I2677 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N UNK I2683 " --> pdb=" O UNK I2679 " (cutoff:3.500A) Processing helix chain 'I' and resid 2751 through 2773 removed outlier: 3.888A pdb=" N PHE I2768 " --> pdb=" O GLU I2764 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP I2769 " --> pdb=" O LYS I2765 " (cutoff:3.500A) Processing helix chain 'I' and resid 2793 through 2797 removed outlier: 3.504A pdb=" N THR I2796 " --> pdb=" O PRO I2793 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE I2797 " --> pdb=" O TYR I2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2793 through 2797' Processing helix chain 'I' and resid 2809 through 2820 removed outlier: 3.841A pdb=" N ALA I2815 " --> pdb=" O GLU I2811 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET I2816 " --> pdb=" O SER I2812 " (cutoff:3.500A) Processing helix chain 'I' and resid 2868 through 2895 removed outlier: 4.045A pdb=" N MET I2874 " --> pdb=" O GLU I2870 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA I2875 " --> pdb=" O LEU I2871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU I2876 " --> pdb=" O GLN I2872 " (cutoff:3.500A) removed outlier: 4.118A 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: 4.004A pdb=" N ARG I2920 " --> pdb=" O LYS I2916 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU I2921 " --> pdb=" O ALA I2917 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU I2926 " --> pdb=" O LYS I2922 " (cutoff:3.500A) Processing helix chain 'I' and resid 2950 through 2976 removed outlier: 4.114A pdb=" N UNK I2956 " --> pdb=" O UNK I2952 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK I2968 " --> pdb=" O UNK I2964 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N UNK I2969 " --> pdb=" O UNK I2965 " (cutoff:3.500A) Processing helix chain 'I' and resid 2999 through 3016 removed outlier: 3.570A pdb=" N UNK I3004 " --> pdb=" O UNK I3000 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK I3006 " --> pdb=" O UNK I3002 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N UNK I3009 " --> pdb=" O UNK I3005 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N UNK I3010 " --> pdb=" O UNK I3006 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N UNK I3013 " --> pdb=" O UNK I3009 " (cutoff:3.500A) Processing helix chain 'I' and resid 3017 through 3022 Processing helix chain 'I' and resid 3029 through 3040 removed outlier: 3.625A pdb=" N UNK I3037 " --> pdb=" O UNK I3033 " (cutoff:3.500A) Processing helix chain 'I' and resid 3052 through 3063 removed outlier: 4.160A pdb=" N UNK I3056 " --> pdb=" O UNK I3052 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N UNK I3061 " --> pdb=" O UNK I3057 " (cutoff:3.500A) removed outlier: 4.192A 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: 4.040A pdb=" N UNK I3154 " --> pdb=" O UNK I3150 " (cutoff:3.500A) Processing helix chain 'I' and resid 3175 through 3186 removed outlier: 3.657A pdb=" N UNK I3182 " --> pdb=" O UNK I3178 " (cutoff:3.500A) Processing helix chain 'I' and resid 3198 through 3212 removed outlier: 3.615A pdb=" N UNK I3205 " --> pdb=" O UNK I3201 " (cutoff:3.500A) Processing helix chain 'I' and resid 3224 through 3230 removed outlier: 3.784A pdb=" N UNK I3228 " --> pdb=" O UNK I3224 " (cutoff:3.500A) Processing helix chain 'I' and resid 3248 through 3254 removed outlier: 3.516A pdb=" N UNK I3252 " --> pdb=" O UNK I3248 " (cutoff:3.500A) Processing helix chain 'I' and resid 3271 through 3280 Processing helix chain 'I' and resid 3280 through 3285 removed outlier: 3.983A pdb=" N UNK I3284 " --> pdb=" O UNK I3280 " (cutoff:3.500A) Processing helix chain 'I' and resid 3305 through 3310 Processing helix chain 'I' and resid 3316 through 3331 removed outlier: 3.907A pdb=" N UNK I3323 " --> pdb=" O UNK I3319 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N UNK I3324 " --> pdb=" O UNK I3320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N UNK I3330 " --> pdb=" O UNK I3326 " (cutoff:3.500A) Processing helix chain 'I' and resid 3344 through 3349 removed outlier: 3.526A pdb=" N UNK I3348 " --> pdb=" O UNK I3344 " (cutoff:3.500A) Processing helix chain 'I' and resid 3361 through 3388 Processing helix chain 'I' and resid 3399 through 3409 removed outlier: 3.789A pdb=" N UNK I3405 " --> pdb=" O UNK I3401 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N UNK I3407 " --> pdb=" O UNK I3403 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK I3409 " --> pdb=" O UNK I3405 " (cutoff:3.500A) Processing helix chain 'I' and resid 3410 through 3425 removed outlier: 4.030A pdb=" N UNK I3416 " --> pdb=" O UNK I3412 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N UNK I3420 " --> pdb=" O UNK I3416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N UNK I3421 " --> pdb=" O UNK I3417 " (cutoff:3.500A) Processing helix chain 'I' and resid 3434 through 3443 removed outlier: 4.016A pdb=" N UNK I3439 " --> pdb=" O UNK I3435 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N UNK I3440 " --> pdb=" O UNK I3436 " (cutoff:3.500A) Processing helix chain 'I' and resid 3445 through 3450 Processing helix chain 'I' and resid 3461 through 3468 removed outlier: 3.516A pdb=" N UNK I3468 " --> pdb=" O UNK I3464 " (cutoff:3.500A) Processing helix chain 'I' and resid 3518 through 3521 Processing helix chain 'I' and resid 3522 through 3529 removed outlier: 3.738A pdb=" N UNK I3529 " --> pdb=" O UNK I3525 " (cutoff:3.500A) Processing helix chain 'I' and resid 3541 through 3547 removed outlier: 3.524A 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: 3.593A pdb=" N UNK I3579 " --> pdb=" O UNK I3575 " (cutoff:3.500A) Processing helix chain 'I' and resid 3589 through 3611 removed outlier: 4.029A pdb=" N UNK I3595 " --> pdb=" O UNK I3591 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N UNK I3598 " --> pdb=" O UNK I3594 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK I3600 " --> pdb=" O UNK I3596 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK I3601 " --> pdb=" O UNK I3597 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK I3610 " --> pdb=" O UNK I3606 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N UNK I3611 " --> pdb=" O UNK I3607 " (cutoff:3.500A) Processing helix chain 'I' and resid 3645 through 3656 removed outlier: 3.801A pdb=" N GLU I3655 " --> pdb=" O ASN I3651 " (cutoff:3.500A) Processing helix chain 'I' and resid 3657 through 3661 Processing helix chain 'I' and resid 3671 through 3680 removed outlier: 3.561A pdb=" N ASP I3676 " --> pdb=" O ARG I3672 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU I3677 " --> pdb=" O MET I3673 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER I3678 " --> pdb=" O ILE I3674 " (cutoff:3.500A) Processing helix chain 'I' and resid 3696 through 3711 removed outlier: 3.583A pdb=" N ALA I3709 " --> pdb=" O PHE I3705 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR I3711 " --> pdb=" O ARG I3707 " (cutoff:3.500A) Processing helix chain 'I' and resid 3719 through 3738 removed outlier: 3.607A pdb=" N GLU I3736 " --> pdb=" O SER I3732 " (cutoff:3.500A) Processing helix chain 'I' and resid 3754 through 3770 removed outlier: 4.157A pdb=" N LYS I3760 " --> pdb=" O LYS I3756 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG I3762 " --> pdb=" O MET I3758 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU I3763 " --> pdb=" O GLU I3759 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN I3767 " --> pdb=" O LEU I3763 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER I3768 " --> pdb=" O LEU I3764 " (cutoff:3.500A) Processing helix chain 'I' and resid 3771 through 3784 removed outlier: 4.278A pdb=" N GLU I3777 " --> pdb=" O ARG I3773 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET I3778 " --> pdb=" O GLY I3774 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL I3779 " --> pdb=" O ALA I3775 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU I3780 " --> pdb=" O ALA I3776 " (cutoff:3.500A) Processing helix chain 'I' and resid 3791 through 3803 removed outlier: 3.897A pdb=" N LYS I3799 " --> pdb=" O SER I3795 " (cutoff:3.500A) Processing helix chain 'I' and resid 3809 through 3824 Processing helix chain 'I' and resid 3828 through 3838 removed outlier: 3.650A pdb=" N ILE I3832 " --> pdb=" O PHE I3828 " (cutoff:3.500A) Processing helix chain 'I' and resid 3843 through 3856 removed outlier: 3.553A pdb=" N LYS I3852 " --> pdb=" O GLU I3848 " (cutoff:3.500A) Processing helix chain 'I' and resid 3877 through 3891 removed outlier: 4.484A pdb=" N ASP I3883 " --> pdb=" O GLU I3879 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG I3886 " --> pdb=" O GLN I3882 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE I3887 " --> pdb=" O ASP I3883 " (cutoff:3.500A) Processing helix chain 'I' and resid 3898 through 3903 Processing helix chain 'I' and resid 3914 through 3932 removed outlier: 4.116A pdb=" N CYS I3918 " --> pdb=" O ASN I3914 " (cutoff:3.500A) Processing helix chain 'I' and resid 3932 through 3937 removed outlier: 3.875A pdb=" N TYR I3936 " --> pdb=" O ASP I3932 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR I3937 " --> pdb=" O PHE I3933 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3932 through 3937' Processing helix chain 'I' and resid 3944 through 3967 removed outlier: 3.639A pdb=" N LYS I3953 " --> pdb=" O ARG I3949 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA I3954 " --> pdb=" O ASN I3950 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET I3955 " --> pdb=" O PHE I3951 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN I3960 " --> pdb=" O SER I3956 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU I3967 " --> pdb=" O ASN I3963 " (cutoff:3.500A) Processing helix chain 'I' and resid 3973 through 3983 Processing helix chain 'I' and resid 3984 through 4005 removed outlier: 3.740A pdb=" N ALA I3988 " --> pdb=" O ARG I3984 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY I3991 " --> pdb=" O ASP I3987 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE I3992 " --> pdb=" O ALA I3988 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU I3993 " --> pdb=" O VAL I3989 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS I3994 " --> pdb=" O VAL I3990 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS I3998 " --> pdb=" O HIS I3994 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET I3999 " --> pdb=" O VAL I3995 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET I4000 " --> pdb=" O PHE I3996 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA I4004 " --> pdb=" O MET I4000 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN I4005 " --> pdb=" O MET I4001 " (cutoff:3.500A) Processing helix chain 'I' and resid 4006 through 4008 No H-bonds generated for 'chain 'I' and resid 4006 through 4008' Processing helix chain 'I' and resid 4009 through 4030 removed outlier: 4.114A pdb=" N MET I4026 " --> pdb=" O ASP I4022 " (cutoff:3.500A) Processing helix chain 'I' and resid 4039 through 4051 Processing helix chain 'I' and resid 4051 through 4063 Processing helix chain 'I' and resid 4067 through 4072 Processing helix chain 'I' and resid 4074 through 4081 removed outlier: 4.536A pdb=" N TYR I4080 " --> pdb=" O ALA I4076 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL I4081 " --> pdb=" O PHE I4077 " (cutoff:3.500A) Processing helix chain 'I' and resid 4090 through 4100 removed outlier: 3.763A pdb=" N ASP I4098 " --> pdb=" O GLN I4094 " (cutoff:3.500A) Processing helix chain 'I' and resid 4104 through 4114 Processing helix chain 'I' and resid 4124 through 4128 Processing helix chain 'I' and resid 4132 through 4154 removed outlier: 3.551A pdb=" N ALA I4136 " --> pdb=" O PHE I4132 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP I4138 " --> pdb=" O GLU I4134 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE I4139 " --> pdb=" O PRO I4135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE I4141 " --> pdb=" O ARG I4137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU I4146 " --> pdb=" O ASN I4142 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU I4152 " --> pdb=" O THR I4148 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL I4154 " --> pdb=" O LEU I4150 " (cutoff:3.500A) Processing helix chain 'I' and resid 4157 through 4167 Processing helix chain 'I' and resid 4167 through 4175 removed outlier: 3.735A pdb=" N LEU I4171 " --> pdb=" O ALA I4167 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE I4174 " --> pdb=" O ILE I4170 " (cutoff:3.500A) Processing helix chain 'I' and resid 4198 through 4206 Processing helix chain 'I' and resid 4207 through 4224 removed outlier: 4.096A pdb=" N VAL I4222 " --> pdb=" O ILE I4218 " (cutoff:3.500A) Processing helix chain 'I' and resid 4228 through 4251 removed outlier: 4.083A pdb=" N PHE I4234 " --> pdb=" O LYS I4230 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE I4243 " --> pdb=" O GLU I4239 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN I4250 " --> pdb=" O GLN I4246 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE I4251 " --> pdb=" O ILE I4247 " (cutoff:3.500A) Processing helix chain 'I' and resid 4542 through 4558 removed outlier: 3.996A pdb=" N TYR I4554 " --> pdb=" O LYS I4550 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN I4558 " --> pdb=" O TYR I4554 " (cutoff:3.500A) Processing helix chain 'I' and resid 4558 through 4576 removed outlier: 3.682A pdb=" N ALA I4570 " --> pdb=" O ALA I4566 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE I4571 " --> pdb=" O LEU I4567 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA I4572 " --> pdb=" O PHE I4568 " (cutoff:3.500A) Processing helix chain 'I' and resid 4641 through 4665 removed outlier: 3.606A pdb=" N ALA I4654 " --> pdb=" O HIS I4650 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE I4655 " --> pdb=" O THR I4651 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE I4659 " --> pdb=" O PHE I4655 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY I4660 " --> pdb=" O LEU I4656 " (cutoff:3.500A) Processing helix chain 'I' and resid 4667 through 4683 removed outlier: 3.866A pdb=" N ALA I4678 " --> pdb=" O GLU I4674 " (cutoff:3.500A) Processing helix chain 'I' and resid 4697 through 4702 Processing helix chain 'I' and resid 4703 through 4708 removed outlier: 3.707A pdb=" N LEU I4706 " --> pdb=" O ARG I4703 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN I4707 " --> pdb=" O LEU I4704 " (cutoff:3.500A) Processing helix chain 'I' and resid 4719 through 4728 Processing helix chain 'I' and resid 4733 through 4741 Processing helix chain 'I' and resid 4748 through 4753 Processing helix chain 'I' and resid 4772 through 4786 removed outlier: 3.794A pdb=" N PHE I4780 " --> pdb=" O GLN I4776 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY I4781 " --> pdb=" O ILE I4777 " (cutoff:3.500A) 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: 3.599A pdb=" N TRP I4794 " --> pdb=" O LEU I4790 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL I4797 " --> pdb=" O GLY I4793 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET I4798 " --> pdb=" O TRP I4794 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER I4799 " --> pdb=" O TYR I4795 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU I4800 " --> pdb=" O MET I4796 " (cutoff:3.500A) Processing helix chain 'I' and resid 4812 through 4819 removed outlier: 3.579A pdb=" N ILE I4816 " --> pdb=" O HIS I4812 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA I4817 " --> pdb=" O LEU I4813 " (cutoff:3.500A) Processing helix chain 'I' and resid 4820 through 4832 removed outlier: 3.979A pdb=" N ILE I4826 " --> pdb=" O THR I4822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL I4830 " --> pdb=" O ILE I4826 " (cutoff:3.500A) Processing helix chain 'I' and resid 4833 through 4858 removed outlier: 4.258A pdb=" N MET I4839 " --> pdb=" O LYS I4835 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA I4845 " --> pdb=" O VAL I4841 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I4848 " --> pdb=" O LEU I4844 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I4853 " --> pdb=" O TYR I4849 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL I4854 " --> pdb=" O LEU I4850 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA I4855 " --> pdb=" O TYR I4851 " (cutoff:3.500A) Processing helix chain 'I' and resid 4878 through 4889 removed outlier: 3.754A pdb=" N PHE I4885 " --> pdb=" O THR I4881 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS I4886 " --> pdb=" O CYS I4882 " (cutoff:3.500A) Processing helix chain 'I' and resid 4909 through 4922 removed outlier: 3.726A pdb=" N ARG I4913 " --> pdb=" O TYR I4909 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL I4914 " --> pdb=" O GLU I4910 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL I4915 " --> pdb=" O LEU I4911 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE I4918 " --> pdb=" O VAL I4914 " (cutoff:3.500A) Processing helix chain 'I' and resid 4926 through 4957 removed outlier: 3.773A pdb=" N ILE I4936 " --> pdb=" O ILE I4932 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG I4944 " --> pdb=" O PHE I4940 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS I4951 " --> pdb=" O GLN I4947 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU I4952 " --> pdb=" O GLU I4948 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP I4953 " --> pdb=" O GLN I4949 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET I4954 " --> pdb=" O VAL I4950 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU I4955 " --> pdb=" O LYS I4951 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS I4957 " --> pdb=" O ASP I4953 " (cutoff:3.500A) Processing helix chain 'I' and resid 4965 through 4970 removed outlier: 3.578A pdb=" N THR I4970 " --> pdb=" O ASP I4966 " (cutoff:3.500A) Processing helix chain 'I' and resid 4973 through 4981 Processing helix chain 'I' and resid 4986 through 4997 removed outlier: 3.578A pdb=" N PHE I4990 " --> pdb=" O ALA I4986 " (cutoff:3.500A) Processing helix chain 'I' and resid 5006 through 5017 Processing helix chain 'J' and resid 38 through 43 Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.864A pdb=" N GLY J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.794A pdb=" N VAL J 80 " --> pdb=" O THR J 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.523A pdb=" N VAL A 101 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.732A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER B 72 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 106 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.732A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AA6, first strand: chain 'B' and resid 300 through 302 removed outlier: 3.814A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 292 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 223 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 389 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 230 through 233 removed outlier: 3.625A pdb=" N THR B 232 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 314 through 316 Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 359 Processing sheet with id=AB1, first strand: chain 'B' and resid 634 through 639 removed outlier: 3.816A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.603A pdb=" N THR B 642 " --> pdb=" O PHE B 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 767 through 768 removed outlier: 3.537A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 744 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS B 746 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU B 665 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 686 through 687 Processing sheet with id=AB5, first strand: chain 'B' and resid 839 through 840 removed outlier: 3.539A pdb=" N LEU B 839 " --> pdb=" O GLY B1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B1200 " --> pdb=" O LEU B 839 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 839 through 840 removed outlier: 3.539A pdb=" N LEU B 839 " --> pdb=" O GLY B1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B1200 " --> pdb=" O LEU B 839 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG B1087 " --> pdb=" O GLU B1224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.689A 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 940 through 941 Processing sheet with id=AB9, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.517A pdb=" N GLY B1103 " --> pdb=" O VAL B1191 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B1073 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 5.163A 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: 3.711A pdb=" N GLU B1256 " --> pdb=" O ALA B1273 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1459 through 1463 removed outlier: 3.674A pdb=" N UNK B1287 " --> pdb=" O UNK B1460 " (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 1734 through 1736 Processing sheet with id=AC5, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AC6, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AC7, first strand: chain 'E' and resid 48 through 51 removed outlier: 3.733A pdb=" N LEU E 37 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU E 108 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER E 72 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA E 106 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 48 through 51 removed outlier: 3.733A pdb=" N LEU E 37 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU E 19 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AD1, first strand: chain 'E' and resid 300 through 302 removed outlier: 3.814A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 292 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE E 282 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE E 223 " --> pdb=" O PHE E 389 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 389 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 230 through 233 removed outlier: 3.625A pdb=" N THR E 232 " --> pdb=" O TYR E 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 314 through 316 Processing sheet with id=AD4, first strand: chain 'E' and resid 356 through 359 Processing sheet with id=AD5, first strand: chain 'E' and resid 634 through 639 removed outlier: 3.816A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E1646 " --> pdb=" O ILE E1641 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 782 through 783 removed outlier: 3.604A pdb=" N THR E 642 " --> pdb=" O PHE E 783 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 767 through 768 removed outlier: 3.537A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 744 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 666 " --> pdb=" O VAL E 744 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS E 746 " --> pdb=" O PHE E 664 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU E 665 " --> pdb=" O LEU E 792 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 686 through 687 Processing sheet with id=AD9, first strand: chain 'E' and resid 839 through 840 removed outlier: 3.538A pdb=" N LEU E 839 " --> pdb=" O GLY E1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E1200 " --> pdb=" O LEU E 839 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 839 through 840 removed outlier: 3.538A pdb=" N LEU E 839 " --> pdb=" O GLY E1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E1200 " --> pdb=" O LEU E 839 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG E1087 " --> pdb=" O GLU E1224 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.688A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 940 through 941 Processing sheet with id=AE4, first strand: chain 'E' and resid 1136 through 1138 removed outlier: 3.516A pdb=" N GLY E1103 " --> pdb=" O VAL E1191 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E1073 " --> pdb=" O LEU E1194 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 1255 through 1259 removed outlier: 3.710A pdb=" N GLU E1256 " --> pdb=" O ALA E1273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 1459 through 1463 removed outlier: 3.720A pdb=" N UNK E1287 " --> pdb=" O UNK E1460 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 1293 through 1294 Processing sheet with id=AE8, first strand: chain 'E' and resid 1515 through 1516 Processing sheet with id=AE9, first strand: chain 'E' and resid 1734 through 1736 Processing sheet with id=AF1, first strand: chain 'E' and resid 4178 through 4184 Processing sheet with id=AF2, first strand: chain 'E' and resid 4580 through 4583 Processing sheet with id=AF3, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AF4, first strand: chain 'F' and resid 28 through 30 removed outlier: 3.522A pdb=" N VAL F 101 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 48 through 51 removed outlier: 3.733A pdb=" N LEU G 37 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU G 108 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER G 72 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA G 106 " --> pdb=" O SER G 72 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 48 through 51 removed outlier: 3.733A pdb=" N LEU G 37 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU G 19 " --> pdb=" O ILE G 205 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 181 through 184 Processing sheet with id=AF8, first strand: chain 'G' and resid 300 through 302 removed outlier: 3.813A pdb=" N VAL G 300 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 292 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE G 282 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE G 223 " --> pdb=" O PHE G 389 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE G 389 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 230 through 233 removed outlier: 3.626A pdb=" N THR G 232 " --> pdb=" O TYR G 246 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 314 through 316 Processing sheet with id=AG2, first strand: chain 'G' and resid 356 through 359 Processing sheet with id=AG3, first strand: chain 'G' and resid 634 through 639 removed outlier: 3.817A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G1646 " --> pdb=" O ILE G1641 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 782 through 783 removed outlier: 3.604A pdb=" N THR G 642 " --> pdb=" O PHE G 783 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 767 through 768 removed outlier: 3.537A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 744 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 666 " --> pdb=" O VAL G 744 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS G 746 " --> pdb=" O PHE G 664 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU G 665 " --> pdb=" O LEU G 792 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 686 through 687 Processing sheet with id=AG7, first strand: chain 'G' and resid 839 through 840 removed outlier: 3.539A pdb=" N LEU G 839 " --> pdb=" O GLY G1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G1200 " --> pdb=" O LEU G 839 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 839 through 840 removed outlier: 3.539A pdb=" N LEU G 839 " --> pdb=" O GLY G1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G1200 " --> pdb=" O LEU G 839 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG G1087 " --> pdb=" O GLU G1224 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.688A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'G' and resid 940 through 941 Processing sheet with id=AH2, first strand: chain 'G' and resid 1136 through 1138 removed outlier: 3.516A pdb=" N GLY G1103 " --> pdb=" O VAL G1191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG G1073 " --> pdb=" O LEU G1194 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 1255 through 1259 removed outlier: 3.712A pdb=" N GLU G1256 " --> pdb=" O ALA G1273 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 1459 through 1463 removed outlier: 3.627A pdb=" N UNK G1287 " --> pdb=" O UNK G1460 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 1293 through 1294 Processing sheet with id=AH6, first strand: chain 'G' and resid 1734 through 1736 Processing sheet with id=AH7, first strand: chain 'G' and resid 4178 through 4184 Processing sheet with id=AH8, first strand: chain 'G' and resid 4580 through 4583 Processing sheet with id=AH9, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AI1, first strand: chain 'H' and resid 28 through 30 removed outlier: 3.522A pdb=" N VAL H 101 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.732A pdb=" N LEU I 37 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU I 22 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU I 108 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER I 72 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA I 106 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.732A pdb=" N LEU I 37 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU I 22 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU I 19 " --> pdb=" O ILE I 205 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 181 through 184 Processing sheet with id=AI5, first strand: chain 'I' and resid 300 through 302 removed outlier: 3.813A pdb=" N VAL I 300 " --> pdb=" O ALA I 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 292 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE I 282 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE I 223 " --> pdb=" O PHE I 389 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE I 389 " --> pdb=" O PHE I 223 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 230 through 233 removed outlier: 3.625A pdb=" N THR I 232 " --> pdb=" O TYR I 246 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 314 through 316 Processing sheet with id=AI8, first strand: chain 'I' and resid 356 through 359 Processing sheet with id=AI9, first strand: chain 'I' and resid 634 through 639 removed outlier: 3.816A pdb=" N GLN I 634 " --> pdb=" O HIS I1640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG I1646 " --> pdb=" O ILE I1641 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 782 through 783 removed outlier: 3.603A pdb=" N THR I 642 " --> pdb=" O PHE I 783 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 767 through 768 removed outlier: 3.537A pdb=" N ASP I 742 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL I 744 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL I 666 " --> pdb=" O VAL I 744 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS I 746 " --> pdb=" O PHE I 664 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU I 665 " --> pdb=" O LEU I 792 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 686 through 687 Processing sheet with id=AJ4, first strand: chain 'I' and resid 839 through 840 removed outlier: 3.538A pdb=" N LEU I 839 " --> pdb=" O GLY I1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY I1200 " --> pdb=" O LEU I 839 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'I' and resid 839 through 840 removed outlier: 3.538A pdb=" N LEU I 839 " --> pdb=" O GLY I1200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY I1200 " --> pdb=" O LEU I 839 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG I1087 " --> pdb=" O GLU I1224 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 892 through 893 removed outlier: 6.687A pdb=" N THR I 892 " --> pdb=" O HIS I 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'I' and resid 940 through 941 Processing sheet with id=AJ8, first strand: chain 'I' and resid 1136 through 1138 removed outlier: 3.516A pdb=" N GLY I1103 " --> pdb=" O VAL I1191 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG I1073 " --> pdb=" O LEU I1194 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE I1074 " --> pdb=" O SER I1239 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'I' and resid 1255 through 1259 removed outlier: 3.710A pdb=" N GLU I1256 " --> pdb=" O ALA I1273 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'I' and resid 1459 through 1463 removed outlier: 3.761A pdb=" N UNK I1287 " --> pdb=" O UNK I1460 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 1293 through 1294 Processing sheet with id=AK3, first strand: chain 'I' and resid 1515 through 1516 Processing sheet with id=AK4, first strand: chain 'I' and resid 1734 through 1736 Processing sheet with id=AK5, first strand: chain 'I' and resid 4178 through 4184 Processing sheet with id=AK6, first strand: chain 'I' and resid 4580 through 4583 Processing sheet with id=AK7, first strand: chain 'J' and resid 21 through 23 Processing sheet with id=AK8, first strand: chain 'J' and resid 28 through 30 removed outlier: 3.524A pdb=" N VAL J 101 " --> pdb=" O ALA J 72 " (cutoff:3.500A) 4977 hydrogen bonds defined for protein. 14454 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: -1470.42 Time building geometry restraints manager: 40.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 35507 1.33 - 1.45: 21205 1.45 - 1.58: 65280 1.58 - 1.70: 0 1.70 - 1.82: 1020 Bond restraints: 123012 Sorted by residual: bond pdb=" C ARG G4175 " pdb=" N PRO G4176 " ideal model delta sigma weight residual 1.337 1.375 -0.038 1.24e-02 6.50e+03 9.24e+00 bond pdb=" C ARG I4175 " pdb=" N PRO I4176 " ideal model delta sigma weight residual 1.337 1.374 -0.037 1.24e-02 6.50e+03 9.05e+00 bond pdb=" C ARG B4175 " pdb=" N PRO B4176 " ideal model delta sigma weight residual 1.337 1.374 -0.037 1.24e-02 6.50e+03 9.03e+00 bond pdb=" C ARG E4175 " pdb=" N PRO E4176 " ideal model delta sigma weight residual 1.337 1.374 -0.037 1.24e-02 6.50e+03 8.70e+00 bond pdb=" N VAL G4838 " pdb=" CA VAL G4838 " ideal model delta sigma weight residual 1.460 1.497 -0.036 1.26e-02 6.30e+03 8.37e+00 ... (remaining 123007 not shown) Histogram of bond angle deviations from ideal: 96.64 - 105.01: 2340 105.01 - 113.37: 68402 113.37 - 121.74: 66933 121.74 - 130.10: 29309 130.10 - 138.47: 736 Bond angle restraints: 167720 Sorted by residual: angle pdb=" N PRO G4872 " pdb=" CA PRO G4872 " pdb=" C PRO G4872 " ideal model delta sigma weight residual 113.53 103.38 10.15 1.39e+00 5.18e-01 5.33e+01 angle pdb=" N PRO E4872 " pdb=" CA PRO E4872 " pdb=" C PRO E4872 " ideal model delta sigma weight residual 113.53 103.50 10.03 1.39e+00 5.18e-01 5.20e+01 angle pdb=" N PRO I4872 " pdb=" CA PRO I4872 " pdb=" C PRO I4872 " ideal model delta sigma weight residual 113.53 103.51 10.02 1.39e+00 5.18e-01 5.20e+01 angle pdb=" N PRO B4872 " pdb=" CA PRO B4872 " pdb=" C PRO B4872 " ideal model delta sigma weight residual 113.53 103.55 9.98 1.39e+00 5.18e-01 5.15e+01 angle pdb=" N SER H 8 " pdb=" CA SER H 8 " pdb=" C SER H 8 " ideal model delta sigma weight residual 113.25 120.54 -7.29 1.30e+00 5.92e-01 3.14e+01 ... (remaining 167715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 70011 16.10 - 32.19: 2572 32.19 - 48.29: 692 48.29 - 64.39: 53 64.39 - 80.48: 96 Dihedral angle restraints: 73424 sinusoidal: 23656 harmonic: 49768 Sorted by residual: dihedral pdb=" CA GLY G2343 " pdb=" C GLY G2343 " pdb=" N GLU G2344 " pdb=" CA GLU G2344 " ideal model delta harmonic sigma weight residual -180.00 -123.55 -56.45 0 5.00e+00 4.00e-02 1.27e+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 -123.60 -56.40 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA GLY I2343 " pdb=" C GLY I2343 " pdb=" N GLU I2344 " pdb=" CA GLU I2344 " ideal model delta harmonic sigma weight residual -180.00 -123.61 -56.39 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 73421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 17377 0.077 - 0.155: 2003 0.155 - 0.232: 183 0.232 - 0.310: 25 0.310 - 0.387: 12 Chirality restraints: 19600 Sorted by residual: chirality pdb=" CB ILE B 826 " pdb=" CA ILE B 826 " pdb=" CG1 ILE B 826 " pdb=" CG2 ILE B 826 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE G 826 " pdb=" CA ILE G 826 " pdb=" CG1 ILE G 826 " pdb=" CG2 ILE G 826 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB ILE E 826 " pdb=" CA ILE E 826 " pdb=" CG1 ILE E 826 " pdb=" CG2 ILE E 826 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 19597 not shown) Planarity restraints: 22092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E4666 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO E4667 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO E4667 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E4667 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B4666 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO B4667 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO B4667 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B4667 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I4666 " -0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO I4667 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO I4667 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO I4667 " -0.058 5.00e-02 4.00e+02 ... (remaining 22089 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 12 2.08 - 2.78: 29647 2.78 - 3.49: 166411 3.49 - 4.19: 286283 4.19 - 4.90: 468806 Nonbonded interactions: 951159 Sorted by model distance: nonbonded pdb=" O UNK I3557 " pdb=" CB UNK I3561 " model vdw 1.373 3.440 nonbonded pdb=" O UNK E3557 " pdb=" CB UNK E3561 " model vdw 1.373 3.440 nonbonded pdb=" O UNK G3557 " pdb=" CB UNK G3561 " model vdw 1.373 3.440 nonbonded pdb=" O UNK B3557 " pdb=" CB UNK B3561 " model vdw 1.373 3.440 nonbonded pdb=" CB UNK G1297 " pdb=" O UNK G1452 " model vdw 1.374 3.440 ... (remaining 951154 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 17.160 Check model and map are aligned: 1.260 Set scattering table: 0.790 Process input model: 314.180 Find NCS groups from input model: 6.310 Set up NCS constraints: 0.570 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3284 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 0.069 123012 Z= 0.343 Angle : 1.022 13.016 167720 Z= 0.561 Chirality : 0.050 0.387 19600 Planarity : 0.007 0.107 22092 Dihedral : 10.482 80.483 41064 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.69 % Favored : 88.16 % Rotamer: Outliers : 0.46 % Allowed : 2.67 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.56 % 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: -4.60 (0.06), residues: 13356 helix: -3.13 (0.05), residues: 5328 sheet: -2.79 (0.14), residues: 1052 loop : -3.07 (0.06), residues: 6976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP I5019 HIS 0.012 0.002 HIS A 87 PHE 0.033 0.003 PHE E1748 TYR 0.036 0.003 TYR I4863 ARG 0.011 0.001 ARG E 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 11 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.3253 time to fit residues: 3.7663 Evaluate side-chains 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.073 Evaluate side-chains 464 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 452 time to evaluate : 2.225 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: 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 2440 MET cc_start: 0.3668 (mmp) cc_final: 0.3466 (mmp) REVERT: B 2874 MET cc_start: -0.1608 (mtp) cc_final: -0.2476 (mtt) REVERT: B 3881 THR cc_start: 0.6151 (t) cc_final: 0.5195 (t) REVERT: B 3916 ILE cc_start: 0.6631 (mt) cc_final: 0.6422 (mm) REVERT: B 3920 VAL cc_start: 0.8182 (t) cc_final: 0.7782 (t) REVERT: B 4567 LEU cc_start: 0.6261 (tp) cc_final: 0.5867 (tp) REVERT: B 4769 MET cc_start: 0.5854 (ptm) cc_final: 0.3761 (pmm) REVERT: B 4992 LEU cc_start: 0.6004 (tm) cc_final: 0.5761 (tm) outliers start: 12 outliers final: 3 residues processed: 464 average time/residue: 0.3655 time to fit residues: 259.0436 Evaluate side-chains 246 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 243 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 0.0070 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 224 HIS ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS B 383 HIS B 405 HIS ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B1660 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1691 GLN B1775 HIS B2005 GLN B2011 HIS B2100 HIS B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2169 GLN B2884 ASN ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3830 GLN B3882 GLN ** B3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS B4037 ASN ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 ASN ** B4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4142 ASN B4728 HIS B4833 ASN B4886 HIS B5003 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3319 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 123012 Z= 0.188 Angle : 0.735 12.447 167720 Z= 0.376 Chirality : 0.041 0.285 19600 Planarity : 0.006 0.083 22092 Dihedral : 6.311 52.201 18056 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.57 % Favored : 89.34 % Rotamer: Outliers : 0.27 % Allowed : 2.98 % Favored : 96.75 % 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: -3.62 (0.06), residues: 13356 helix: -2.05 (0.06), residues: 5772 sheet: -2.28 (0.15), residues: 1040 loop : -2.75 (0.07), residues: 6544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B3935 HIS 0.008 0.001 HIS I1775 PHE 0.025 0.002 PHE G3962 TYR 0.060 0.002 TYR I4580 ARG 0.017 0.001 ARG B4159 *********************** 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 : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.3628 time to fit residues: 2.3313 Evaluate side-chains 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.073 Evaluate side-chains 363 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 356 time to evaluate : 2.217 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: B 961 MET cc_start: -0.0634 (mmt) cc_final: -0.0976 (mmt) REVERT: B 2874 MET cc_start: -0.2340 (mtp) cc_final: -0.3190 (mtp) REVERT: B 3723 MET cc_start: 0.7724 (mpp) cc_final: 0.7082 (mmm) REVERT: B 3920 VAL cc_start: 0.7340 (t) cc_final: 0.7126 (t) REVERT: B 4233 LEU cc_start: 0.7260 (pp) cc_final: 0.7013 (pp) REVERT: B 4676 GLU cc_start: 0.6555 (pt0) cc_final: 0.6292 (pt0) REVERT: B 4726 ASP cc_start: 0.6031 (m-30) cc_final: 0.5460 (m-30) REVERT: B 4769 MET cc_start: 0.5861 (ptm) cc_final: 0.3785 (pmm) REVERT: B 4816 ILE cc_start: 0.6749 (mt) cc_final: 0.5799 (mm) REVERT: B 4839 MET cc_start: 0.5488 (ttt) cc_final: 0.5126 (ttt) REVERT: B 4938 ASP cc_start: 0.5168 (m-30) cc_final: 0.4968 (m-30) REVERT: B 4991 PHE cc_start: 0.4916 (t80) cc_final: 0.4622 (t80) REVERT: B 4992 LEU cc_start: 0.7332 (tt) cc_final: 0.6866 (tp) outliers start: 7 outliers final: 1 residues processed: 360 average time/residue: 0.3274 time to fit residues: 188.9162 Evaluate side-chains 248 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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: 40.0000 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 0.0170 chunk 35 optimal weight: 0.0170 chunk 27 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 overall best weight: 4.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 32 GLN B 105 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN ** B1660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1663 HIS ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2036 GLN B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3882 GLN ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4130 ASN B4133 GLN ** B4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4812 HIS B5031 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3396 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 123012 Z= 0.262 Angle : 0.936 21.783 167720 Z= 0.469 Chirality : 0.053 1.118 19600 Planarity : 0.008 0.109 22092 Dihedral : 6.365 47.721 18056 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.74 % Favored : 88.05 % Rotamer: Outliers : 0.77 % Allowed : 3.95 % Favored : 95.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -3.61 (0.06), residues: 13356 helix: -1.93 (0.06), residues: 5748 sheet: -2.23 (0.16), residues: 1020 loop : -2.86 (0.07), residues: 6588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP I1626 HIS 0.046 0.004 HIS B3994 PHE 0.056 0.004 PHE B4163 TYR 0.056 0.005 TYR G5032 ARG 0.044 0.002 ARG G4734 *********************** 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 6 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.3696 time to fit residues: 2.3822 Evaluate side-chains 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.086 Evaluate side-chains 328 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 308 time to evaluate : 2.244 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: B 941 MET cc_start: -0.0765 (tpp) cc_final: -0.3324 (mtm) REVERT: B 1636 MET cc_start: 0.3361 (ppp) cc_final: 0.3155 (ppp) REVERT: B 2790 MET cc_start: -0.1649 (ttt) cc_final: -0.2074 (ttm) REVERT: B 2874 MET cc_start: -0.2544 (mtp) cc_final: -0.3147 (mtt) REVERT: B 3723 MET cc_start: 0.8153 (mpp) cc_final: 0.7575 (mmm) REVERT: B 3783 ILE cc_start: 0.7118 (mt) cc_final: 0.6789 (mt) REVERT: B 3962 PHE cc_start: 0.5989 (m-80) cc_final: 0.4875 (m-10) REVERT: B 4000 MET cc_start: 0.4871 (ttp) cc_final: 0.4589 (ttp) REVERT: B 4045 VAL cc_start: 0.7873 (t) cc_final: 0.7497 (t) REVERT: B 4058 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7535 (tp) REVERT: B 4769 MET cc_start: 0.5850 (ptm) cc_final: 0.3829 (pmm) REVERT: B 4796 MET cc_start: 0.6906 (tpt) cc_final: 0.6186 (tpt) REVERT: B 4816 ILE cc_start: 0.7127 (mt) cc_final: 0.6747 (mm) REVERT: B 4923 PHE cc_start: 0.6102 (OUTLIER) cc_final: 0.5672 (m-10) REVERT: B 5012 LYS cc_start: 0.7347 (mmtm) cc_final: 0.6960 (mmtm) REVERT: B 5031 GLN cc_start: 0.5977 (OUTLIER) cc_final: 0.4712 (pp30) outliers start: 20 outliers final: 5 residues processed: 316 average time/residue: 0.3260 time to fit residues: 166.9103 Evaluate side-chains 237 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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: 50.0000 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 0.0070 chunk 34 optimal weight: 0.2980 chunk 10 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN ** B1660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1837 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN B3882 GLN ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4204 GLN B4984 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3373 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 123012 Z= 0.235 Angle : 0.895 22.437 167720 Z= 0.446 Chirality : 0.048 0.497 19600 Planarity : 0.009 0.244 22092 Dihedral : 6.356 48.734 18056 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.56 % Favored : 88.26 % Rotamer: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % 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: -3.70 (0.06), residues: 13356 helix: -2.03 (0.06), residues: 5812 sheet: -1.93 (0.16), residues: 964 loop : -2.96 (0.07), residues: 6580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP G1626 HIS 0.039 0.003 HIS G 218 PHE 0.071 0.004 PHE G4163 TYR 0.111 0.005 TYR G4560 ARG 0.083 0.002 ARG E2126 *********************** 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 : 0.084 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3767 time to fit residues: 2.0403 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.085 Evaluate side-chains 302 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 300 time to evaluate : 2.275 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: B 924 MET cc_start: -0.0890 (ptt) cc_final: -0.1166 (ptt) REVERT: B 941 MET cc_start: -0.1081 (tpp) cc_final: -0.3249 (mtm) REVERT: B 1636 MET cc_start: 0.3057 (ppp) cc_final: 0.2658 (ppp) REVERT: B 2790 MET cc_start: -0.1560 (ttt) cc_final: -0.2018 (ttm) REVERT: B 2874 MET cc_start: -0.2742 (mtp) cc_final: -0.3274 (mtt) REVERT: B 2932 MET cc_start: -0.0051 (ptt) cc_final: -0.0668 (ptm) REVERT: B 3723 MET cc_start: 0.8065 (mpp) cc_final: 0.7268 (mmm) REVERT: B 3920 VAL cc_start: 0.7401 (t) cc_final: 0.7143 (t) REVERT: B 3974 THR cc_start: 0.6124 (t) cc_final: 0.5818 (t) REVERT: B 3987 ASP cc_start: 0.5296 (t0) cc_final: 0.5056 (t0) REVERT: B 4000 MET cc_start: 0.4540 (ttp) cc_final: 0.3897 (ttp) REVERT: B 4059 LEU cc_start: 0.7098 (tp) cc_final: 0.6611 (tp) REVERT: B 4769 MET cc_start: 0.5824 (ptm) cc_final: 0.3913 (pmm) REVERT: B 4796 MET cc_start: 0.6924 (tpt) cc_final: 0.6367 (tpt) REVERT: B 4816 ILE cc_start: 0.6462 (mt) cc_final: 0.6255 (mm) REVERT: B 4839 MET cc_start: 0.4295 (ttt) cc_final: 0.4045 (ttt) REVERT: B 4989 MET cc_start: 0.4904 (mpp) cc_final: 0.4485 (mpp) REVERT: B 5012 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6924 (mmtm) outliers start: 2 outliers final: 0 residues processed: 301 average time/residue: 0.3594 time to fit residues: 176.5402 Evaluate side-chains 221 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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: 0.0270 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1837 GLN ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3771 HIS ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3882 GLN ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4130 ASN B4133 GLN B4984 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3360 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 123012 Z= 0.218 Angle : 0.858 12.975 167720 Z= 0.431 Chirality : 0.048 0.485 19600 Planarity : 0.008 0.165 22092 Dihedral : 6.302 48.538 18056 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.31 % Favored : 87.51 % Rotamer: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.85 % 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: -3.71 (0.06), residues: 13356 helix: -2.06 (0.06), residues: 5848 sheet: -1.88 (0.16), residues: 988 loop : -2.96 (0.07), residues: 6520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP G1626 HIS 0.031 0.003 HIS G 218 PHE 0.081 0.004 PHE G3962 TYR 0.051 0.004 TYR B2110 ARG 0.047 0.002 ARG E4734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.075 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2214 time to fit residues: 0.8091 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.097 Evaluate side-chains 294 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 2.293 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 924 MET cc_start: -0.0882 (ptt) cc_final: -0.1246 (ptt) REVERT: B 2874 MET cc_start: -0.2431 (mtp) cc_final: -0.3104 (mtt) REVERT: B 3723 MET cc_start: 0.8137 (mpp) cc_final: 0.7439 (mpp) REVERT: B 3751 VAL cc_start: 0.4057 (t) cc_final: 0.3729 (t) REVERT: B 4000 MET cc_start: 0.4806 (ttp) cc_final: 0.3225 (ttp) REVERT: B 4046 ASP cc_start: 0.7650 (m-30) cc_final: 0.7339 (m-30) REVERT: B 4769 MET cc_start: 0.5587 (ptm) cc_final: 0.3568 (pmm) REVERT: B 4796 MET cc_start: 0.7017 (tpt) cc_final: 0.6496 (tpt) REVERT: B 4816 ILE cc_start: 0.6431 (mt) cc_final: 0.6127 (mm) REVERT: B 4940 PHE cc_start: 0.5429 (t80) cc_final: 0.5157 (t80) REVERT: B 5012 LYS cc_start: 0.7069 (mmtm) cc_final: 0.6828 (mmtm) outliers start: 3 outliers final: 0 residues processed: 291 average time/residue: 0.3275 time to fit residues: 154.7887 Evaluate side-chains 228 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.242 ------------------------------------------------------------------------------- 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: 20.0000 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 37 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3978 GLN B3982 HIS ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4156 HIS ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4984 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3379 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 123012 Z= 0.244 Angle : 0.886 33.162 167720 Z= 0.441 Chirality : 0.049 0.534 19600 Planarity : 0.008 0.105 22092 Dihedral : 6.254 48.277 18056 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.34 % Favored : 87.45 % Rotamer: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % 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: -3.70 (0.06), residues: 13356 helix: -2.04 (0.06), residues: 5860 sheet: -1.84 (0.16), residues: 988 loop : -2.97 (0.07), residues: 6508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP I1626 HIS 0.031 0.003 HIS I 218 PHE 0.063 0.004 PHE G4163 TYR 0.051 0.004 TYR G2110 ARG 0.046 0.002 ARG E4734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.077 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1948 time to fit residues: 0.7166 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.074 Evaluate side-chains 280 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 2.304 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: B 924 MET cc_start: -0.0827 (ptt) cc_final: -0.1200 (ptt) REVERT: B 941 MET cc_start: -0.0993 (mmt) cc_final: -0.2962 (mpp) REVERT: B 961 MET cc_start: -0.1476 (tpp) cc_final: -0.1748 (mtp) REVERT: B 2250 MET cc_start: 0.5493 (mpp) cc_final: 0.5272 (ptp) REVERT: B 2874 MET cc_start: -0.2439 (mtp) cc_final: -0.3133 (mtt) REVERT: B 3723 MET cc_start: 0.8016 (mpp) cc_final: 0.7388 (mmm) REVERT: B 4000 MET cc_start: 0.5194 (ttp) cc_final: 0.4087 (ttp) REVERT: B 4769 MET cc_start: 0.5614 (ptm) cc_final: 0.3614 (pmm) REVERT: B 4796 MET cc_start: 0.6991 (tpt) cc_final: 0.6489 (tpt) REVERT: B 4816 ILE cc_start: 0.6475 (mt) cc_final: 0.6140 (mm) REVERT: B 4839 MET cc_start: 0.4240 (OUTLIER) cc_final: 0.3861 (ttt) REVERT: B 5012 LYS cc_start: 0.7127 (mmtm) cc_final: 0.6898 (mmtm) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.3322 time to fit residues: 150.6253 Evaluate side-chains 218 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 2.238 ------------------------------------------------------------------------------- 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: 0.7980 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2169 GLN ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3897 ASN ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4984 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3377 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 123012 Z= 0.273 Angle : 0.904 32.665 167720 Z= 0.448 Chirality : 0.049 0.611 19600 Planarity : 0.008 0.135 22092 Dihedral : 6.268 48.211 18056 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.55 % Favored : 87.24 % Rotamer: Outliers : 0.04 % Allowed : 2.05 % Favored : 97.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -3.68 (0.06), residues: 13356 helix: -2.01 (0.06), residues: 5864 sheet: -1.81 (0.16), residues: 988 loop : -2.97 (0.07), residues: 6504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP G3935 HIS 0.049 0.004 HIS G4832 PHE 0.065 0.004 PHE I4163 TYR 0.051 0.004 TYR G2110 ARG 0.046 0.002 ARG G4734 *********************** 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 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.093 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2227 time to fit residues: 0.8109 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.083 Evaluate side-chains 275 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 2.254 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: -0.0820 (ptt) cc_final: -0.1213 (ptt) REVERT: B 2874 MET cc_start: -0.2450 (mtp) cc_final: -0.3157 (mtt) REVERT: B 3723 MET cc_start: 0.7935 (mpp) cc_final: 0.7460 (mmm) REVERT: B 3751 VAL cc_start: 0.3972 (t) cc_final: 0.3635 (t) REVERT: B 3978 GLN cc_start: 0.6221 (mm-40) cc_final: 0.5468 (mm-40) REVERT: B 4000 MET cc_start: 0.5496 (ttp) cc_final: 0.4754 (ttp) REVERT: B 4769 MET cc_start: 0.5611 (ptm) cc_final: 0.3612 (pmm) REVERT: B 4796 MET cc_start: 0.6988 (tpt) cc_final: 0.6491 (tpt) REVERT: B 4816 ILE cc_start: 0.6408 (mt) cc_final: 0.6172 (mm) REVERT: B 4838 VAL cc_start: 0.7090 (m) cc_final: 0.6871 (m) outliers start: 1 outliers final: 1 residues processed: 275 average time/residue: 0.3193 time to fit residues: 143.5186 Evaluate side-chains 214 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 0.0020 chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 0.0030 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN B 596 ASN ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3882 GLN ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4984 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3373 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 123012 Z= 0.250 Angle : 0.896 32.803 167720 Z= 0.442 Chirality : 0.049 0.530 19600 Planarity : 0.009 0.220 22092 Dihedral : 6.259 48.065 18056 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.34 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -3.68 (0.06), residues: 13356 helix: -2.02 (0.06), residues: 5856 sheet: -1.79 (0.16), residues: 988 loop : -2.96 (0.07), residues: 6512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP E1626 HIS 0.032 0.003 HIS G4156 PHE 0.067 0.004 PHE G4163 TYR 0.051 0.004 TYR I2110 ARG 0.045 0.002 ARG I4734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.094 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2162 time to fit residues: 0.7904 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.070 Evaluate side-chains 271 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.120 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 924 MET cc_start: -0.0824 (ptt) cc_final: -0.1213 (ptt) REVERT: B 2874 MET cc_start: -0.2447 (mtp) cc_final: -0.3151 (mtt) REVERT: B 3723 MET cc_start: 0.8131 (mpp) cc_final: 0.6471 (mpp) REVERT: B 3978 GLN cc_start: 0.6069 (mm-40) cc_final: 0.5331 (mm-40) REVERT: B 4000 MET cc_start: 0.5118 (ttp) cc_final: 0.4740 (ttp) REVERT: B 4769 MET cc_start: 0.5408 (ptm) cc_final: 0.3284 (pmm) REVERT: B 4796 MET cc_start: 0.6971 (tpt) cc_final: 0.6518 (tpt) REVERT: B 4816 ILE cc_start: 0.6477 (mt) cc_final: 0.6182 (mm) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3091 time to fit residues: 135.8728 Evaluate side-chains 211 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 3 optimal weight: 30.0000 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.0670 chunk 25 optimal weight: 0.3980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3882 GLN B3897 ASN ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4984 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3371 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 123012 Z= 0.254 Angle : 0.910 30.498 167720 Z= 0.449 Chirality : 0.050 0.687 19600 Planarity : 0.008 0.145 22092 Dihedral : 6.231 48.108 18056 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.40 % Favored : 87.39 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -3.68 (0.06), residues: 13356 helix: -2.06 (0.06), residues: 5896 sheet: -1.74 (0.16), residues: 1008 loop : -2.94 (0.07), residues: 6452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP I1626 HIS 0.070 0.004 HIS E4832 PHE 0.066 0.004 PHE I4163 TYR 0.051 0.004 TYR G2110 ARG 0.046 0.002 ARG G4734 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.101 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2170 time to fit residues: 0.7942 Evaluate side-chains 2 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.075 Evaluate side-chains 268 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.249 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: -0.0835 (ptt) cc_final: -0.1216 (ptt) REVERT: B 941 MET cc_start: -0.0063 (mmm) cc_final: -0.1931 (mpp) REVERT: B 961 MET cc_start: -0.0977 (mtt) cc_final: -0.2984 (mtm) REVERT: B 2874 MET cc_start: -0.2444 (mtp) cc_final: -0.3206 (mtt) REVERT: B 3723 MET cc_start: 0.8085 (mpp) cc_final: 0.7316 (mmm) REVERT: B 3751 VAL cc_start: 0.3942 (t) cc_final: 0.3585 (t) REVERT: B 4000 MET cc_start: 0.5427 (ttp) cc_final: 0.4969 (ttp) REVERT: B 4064 MET cc_start: 0.4017 (ppp) cc_final: 0.3724 (ppp) REVERT: B 4769 MET cc_start: 0.5614 (ptm) cc_final: 0.3629 (pmm) REVERT: B 4796 MET cc_start: 0.6975 (tpt) cc_final: 0.6459 (tpt) REVERT: B 4816 ILE cc_start: 0.6252 (mt) cc_final: 0.6042 (mm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3201 time to fit residues: 140.1261 Evaluate side-chains 211 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 53.25 > 50: distance: 4 - 5: 5.699 distance: 5 - 8: 11.814 distance: 6 - 7: 16.693 distance: 6 - 12: 4.377 distance: 8 - 9: 4.635 distance: 9 - 10: 6.938 distance: 9 - 11: 4.637 distance: 12 - 13: 17.715 distance: 13 - 14: 34.549 distance: 14 - 15: 30.973 distance: 14 - 16: 40.011 distance: 16 - 17: 9.583 distance: 17 - 18: 20.506 distance: 17 - 20: 23.808 distance: 18 - 19: 10.338 distance: 18 - 27: 24.899 distance: 20 - 21: 24.506 distance: 21 - 22: 7.061 distance: 22 - 23: 6.797 distance: 23 - 24: 9.383 distance: 24 - 25: 8.716 distance: 24 - 26: 7.346 distance: 27 - 28: 17.046 distance: 28 - 29: 27.998 distance: 28 - 31: 7.026 distance: 29 - 30: 41.485 distance: 29 - 34: 22.294 distance: 31 - 32: 15.574 distance: 31 - 33: 10.562 distance: 34 - 35: 33.592 distance: 35 - 36: 36.024 distance: 35 - 38: 34.801 distance: 36 - 37: 48.305 distance: 36 - 45: 18.512 distance: 38 - 39: 18.101 distance: 39 - 40: 38.866 distance: 39 - 41: 36.960 distance: 40 - 42: 47.944 distance: 41 - 43: 27.250 distance: 42 - 44: 30.647 distance: 43 - 44: 13.545 distance: 45 - 46: 9.843 distance: 45 - 51: 19.985 distance: 46 - 47: 11.147 distance: 46 - 49: 31.114 distance: 47 - 48: 16.664 distance: 47 - 52: 19.621 distance: 49 - 50: 31.746 distance: 50 - 51: 19.076 distance: 52 - 53: 24.759 distance: 53 - 54: 27.463 distance: 53 - 56: 28.511 distance: 54 - 55: 13.066 distance: 54 - 61: 21.781 distance: 56 - 57: 9.733 distance: 57 - 58: 27.941 distance: 58 - 59: 17.330 distance: 59 - 60: 12.798 distance: 61 - 62: 16.716 distance: 62 - 63: 16.530 distance: 62 - 65: 18.871 distance: 63 - 64: 30.428 distance: 63 - 70: 26.765 distance: 65 - 66: 12.705 distance: 66 - 67: 19.269 distance: 67 - 68: 4.787 distance: 68 - 69: 32.408 distance: 70 - 71: 25.955 distance: 71 - 72: 7.346 distance: 72 - 73: 11.914