Starting phenix.real_space_refine on Thu Mar 14 11:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmi_22395/03_2024/7jmi_22395_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmi_22395/03_2024/7jmi_22395.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/7jmi_22395/03_2024/7jmi_22395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmi_22395/03_2024/7jmi_22395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmi_22395/03_2024/7jmi_22395_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmi_22395/03_2024/7jmi_22395_neut.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 S 644 5.16 5 C 76496 2.51 5 N 21384 2.21 5 O 22224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 1271": "NH1" <-> "NH2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B ARG 1607": "NH1" <-> "NH2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1743": "NH1" <-> "NH2" Residue "B ARG 1797": "NH1" <-> "NH2" Residue "B ARG 1827": "NH1" <-> "NH2" Residue "B ARG 1996": "NH1" <-> "NH2" Residue "B ARG 2140": "NH1" <-> "NH2" Residue "B ARG 2355": "NH1" <-> "NH2" Residue "B ARG 2452": "NH1" <-> "NH2" Residue "B ARG 3648": "NH1" <-> "NH2" Residue "B ARG 3886": "NH1" <-> "NH2" Residue "B ARG 3904": "NH1" <-> "NH2" Residue "B ARG 3949": "NH1" <-> "NH2" Residue "B ARG 3984": "NH1" <-> "NH2" Residue "B ARG 4042": "NH1" <-> "NH2" Residue "B ARG 4137": "NH1" <-> "NH2" Residue "B ARG 4159": "NH1" <-> "NH2" Residue "B ARG 4175": "NH1" <-> "NH2" Residue "B ARG 4192": "NH1" <-> "NH2" Residue "B ARG 4548": "NH1" <-> "NH2" Residue "B ARG 4557": "NH1" <-> "NH2" Residue "B ARG 4563": "NH1" <-> "NH2" Residue "B TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4673": "NH1" <-> "NH2" Residue "B ARG 4703": "NH1" <-> "NH2" Residue "B ARG 4722": "NH1" <-> "NH2" Residue "B ARG 4734": "NH1" <-> "NH2" Residue "B ARG 4736": "NH1" <-> "NH2" Residue "B ARG 4824": "NH1" <-> "NH2" Residue "B ARG 4860": "NH1" <-> "NH2" Residue "B ARG 4892": "NH1" <-> "NH2" Residue "B ARG 4913": "NH1" <-> "NH2" Residue "B ARG 5017": "NH1" <-> "NH2" Residue "B ARG 5029": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E ARG 1271": "NH1" <-> "NH2" Residue "E ARG 1594": "NH1" <-> "NH2" Residue "E ARG 1607": "NH1" <-> "NH2" Residue "E ARG 1656": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1743": "NH1" <-> "NH2" Residue "E ARG 1797": "NH1" <-> "NH2" Residue "E ARG 1827": "NH1" <-> "NH2" Residue "E ARG 1996": "NH1" <-> "NH2" Residue "E ARG 2140": "NH1" <-> "NH2" Residue "E ARG 2355": "NH1" <-> "NH2" Residue "E ARG 2452": "NH1" <-> "NH2" Residue "E ARG 3648": "NH1" <-> "NH2" Residue "E ARG 3886": "NH1" <-> "NH2" Residue "E ARG 3904": "NH1" <-> "NH2" Residue "E ARG 3949": "NH1" <-> "NH2" Residue "E ARG 3984": "NH1" <-> "NH2" Residue "E ARG 4042": "NH1" <-> "NH2" Residue "E ARG 4137": "NH1" <-> "NH2" Residue "E ARG 4159": "NH1" <-> "NH2" Residue "E ARG 4175": "NH1" <-> "NH2" Residue "E ARG 4192": "NH1" <-> "NH2" Residue "E ARG 4548": "NH1" <-> "NH2" Residue "E ARG 4557": "NH1" <-> "NH2" Residue "E ARG 4563": "NH1" <-> "NH2" Residue "E TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4673": "NH1" <-> "NH2" Residue "E ARG 4703": "NH1" <-> "NH2" Residue "E ARG 4722": "NH1" <-> "NH2" Residue "E ARG 4734": "NH1" <-> "NH2" Residue "E ARG 4736": "NH1" <-> "NH2" Residue "E ARG 4824": "NH1" <-> "NH2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E ARG 4913": "NH1" <-> "NH2" Residue "E ARG 5017": "NH1" <-> "NH2" Residue "E ARG 5029": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 266": "NH1" <-> "NH2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 553": "NH1" <-> "NH2" Residue "G ARG 1271": "NH1" <-> "NH2" Residue "G ARG 1594": "NH1" <-> "NH2" Residue "G ARG 1607": "NH1" <-> "NH2" Residue "G ARG 1656": "NH1" <-> "NH2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 1743": "NH1" <-> "NH2" Residue "G ARG 1797": "NH1" <-> "NH2" Residue "G ARG 1827": "NH1" <-> "NH2" Residue "G ARG 1996": "NH1" <-> "NH2" Residue "G ARG 2140": "NH1" <-> "NH2" Residue "G ARG 2355": "NH1" <-> "NH2" Residue "G ARG 2452": "NH1" <-> "NH2" Residue "G ARG 3648": "NH1" <-> "NH2" Residue "G ARG 3886": "NH1" <-> "NH2" Residue "G ARG 3904": "NH1" <-> "NH2" Residue "G ARG 3949": "NH1" <-> "NH2" Residue "G ARG 3984": "NH1" <-> "NH2" Residue "G ARG 4042": "NH1" <-> "NH2" Residue "G ARG 4137": "NH1" <-> "NH2" Residue "G ARG 4159": "NH1" <-> "NH2" Residue "G ARG 4175": "NH1" <-> "NH2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4548": "NH1" <-> "NH2" Residue "G ARG 4557": "NH1" <-> "NH2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4673": "NH1" <-> "NH2" Residue "G ARG 4703": "NH1" <-> "NH2" Residue "G ARG 4722": "NH1" <-> "NH2" Residue "G ARG 4734": "NH1" <-> "NH2" Residue "G ARG 4736": "NH1" <-> "NH2" Residue "G ARG 4824": "NH1" <-> "NH2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G ARG 4913": "NH1" <-> "NH2" Residue "G ARG 5017": "NH1" <-> "NH2" Residue "G ARG 5029": "NH1" <-> "NH2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 266": "NH1" <-> "NH2" Residue "I ARG 426": "NH1" <-> "NH2" Residue "I ARG 553": "NH1" <-> "NH2" Residue "I ARG 1271": "NH1" <-> "NH2" Residue "I ARG 1594": "NH1" <-> "NH2" Residue "I ARG 1607": "NH1" <-> "NH2" Residue "I ARG 1656": "NH1" <-> "NH2" Residue "I ARG 1725": "NH1" <-> "NH2" Residue "I ARG 1743": "NH1" <-> "NH2" Residue "I ARG 1797": "NH1" <-> "NH2" Residue "I ARG 1827": "NH1" <-> "NH2" Residue "I ARG 1996": "NH1" <-> "NH2" Residue "I ARG 2140": "NH1" <-> "NH2" Residue "I ARG 2355": "NH1" <-> "NH2" Residue "I ARG 2452": "NH1" <-> "NH2" Residue "I ARG 3648": "NH1" <-> "NH2" Residue "I ARG 3886": "NH1" <-> "NH2" Residue "I ARG 3904": "NH1" <-> "NH2" Residue "I ARG 3949": "NH1" <-> "NH2" Residue "I ARG 3984": "NH1" <-> "NH2" Residue "I ARG 4042": "NH1" <-> "NH2" Residue "I ARG 4137": "NH1" <-> "NH2" Residue "I ARG 4159": "NH1" <-> "NH2" Residue "I ARG 4175": "NH1" <-> "NH2" Residue "I ARG 4192": "NH1" <-> "NH2" Residue "I ARG 4548": "NH1" <-> "NH2" Residue "I ARG 4557": "NH1" <-> "NH2" Residue "I ARG 4563": "NH1" <-> "NH2" Residue "I TYR 4638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4673": "NH1" <-> "NH2" Residue "I ARG 4703": "NH1" <-> "NH2" Residue "I ARG 4722": "NH1" <-> "NH2" Residue "I ARG 4734": "NH1" <-> "NH2" Residue "I ARG 4736": "NH1" <-> "NH2" Residue "I ARG 4824": "NH1" <-> "NH2" Residue "I ARG 4860": "NH1" <-> "NH2" Residue "I ARG 4892": "NH1" <-> "NH2" Residue "I ARG 4913": "NH1" <-> "NH2" Residue "I ARG 5017": "NH1" <-> "NH2" Residue "I ARG 5029": "NH1" <-> "NH2" Time to flip residues: 0.23s 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 178.035 206.100 87.926 1.00 0.96 S ATOM 29541 SG CYS B4961 180.280 204.898 91.504 1.00 1.19 S ATOM 58885 SG CYS E4958 205.334 208.915 87.854 1.00 1.01 S ATOM 58910 SG CYS E4961 204.154 206.686 91.448 1.00 1.12 S ATOM 89072 SG CYS G4958 208.332 181.392 87.746 1.00 1.53 S ATOM 89097 SG CYS G4961 206.136 182.575 91.360 1.00 1.34 S ATOM A0EUZ SG CYS I4958 180.876 178.626 87.804 1.00 1.27 S ATOM A0EVO SG CYS I4961 182.089 180.839 91.399 1.00 1.48 S Time building chain proxies: 44.91, per 1000 atoms: 0.37 Number of scatterers: 120756 At special positions: 0 Unit cell: (387.795, 387.795, 210.84, 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: 31.99 Conformation dependent library (CDL) restraints added in 14.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" ND1 HIS E4983 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4958 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4961 " pdb="ZN ZN E5101 " - pdb=" NE2 HIS E4978 " pdb=" ZN G5101 " pdb="ZN ZN G5101 " - pdb=" ND1 HIS G4983 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4961 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4958 " pdb="ZN ZN G5101 " - pdb=" NE2 HIS G4978 " pdb=" ZN I5101 " pdb="ZN ZN I5101 " - pdb=" ND1 HIS I4983 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4961 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4958 " pdb="ZN ZN I5101 " - pdb=" NE2 HIS I4978 " Number of angles added : 8 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32360 Finding SS restraints... Secondary structure from input PDB file: 686 helices and 106 sheets defined 60.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 19.13 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.763A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.986A pdb=" N GLY A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.813A 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 364 through 369 Processing helix chain 'B' and resid 395 through 412 removed outlier: 3.790A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.673A 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 450 removed outlier: 3.756A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 481 removed outlier: 3.613A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.512A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 removed outlier: 4.142A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.647A pdb=" N SER B 541 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.184A 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: 3.789A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.777A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 removed outlier: 3.958A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 596 through 608 removed outlier: 4.057A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.954A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 622 " --> pdb=" O GLN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 889 removed outlier: 3.541A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B 879 " --> pdb=" O ALA B 875 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 934 removed outlier: 3.771A pdb=" N ASN B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 3.656A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 989 " --> pdb=" O VAL B 985 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1041 removed outlier: 4.226A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.755A pdb=" N LEU B1046 " --> pdb=" O ALA B1042 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B1047 " --> pdb=" O VAL B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1082 Processing helix chain 'B' and resid 1575 through 1579 removed outlier: 3.531A pdb=" N ALA B1578 " --> pdb=" O LEU B1575 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B1579 " --> pdb=" O SER B1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1575 through 1579' Processing helix chain 'B' and resid 1652 through 1657 Processing helix chain 'B' and resid 1658 through 1674 removed outlier: 3.754A pdb=" N HIS B1665 " --> pdb=" O ARG B1661 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B1670 " --> pdb=" O THR B1666 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B1671 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1686 removed outlier: 3.707A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) Processing helix chain 'B' and resid 1692 through 1700 removed outlier: 4.139A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1710 through 1712 No H-bonds generated for 'chain 'B' and resid 1710 through 1712' Processing helix chain 'B' and resid 1713 through 1718 Processing helix chain 'B' and resid 1720 through 1730 removed outlier: 3.925A pdb=" N ARG B1725 " --> pdb=" O GLU B1721 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1824 removed outlier: 3.756A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET B1814 " --> pdb=" O LYS B1810 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B1816 " --> pdb=" O LEU B1812 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1838 Processing helix chain 'B' and resid 1840 through 1851 removed outlier: 3.531A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1863 Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1933 through 1982 removed outlier: 3.853A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B1947 " --> pdb=" O LEU B1943 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B1966 " --> pdb=" O ALA B1962 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B1978 " --> pdb=" O ARG B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1994 removed outlier: 3.676A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1995 through 1998 Processing helix chain 'B' and resid 2001 through 2011 removed outlier: 3.668A pdb=" N ILE B2006 " --> pdb=" O PRO B2002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) Processing helix chain 'B' and resid 2028 through 2042 removed outlier: 3.740A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2108 removed outlier: 3.620A pdb=" N HIS B2100 " --> pdb=" O GLU B2096 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2129 removed outlier: 3.682A pdb=" N TYR B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2137 Processing helix chain 'B' and resid 2148 through 2165 removed outlier: 4.010A pdb=" N CYS B2158 " --> pdb=" O SER B2154 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B2165 " --> pdb=" O GLN B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2187 removed outlier: 3.642A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.826A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2216 removed outlier: 3.567A pdb=" N VAL B2210 " --> pdb=" O THR B2206 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) Processing helix chain 'B' and resid 2228 through 2242 removed outlier: 3.655A pdb=" N CYS B2233 " --> pdb=" O VAL B2229 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B2238 " --> pdb=" O ARG B2234 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2252 removed outlier: 3.573A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2262 removed outlier: 4.073A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 Processing helix chain 'B' and resid 2294 through 2306 removed outlier: 3.519A pdb=" N VAL B2298 " --> pdb=" O ASP B2294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 4.240A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2331 removed outlier: 3.526A pdb=" N TYR B2331 " --> pdb=" O GLY B2327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2335 through 2339 removed outlier: 4.267A pdb=" N ALA B2338 " --> pdb=" O LEU B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2350 through 2358 removed outlier: 3.773A pdb=" N LEU B2356 " --> pdb=" O VAL B2352 " (cutoff:3.500A) Processing helix chain 'B' and resid 2360 through 2364 Processing helix chain 'B' and resid 2375 through 2388 Processing helix chain 'B' and resid 2389 through 2393 Processing helix chain 'B' and resid 2417 through 2436 removed outlier: 4.195A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B2422 " --> pdb=" O LEU B2418 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B2428 " --> pdb=" O SER B2424 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B2433 " --> pdb=" O LEU B2429 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2445 Processing helix chain 'B' and resid 2448 through 2461 removed outlier: 3.732A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2471 Processing helix chain 'B' and resid 2500 through 2507 removed outlier: 3.580A pdb=" N UNK B2504 " --> pdb=" O UNK B2500 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N UNK B2505 " --> pdb=" O UNK B2501 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK B2506 " --> pdb=" O UNK B2502 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2525 removed outlier: 4.043A pdb=" N UNK B2523 " --> pdb=" O UNK B2519 " (cutoff:3.500A) Processing helix chain 'B' and resid 2525 through 2530 removed outlier: 3.560A pdb=" N UNK B2530 " --> pdb=" O UNK B2526 " (cutoff:3.500A) Processing helix chain 'B' and resid 2542 through 2548 removed outlier: 3.654A pdb=" N UNK B2546 " --> pdb=" O UNK B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2557 removed outlier: 3.744A pdb=" N UNK B2555 " --> pdb=" O UNK B2551 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2581 removed outlier: 3.586A pdb=" N UNK B2578 " --> pdb=" O UNK B2574 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2602 removed outlier: 3.614A pdb=" N UNK B2597 " --> pdb=" O UNK B2593 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK B2602 " --> pdb=" O UNK B2598 " (cutoff:3.500A) Processing helix chain 'B' and resid 2610 through 2618 removed outlier: 3.806A pdb=" N UNK B2618 " --> pdb=" O UNK B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2626 through 2641 removed outlier: 3.904A pdb=" N UNK B2630 " --> pdb=" O UNK B2626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N UNK B2631 " --> pdb=" O UNK B2627 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N UNK B2634 " --> pdb=" O UNK B2630 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N UNK B2635 " --> pdb=" O UNK B2631 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK B2639 " --> pdb=" O UNK B2635 " (cutoff:3.500A) removed outlier: 3.813A 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: 4.127A pdb=" N UNK B2681 " --> pdb=" O UNK B2677 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N UNK B2683 " --> pdb=" O UNK B2679 " (cutoff:3.500A) Processing helix chain 'B' and resid 2748 through 2773 removed outlier: 3.537A pdb=" N ASP B2752 " --> pdb=" O PRO B2748 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.541A pdb=" N THR B2796 " --> pdb=" O PRO B2793 " (cutoff:3.500A) removed outlier: 3.705A 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 2800 through 2804 Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 4.064A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET B2816 " --> pdb=" O SER B2812 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B2817 " --> pdb=" O LEU B2813 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.021A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B2875 " --> pdb=" O LEU B2871 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP B2886 " --> pdb=" O TYR B2882 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2911 Processing helix chain 'B' and resid 2914 through 2932 removed outlier: 3.605A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B2920 " --> pdb=" O LYS B2916 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2976 removed outlier: 4.216A pdb=" N UNK B2956 " --> pdb=" O UNK B2952 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK B2968 " --> pdb=" O UNK B2964 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK B2969 " --> pdb=" O UNK B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2999 through 3015 removed outlier: 3.528A pdb=" N UNK B3004 " --> pdb=" O UNK B3000 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK B3006 " --> pdb=" O UNK B3002 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.533A pdb=" N UNK B3037 " --> pdb=" O UNK B3033 " (cutoff:3.500A) Processing helix chain 'B' and resid 3052 through 3063 removed outlier: 4.319A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N UNK B3057 " --> pdb=" O UNK B3053 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N UNK B3061 " --> pdb=" O UNK B3057 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N UNK B3062 " --> pdb=" O UNK B3058 " (cutoff:3.500A) Processing helix chain 'B' and resid 3141 through 3146 Processing helix chain 'B' and resid 3146 through 3162 removed outlier: 4.083A pdb=" N UNK B3154 " --> pdb=" O UNK B3150 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3186 removed outlier: 3.692A pdb=" N UNK B3182 " --> pdb=" O UNK B3178 " (cutoff:3.500A) Processing helix chain 'B' and resid 3198 through 3212 Processing helix chain 'B' and resid 3213 through 3215 No H-bonds generated for 'chain 'B' and resid 3213 through 3215' Processing helix chain 'B' and resid 3224 through 3230 removed outlier: 3.885A pdb=" N UNK B3228 " --> pdb=" O UNK B3224 " (cutoff:3.500A) Processing helix chain 'B' and resid 3248 through 3254 removed outlier: 3.585A pdb=" N UNK B3252 " --> pdb=" O UNK B3248 " (cutoff:3.500A) Processing helix chain 'B' and resid 3271 through 3285 removed outlier: 3.510A pdb=" N UNK B3281 " --> pdb=" O UNK B3277 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N UNK B3282 " --> pdb=" O UNK B3278 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N UNK B3284 " --> pdb=" O UNK B3280 " (cutoff:3.500A) Processing helix chain 'B' and resid 3301 through 3304 Processing helix chain 'B' and resid 3305 through 3310 Processing helix chain 'B' and resid 3316 through 3321 removed outlier: 3.594A pdb=" N UNK B3321 " --> pdb=" O UNK B3317 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3331 removed outlier: 3.566A pdb=" N UNK B3330 " --> pdb=" O UNK B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3349 removed outlier: 3.564A pdb=" N UNK B3348 " --> pdb=" O UNK B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3361 through 3388 Processing helix chain 'B' and resid 3399 through 3407 removed outlier: 3.597A pdb=" N UNK B3403 " --> pdb=" O UNK B3399 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK B3404 " --> pdb=" O UNK B3400 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N UNK B3405 " --> pdb=" O UNK B3401 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK B3407 " --> pdb=" O UNK B3403 " (cutoff:3.500A) Processing helix chain 'B' and resid 3410 through 3425 removed outlier: 4.074A pdb=" N UNK B3416 " --> pdb=" O UNK B3412 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK B3417 " --> pdb=" O UNK B3413 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N UNK B3420 " --> pdb=" O UNK B3416 " (cutoff:3.500A) Processing helix chain 'B' and resid 3437 through 3443 Processing helix chain 'B' and resid 3445 through 3450 Processing helix chain 'B' and resid 3461 through 3468 removed outlier: 3.555A pdb=" N UNK B3468 " --> pdb=" O UNK B3464 " (cutoff:3.500A) Processing helix chain 'B' and resid 3518 through 3521 removed outlier: 3.638A pdb=" N UNK B3521 " --> pdb=" O UNK B3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3518 through 3521' Processing helix chain 'B' and resid 3522 through 3527 Processing helix chain 'B' and resid 3541 through 3547 removed outlier: 3.630A 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: 3.617A pdb=" N UNK B3579 " --> pdb=" O UNK B3575 " (cutoff:3.500A) Processing helix chain 'B' and resid 3589 through 3608 removed outlier: 4.078A pdb=" N UNK B3595 " --> pdb=" O UNK B3591 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N UNK B3598 " --> pdb=" O UNK B3594 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK B3600 " --> pdb=" O UNK B3596 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNK B3601 " --> pdb=" O UNK B3597 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 removed outlier: 3.735A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) Processing helix chain 'B' and resid 3657 through 3661 Processing helix chain 'B' and resid 3671 through 3680 removed outlier: 4.017A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3681 through 3683 No H-bonds generated for 'chain 'B' and resid 3681 through 3683' Processing helix chain 'B' and resid 3696 through 3708 Processing helix chain 'B' and resid 3719 through 3738 removed outlier: 3.806A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3769 removed outlier: 4.014A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN B3767 " --> pdb=" O LEU B3763 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B3768 " --> pdb=" O LEU B3764 " (cutoff:3.500A) Processing helix chain 'B' and resid 3771 through 3784 removed outlier: 4.661A pdb=" N GLU B3777 " --> pdb=" O ARG B3773 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B3779 " --> pdb=" O ALA B3775 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3803 removed outlier: 3.555A pdb=" N SER B3803 " --> pdb=" O LYS B3799 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3828 through 3838 removed outlier: 3.591A pdb=" N ILE B3832 " --> pdb=" O PHE B3828 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3856 Processing helix chain 'B' and resid 3877 through 3892 removed outlier: 3.690A pdb=" N GLN B3882 " --> pdb=" O ASP B3878 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3903 Processing helix chain 'B' and resid 3914 through 3937 removed outlier: 4.032A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP B3921 " --> pdb=" O ILE B3917 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B3929 " --> pdb=" O ARG B3925 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B3934 " --> pdb=" O ILE B3930 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3967 removed outlier: 3.742A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.684A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 4004 removed outlier: 4.137A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B3992 " --> pdb=" O ALA B3988 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B3993 " --> pdb=" O VAL B3989 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B3994 " --> pdb=" O VAL B3990 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET B3999 " --> pdb=" O VAL B3995 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B4004 " --> pdb=" O MET B4000 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4030 removed outlier: 4.024A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4051 removed outlier: 3.611A pdb=" N ASP B4046 " --> pdb=" O ARG B4042 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B4048 " --> pdb=" O MET B4044 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4063 removed outlier: 3.757A pdb=" N PHE B4061 " --> pdb=" O MET B4057 " (cutoff:3.500A) Processing helix chain 'B' and resid 4067 through 4072 Processing helix chain 'B' and resid 4074 through 4079 removed outlier: 3.546A pdb=" N GLN B4078 " --> pdb=" O SER B4074 " (cutoff:3.500A) Processing helix chain 'B' and resid 4090 through 4100 removed outlier: 3.623A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4124 through 4131 Processing helix chain 'B' and resid 4132 through 4154 removed outlier: 3.837A pdb=" N ALA B4136 " --> pdb=" O PHE B4132 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B4137 " --> pdb=" O GLN B4133 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B4141 " --> pdb=" O ARG B4137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B4152 " --> pdb=" O THR B4148 " (cutoff:3.500A) removed outlier: 3.833A 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 4169 through 4174 removed outlier: 3.717A pdb=" N PHE B4174 " --> pdb=" O ILE B4170 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4206 removed outlier: 3.952A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B4203 " --> pdb=" O GLU B4199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B4204 " --> pdb=" O THR B4200 " (cutoff:3.500A) Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 4.002A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4251 removed outlier: 3.766A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B4249 " --> pdb=" O MET B4245 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B4250 " --> pdb=" O GLN B4246 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B4251 " --> pdb=" O ILE B4247 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4558 removed outlier: 3.540A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4576 removed outlier: 3.587A pdb=" N ALA B4570 " --> pdb=" O ALA B4566 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B4574 " --> pdb=" O ALA B4570 " (cutoff:3.500A) Processing helix chain 'B' and resid 4641 through 4665 removed outlier: 3.595A pdb=" N ALA B4654 " --> pdb=" O HIS B4650 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B4655 " --> pdb=" O THR B4651 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) Processing helix chain 'B' and resid 4667 through 4683 removed outlier: 3.512A pdb=" N GLU B4676 " --> pdb=" O LYS B4672 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B4678 " --> pdb=" O GLU B4674 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4702 removed outlier: 3.719A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4706 removed outlier: 3.565A pdb=" N LEU B4706 " --> pdb=" O ARG B4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4703 through 4706' 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 Processing helix chain 'B' and resid 4786 through 4802 removed outlier: 4.140A pdb=" N MET B4798 " --> pdb=" O TRP B4794 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B4799 " --> pdb=" O TYR B4795 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B4800 " --> pdb=" O MET B4796 " (cutoff:3.500A) Processing helix chain 'B' and resid 4812 through 4819 removed outlier: 3.507A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.676A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 removed outlier: 3.969A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY B4842 " --> pdb=" O VAL B4838 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B4843 " --> pdb=" O MET B4839 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B4844 " --> pdb=" O THR B4840 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B4845 " --> pdb=" O VAL B4841 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B4846 " --> pdb=" O GLY B4842 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B4848 " --> pdb=" O LEU B4844 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B4853 " --> pdb=" O TYR B4849 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) Processing helix chain 'B' and resid 4859 through 4863 removed outlier: 3.574A pdb=" N PHE B4862 " --> pdb=" O PHE B4859 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4859 through 4863' Processing helix chain 'B' and resid 4878 through 4890 removed outlier: 3.663A pdb=" N PHE B4885 " --> pdb=" O THR B4881 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 removed outlier: 3.919A pdb=" N ASP B4899 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4911 through 4925 removed outlier: 4.142A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B4916 " --> pdb=" O TYR B4912 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP B4917 " --> pdb=" O ARG B4913 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B4918 " --> pdb=" O VAL B4914 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B4922 " --> pdb=" O ILE B4918 " (cutoff:3.500A) Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 3.800A pdb=" N LEU B4935 " --> pdb=" O ILE B4931 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B4944 " --> pdb=" O PHE B4940 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B4953 " --> pdb=" O GLN B4949 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET B4954 " --> pdb=" O VAL B4950 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B4955 " --> pdb=" O LYS B4951 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4968 removed outlier: 4.010A pdb=" N TYR B4967 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4986 through 4997 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 364 through 369 Processing helix chain 'E' and resid 395 through 412 removed outlier: 3.790A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS E 405 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 3.673A 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 450 removed outlier: 3.756A pdb=" N GLY E 450 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 481 removed outlier: 3.613A pdb=" N GLN E 465 " --> pdb=" O HIS E 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 478 " --> pdb=" O ARG E 474 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN E 479 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.512A pdb=" N CYS E 490 " --> pdb=" O LEU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 531 removed outlier: 4.141A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU E 524 " --> pdb=" O ASN E 520 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 528 " --> pdb=" O GLU E 524 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU E 529 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.646A pdb=" N SER E 541 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 4.185A 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: 3.787A pdb=" N VAL E 548 " --> pdb=" O LEU E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 569 removed outlier: 3.777A pdb=" N TYR E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 577 removed outlier: 3.960A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 594 Processing helix chain 'E' and resid 596 through 608 removed outlier: 4.058A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 603 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 625 removed outlier: 3.954A pdb=" N GLN E 618 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP E 619 " --> pdb=" O ARG E 615 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 622 " --> pdb=" O GLN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 889 removed outlier: 3.541A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS E 873 " --> pdb=" O ARG E 869 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS E 879 " --> pdb=" O ALA E 875 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 887 " --> pdb=" O ALA E 883 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 889 " --> pdb=" O THR E 885 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 934 removed outlier: 3.771A pdb=" N ASN E 919 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 929 " --> pdb=" O SER E 925 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA E 934 " --> pdb=" O LYS E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 980 through 1001 removed outlier: 3.655A pdb=" N LEU E 984 " --> pdb=" O ALA E 980 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP E 986 " --> pdb=" O THR E 982 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 989 " --> pdb=" O VAL E 985 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1041 removed outlier: 4.225A pdb=" N GLN E1041 " --> pdb=" O ASP E1037 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1049 removed outlier: 3.754A pdb=" N LEU E1046 " --> pdb=" O ALA E1042 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU E1047 " --> pdb=" O VAL E1043 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1082 Processing helix chain 'E' and resid 1575 through 1579 removed outlier: 3.531A pdb=" N ALA E1578 " --> pdb=" O LEU E1575 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET E1579 " --> pdb=" O SER E1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1575 through 1579' Processing helix chain 'E' and resid 1652 through 1657 Processing helix chain 'E' and resid 1658 through 1674 removed outlier: 3.753A pdb=" N HIS E1665 " --> pdb=" O ARG E1661 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR E1670 " --> pdb=" O THR E1666 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG E1671 " --> pdb=" O LEU E1667 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1686 removed outlier: 3.706A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS E1686 " --> pdb=" O ALA E1682 " (cutoff:3.500A) Processing helix chain 'E' and resid 1692 through 1700 removed outlier: 4.138A pdb=" N LEU E1698 " --> pdb=" O LEU E1694 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU E1699 " --> pdb=" O LEU E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1710 through 1712 No H-bonds generated for 'chain 'E' and resid 1710 through 1712' Processing helix chain 'E' and resid 1713 through 1718 Processing helix chain 'E' and resid 1720 through 1730 removed outlier: 3.927A pdb=" N ARG E1725 " --> pdb=" O GLU E1721 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER E1726 " --> pdb=" O SER E1722 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 Processing helix chain 'E' and resid 1803 through 1824 removed outlier: 3.756A pdb=" N LEU E1807 " --> pdb=" O PRO E1803 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E1814 " --> pdb=" O LYS E1810 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY E1816 " --> pdb=" O LEU E1812 " (cutoff:3.500A) Processing helix chain 'E' and resid 1833 through 1838 Processing helix chain 'E' and resid 1840 through 1851 removed outlier: 3.529A pdb=" N MET E1851 " --> pdb=" O THR E1847 " (cutoff:3.500A) Processing helix chain 'E' and resid 1855 through 1863 Processing helix chain 'E' and resid 1866 through 1871 Processing helix chain 'E' and resid 1933 through 1982 removed outlier: 3.852A pdb=" N TYR E1945 " --> pdb=" O ASN E1941 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE E1946 " --> pdb=" O LEU E1942 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS E1947 " --> pdb=" O LEU E1943 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E1963 " --> pdb=" O ALA E1959 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA E1978 " --> pdb=" O ARG E1974 " (cutoff:3.500A) Processing helix chain 'E' and resid 1989 through 1994 removed outlier: 3.675A pdb=" N ARG E1994 " --> pdb=" O GLU E1990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1995 through 1998 Processing helix chain 'E' and resid 2001 through 2011 removed outlier: 3.668A pdb=" N ILE E2006 " --> pdb=" O PRO E2002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN E2007 " --> pdb=" O GLN E2003 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N HIS E2011 " --> pdb=" O ASN E2007 " (cutoff:3.500A) Processing helix chain 'E' and resid 2028 through 2042 removed outlier: 3.740A pdb=" N GLN E2032 " --> pdb=" O ARG E2028 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2108 removed outlier: 3.620A pdb=" N HIS E2100 " --> pdb=" O GLU E2096 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL E2103 " --> pdb=" O SER E2099 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2129 removed outlier: 3.683A pdb=" N TYR E2128 " --> pdb=" O LEU E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2137 Processing helix chain 'E' and resid 2148 through 2165 removed outlier: 4.010A pdb=" N CYS E2158 " --> pdb=" O SER E2154 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN E2161 " --> pdb=" O GLU E2157 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E2165 " --> pdb=" O GLN E2161 " (cutoff:3.500A) Processing helix chain 'E' and resid 2171 through 2187 removed outlier: 3.641A pdb=" N LEU E2177 " --> pdb=" O GLN E2173 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.824A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.567A pdb=" N VAL E2210 " --> pdb=" O THR E2206 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN E2213 " --> pdb=" O GLU E2209 " (cutoff:3.500A) Processing helix chain 'E' and resid 2228 through 2242 removed outlier: 3.654A pdb=" N CYS E2233 " --> pdb=" O VAL E2229 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR E2238 " --> pdb=" O ARG E2234 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2252 removed outlier: 3.572A pdb=" N ASP E2252 " --> pdb=" O ARG E2248 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2262 removed outlier: 4.072A pdb=" N ASN E2260 " --> pdb=" O TYR E2256 " (cutoff:3.500A) Processing helix chain 'E' and resid 2271 through 2279 Processing helix chain 'E' and resid 2294 through 2306 removed outlier: 3.520A pdb=" N VAL E2298 " --> pdb=" O ASP E2294 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E2299 " --> pdb=" O LEU E2295 " (cutoff:3.500A) Processing helix chain 'E' and resid 2310 through 2315 removed outlier: 4.240A pdb=" N ALA E2315 " --> pdb=" O PRO E2311 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2331 removed outlier: 3.526A pdb=" N TYR E2331 " --> pdb=" O GLY E2327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2335 through 2339 removed outlier: 4.265A pdb=" N ALA E2338 " --> pdb=" O LEU E2335 " (cutoff:3.500A) Processing helix chain 'E' and resid 2350 through 2358 removed outlier: 3.774A pdb=" N LEU E2356 " --> pdb=" O VAL E2352 " (cutoff:3.500A) Processing helix chain 'E' and resid 2360 through 2364 Processing helix chain 'E' and resid 2375 through 2388 Processing helix chain 'E' and resid 2389 through 2393 Processing helix chain 'E' and resid 2417 through 2436 removed outlier: 4.196A pdb=" N ALA E2421 " --> pdb=" O HIS E2417 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E2422 " --> pdb=" O LEU E2418 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET E2423 " --> pdb=" O GLY E2419 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E2428 " --> pdb=" O SER E2424 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E2433 " --> pdb=" O LEU E2429 " (cutoff:3.500A) Processing helix chain 'E' and resid 2440 through 2445 Processing helix chain 'E' and resid 2448 through 2461 removed outlier: 3.731A pdb=" N ILE E2453 " --> pdb=" O GLU E2449 " (cutoff:3.500A) Processing helix chain 'E' and resid 2466 through 2471 Processing helix chain 'E' and resid 2502 through 2507 removed outlier: 3.673A pdb=" N UNK E2506 " --> pdb=" O UNK E2502 " (cutoff:3.500A) Processing helix chain 'E' and resid 2516 through 2525 removed outlier: 4.051A pdb=" N UNK E2523 " --> pdb=" O UNK E2519 " (cutoff:3.500A) Processing helix chain 'E' and resid 2525 through 2530 removed outlier: 3.562A pdb=" N UNK E2530 " --> pdb=" O UNK E2526 " (cutoff:3.500A) Processing helix chain 'E' and resid 2542 through 2548 removed outlier: 3.675A pdb=" N UNK E2546 " --> pdb=" O UNK E2542 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2557 removed outlier: 3.753A pdb=" N UNK E2555 " --> pdb=" O UNK E2551 " (cutoff:3.500A) Processing helix chain 'E' and resid 2567 through 2581 removed outlier: 3.558A pdb=" N UNK E2578 " --> pdb=" O UNK E2574 " (cutoff:3.500A) Processing helix chain 'E' and resid 2587 through 2602 removed outlier: 3.622A pdb=" N UNK E2597 " --> pdb=" O UNK E2593 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N UNK E2602 " --> pdb=" O UNK E2598 " (cutoff:3.500A) Processing helix chain 'E' and resid 2610 through 2618 removed outlier: 3.796A pdb=" N UNK E2618 " --> pdb=" O UNK E2614 " (cutoff:3.500A) Processing helix chain 'E' and resid 2626 through 2640 removed outlier: 3.905A pdb=" N UNK E2630 " --> pdb=" O UNK E2626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N UNK E2631 " --> pdb=" O UNK E2627 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK E2634 " --> pdb=" O UNK E2630 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK E2635 " --> pdb=" O UNK E2631 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N UNK E2639 " --> pdb=" O UNK E2635 " (cutoff:3.500A) Processing helix chain 'E' and resid 2641 through 2643 No H-bonds generated for 'chain 'E' and resid 2641 through 2643' Processing helix chain 'E' and resid 2650 through 2666 Processing helix chain 'E' and resid 2678 through 2683 removed outlier: 4.258A pdb=" N UNK E2683 " --> pdb=" O UNK E2679 " (cutoff:3.500A) Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 3.537A pdb=" N ASP E2752 " --> pdb=" O PRO E2748 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE E2768 " --> pdb=" O GLU E2764 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E2769 " --> pdb=" O LYS E2765 " (cutoff:3.500A) Processing helix chain 'E' and resid 2793 through 2797 removed outlier: 3.543A pdb=" N THR E2796 " --> pdb=" O PRO E2793 " (cutoff:3.500A) removed outlier: 3.705A 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 2800 through 2804 Processing helix chain 'E' and resid 2809 through 2820 removed outlier: 4.064A pdb=" N ALA E2815 " --> pdb=" O GLU E2811 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET E2816 " --> pdb=" O SER E2812 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E2817 " --> pdb=" O LEU E2813 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2895 removed outlier: 4.022A pdb=" N MET E2874 " --> pdb=" O GLU E2870 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E2875 " --> pdb=" O LEU E2871 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP E2886 " --> pdb=" O TYR E2882 " (cutoff:3.500A) Processing helix chain 'E' and resid 2907 through 2911 Processing helix chain 'E' and resid 2914 through 2932 removed outlier: 3.604A pdb=" N ASP E2919 " --> pdb=" O GLU E2915 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG E2920 " --> pdb=" O LYS E2916 " (cutoff:3.500A) Processing helix chain 'E' and resid 2950 through 2976 removed outlier: 4.217A pdb=" N UNK E2956 " --> pdb=" O UNK E2952 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N UNK E2968 " --> pdb=" O UNK E2964 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N UNK E2969 " --> pdb=" O UNK E2965 " (cutoff:3.500A) Processing helix chain 'E' and resid 2999 through 3015 removed outlier: 3.511A pdb=" N UNK E3004 " --> pdb=" O UNK E3000 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N UNK E3006 " --> pdb=" O UNK E3002 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK E3009 " --> pdb=" O UNK E3005 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N UNK E3010 " --> pdb=" O UNK E3006 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.532A pdb=" N UNK E3037 " --> pdb=" O UNK E3033 " (cutoff:3.500A) Processing helix chain 'E' and resid 3052 through 3063 removed outlier: 4.302A pdb=" N UNK E3056 " --> pdb=" O UNK E3052 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N UNK E3057 " --> pdb=" O UNK E3053 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N UNK E3061 " --> pdb=" O UNK E3057 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N UNK E3062 " --> pdb=" O UNK E3058 " (cutoff:3.500A) Processing helix chain 'E' and resid 3141 through 3146 Processing helix chain 'E' and resid 3146 through 3162 removed outlier: 4.071A pdb=" N UNK E3154 " --> pdb=" O UNK E3150 " (cutoff:3.500A) Processing helix chain 'E' and resid 3175 through 3186 removed outlier: 3.682A pdb=" N UNK E3182 " --> pdb=" O UNK E3178 " (cutoff:3.500A) Processing helix chain 'E' and resid 3198 through 3212 Processing helix chain 'E' and resid 3213 through 3215 No H-bonds generated for 'chain 'E' and resid 3213 through 3215' Processing helix chain 'E' and resid 3225 through 3230 Processing helix chain 'E' and resid 3248 through 3254 removed outlier: 3.575A pdb=" N UNK E3252 " --> pdb=" O UNK E3248 " (cutoff:3.500A) Processing helix chain 'E' and resid 3271 through 3285 removed outlier: 3.512A pdb=" N UNK E3281 " --> pdb=" O UNK E3277 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N UNK E3282 " --> pdb=" O UNK E3278 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N UNK E3284 " --> pdb=" O UNK E3280 " (cutoff:3.500A) Processing helix chain 'E' and resid 3301 through 3304 Processing helix chain 'E' and resid 3305 through 3310 Processing helix chain 'E' and resid 3316 through 3321 removed outlier: 3.586A pdb=" N UNK E3321 " --> pdb=" O UNK E3317 " (cutoff:3.500A) Processing helix chain 'E' and resid 3321 through 3331 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: 3.573A pdb=" N UNK E3348 " --> pdb=" O UNK E3344 " (cutoff:3.500A) Processing helix chain 'E' and resid 3361 through 3388 Processing helix chain 'E' and resid 3399 through 3407 removed outlier: 3.573A pdb=" N UNK E3403 " --> pdb=" O UNK E3399 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK E3404 " --> pdb=" O UNK E3400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK E3405 " --> pdb=" O UNK E3401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N UNK E3407 " --> pdb=" O UNK E3403 " (cutoff:3.500A) Processing helix chain 'E' and resid 3410 through 3425 removed outlier: 4.082A pdb=" N UNK E3416 " --> pdb=" O UNK E3412 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N UNK E3420 " --> pdb=" O UNK E3416 " (cutoff:3.500A) Processing helix chain 'E' and resid 3437 through 3443 Processing helix chain 'E' and resid 3445 through 3450 Processing helix chain 'E' and resid 3461 through 3468 removed outlier: 3.573A pdb=" N UNK E3468 " --> pdb=" O UNK E3464 " (cutoff:3.500A) Processing helix chain 'E' and resid 3522 through 3527 Processing helix chain 'E' and resid 3541 through 3547 removed outlier: 3.638A pdb=" N UNK E3547 " --> pdb=" O UNK E3543 " (cutoff:3.500A) Processing helix chain 'E' and resid 3551 through 3560 Processing helix chain 'E' and resid 3574 through 3579 removed outlier: 3.629A pdb=" N UNK E3579 " --> pdb=" O UNK E3575 " (cutoff:3.500A) Processing helix chain 'E' and resid 3589 through 3608 removed outlier: 4.093A pdb=" N UNK E3595 " --> pdb=" O UNK E3591 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N UNK E3598 " --> pdb=" O UNK E3594 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N UNK E3600 " --> pdb=" O UNK E3596 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N UNK E3601 " --> pdb=" O UNK E3597 " (cutoff:3.500A) Processing helix chain 'E' and resid 3645 through 3656 removed outlier: 3.734A pdb=" N GLU E3655 " --> pdb=" O ASN E3651 " (cutoff:3.500A) Processing helix chain 'E' and resid 3657 through 3661 Processing helix chain 'E' and resid 3671 through 3680 removed outlier: 4.018A pdb=" N LEU E3677 " --> pdb=" O MET E3673 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E3678 " --> pdb=" O ILE E3674 " (cutoff:3.500A) Processing helix chain 'E' and resid 3681 through 3683 No H-bonds generated for 'chain 'E' and resid 3681 through 3683' Processing helix chain 'E' and resid 3696 through 3708 Processing helix chain 'E' and resid 3719 through 3738 removed outlier: 3.805A pdb=" N GLU E3736 " --> pdb=" O SER E3732 " (cutoff:3.500A) Processing helix chain 'E' and resid 3752 through 3769 removed outlier: 4.014A pdb=" N LYS E3760 " --> pdb=" O LYS E3756 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN E3767 " --> pdb=" O LEU E3763 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER E3768 " --> pdb=" O LEU E3764 " (cutoff:3.500A) Processing helix chain 'E' and resid 3771 through 3784 removed outlier: 4.660A pdb=" N GLU E3777 " --> pdb=" O ARG E3773 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET E3778 " --> pdb=" O GLY E3774 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL E3779 " --> pdb=" O ALA E3775 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU E3780 " --> pdb=" O ALA E3776 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3803 removed outlier: 3.555A pdb=" N SER E3803 " --> pdb=" O LYS E3799 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3824 Processing helix chain 'E' and resid 3828 through 3838 removed outlier: 3.592A pdb=" N ILE E3832 " --> pdb=" O PHE E3828 " (cutoff:3.500A) Processing helix chain 'E' and resid 3843 through 3856 Processing helix chain 'E' and resid 3877 through 3892 removed outlier: 3.690A pdb=" N GLN E3882 " --> pdb=" O ASP E3878 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP E3883 " --> pdb=" O GLU E3879 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E3885 " --> pdb=" O THR E3881 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS E3892 " --> pdb=" O LEU E3888 " (cutoff:3.500A) Processing helix chain 'E' and resid 3898 through 3903 Processing helix chain 'E' and resid 3914 through 3937 removed outlier: 4.032A pdb=" N CYS E3918 " --> pdb=" O ASN E3914 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP E3921 " --> pdb=" O ILE E3917 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E3929 " --> pdb=" O ARG E3925 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR E3934 " --> pdb=" O ILE E3930 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP E3935 " --> pdb=" O SER E3931 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR E3936 " --> pdb=" O ASP E3932 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR E3937 " --> pdb=" O PHE E3933 " (cutoff:3.500A) Processing helix chain 'E' and resid 3944 through 3967 removed outlier: 3.741A pdb=" N LYS E3953 " --> pdb=" O ARG E3949 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN E3960 " --> pdb=" O SER E3956 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU E3967 " --> pdb=" O ASN E3963 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3983 removed outlier: 3.686A pdb=" N HIS E3982 " --> pdb=" O GLN E3978 " (cutoff:3.500A) Processing helix chain 'E' and resid 3984 through 4004 removed outlier: 4.136A pdb=" N GLY E3991 " --> pdb=" O ASP E3987 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU E3993 " --> pdb=" O VAL E3989 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS E3994 " --> pdb=" O VAL E3990 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET E3999 " --> pdb=" O VAL E3995 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA E4004 " --> pdb=" O MET E4000 " (cutoff:3.500A) Processing helix chain 'E' and resid 4009 through 4030 removed outlier: 4.023A pdb=" N MET E4026 " --> pdb=" O ASP E4022 " (cutoff:3.500A) Processing helix chain 'E' and resid 4039 through 4051 removed outlier: 3.611A pdb=" N ASP E4046 " --> pdb=" O ARG E4042 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E4048 " --> pdb=" O MET E4044 " (cutoff:3.500A) Processing helix chain 'E' and resid 4051 through 4063 removed outlier: 3.758A pdb=" N PHE E4061 " --> pdb=" O MET E4057 " (cutoff:3.500A) Processing helix chain 'E' and resid 4067 through 4072 Processing helix chain 'E' and resid 4074 through 4079 removed outlier: 3.546A pdb=" N GLN E4078 " --> pdb=" O SER E4074 " (cutoff:3.500A) Processing helix chain 'E' and resid 4090 through 4100 removed outlier: 3.622A pdb=" N ASP E4098 " --> pdb=" O GLN E4094 " (cutoff:3.500A) Processing helix chain 'E' and resid 4104 through 4115 Processing helix chain 'E' and resid 4124 through 4131 Processing helix chain 'E' and resid 4132 through 4154 removed outlier: 3.837A pdb=" N ALA E4136 " --> pdb=" O PHE E4132 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E4137 " --> pdb=" O GLN E4133 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASP E4138 " --> pdb=" O GLU E4134 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE E4139 " --> pdb=" O PRO E4135 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E4141 " --> pdb=" O ARG E4137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU E4152 " --> pdb=" O THR E4148 " (cutoff:3.500A) removed outlier: 3.833A 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 4169 through 4174 removed outlier: 3.716A pdb=" N PHE E4174 " --> pdb=" O ILE E4170 " (cutoff:3.500A) Processing helix chain 'E' and resid 4198 through 4206 removed outlier: 3.952A pdb=" N ARG E4202 " --> pdb=" O SER E4198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA E4203 " --> pdb=" O GLU E4199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN E4204 " --> pdb=" O THR E4200 " (cutoff:3.500A) Processing helix chain 'E' and resid 4207 through 4224 removed outlier: 4.003A pdb=" N VAL E4222 " --> pdb=" O ILE E4218 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4251 removed outlier: 3.765A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE E4243 " --> pdb=" O GLU E4239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E4249 " --> pdb=" O MET E4245 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN E4250 " --> pdb=" O GLN E4246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E4251 " --> pdb=" O ILE E4247 " (cutoff:3.500A) Processing helix chain 'E' and resid 4542 through 4558 removed outlier: 3.540A pdb=" N VAL E4546 " --> pdb=" O GLY E4542 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR E4554 " --> pdb=" O LYS E4550 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN E4558 " --> pdb=" O TYR E4554 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4576 removed outlier: 3.587A pdb=" N ALA E4570 " --> pdb=" O ALA E4566 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE E4571 " --> pdb=" O LEU E4567 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E4572 " --> pdb=" O PHE E4568 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E4574 " --> pdb=" O ALA E4570 " (cutoff:3.500A) Processing helix chain 'E' and resid 4641 through 4665 removed outlier: 3.596A pdb=" N ALA E4654 " --> pdb=" O HIS E4650 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E4655 " --> pdb=" O THR E4651 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE E4659 " --> pdb=" O PHE E4655 " (cutoff:3.500A) Processing helix chain 'E' and resid 4667 through 4683 removed outlier: 3.512A pdb=" N GLU E4676 " --> pdb=" O LYS E4672 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA E4678 " --> pdb=" O GLU E4674 " (cutoff:3.500A) Processing helix chain 'E' and resid 4696 through 4702 removed outlier: 3.721A pdb=" N GLN E4700 " --> pdb=" O ASP E4696 " (cutoff:3.500A) Processing helix chain 'E' and resid 4703 through 4706 removed outlier: 3.565A pdb=" N LEU E4706 " --> pdb=" O ARG E4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4703 through 4706' Processing helix chain 'E' and resid 4719 through 4728 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 Processing helix chain 'E' and resid 4786 through 4802 removed outlier: 4.141A pdb=" N MET E4798 " --> pdb=" O TRP E4794 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER E4799 " --> pdb=" O TYR E4795 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E4800 " --> pdb=" O MET E4796 " (cutoff:3.500A) Processing helix chain 'E' and resid 4812 through 4819 removed outlier: 3.508A pdb=" N ILE E4816 " --> pdb=" O HIS E4812 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E4817 " --> pdb=" O LEU E4813 " (cutoff:3.500A) Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.676A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E4829 " --> pdb=" O THR E4825 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL E4830 " --> pdb=" O ILE E4826 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 removed outlier: 3.970A pdb=" N MET E4839 " --> pdb=" O LYS E4835 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY E4842 " --> pdb=" O VAL E4838 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E4843 " --> pdb=" O MET E4839 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E4844 " --> pdb=" O THR E4840 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E4845 " --> pdb=" O VAL E4841 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E4846 " --> pdb=" O GLY E4842 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL E4848 " --> pdb=" O LEU E4844 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E4853 " --> pdb=" O TYR E4849 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL E4854 " --> pdb=" O LEU E4850 " (cutoff:3.500A) Processing helix chain 'E' and resid 4859 through 4863 removed outlier: 3.573A pdb=" N PHE E4862 " --> pdb=" O PHE E4859 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR E4863 " --> pdb=" O ARG E4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4859 through 4863' Processing helix chain 'E' and resid 4878 through 4890 removed outlier: 3.664A pdb=" N PHE E4885 " --> pdb=" O THR E4881 " (cutoff:3.500A) Processing helix chain 'E' and resid 4896 through 4900 removed outlier: 3.920A pdb=" N ASP E4899 " --> pdb=" O GLY E4896 " (cutoff:3.500A) Processing helix chain 'E' and resid 4911 through 4925 removed outlier: 4.142A pdb=" N VAL E4915 " --> pdb=" O LEU E4911 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E4916 " --> pdb=" O TYR E4912 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP E4917 " --> pdb=" O ARG E4913 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E4918 " --> pdb=" O VAL E4914 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E4922 " --> pdb=" O ILE E4918 " (cutoff:3.500A) Processing helix chain 'E' and resid 4926 through 4957 removed outlier: 3.799A pdb=" N LEU E4935 " --> pdb=" O ILE E4931 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG E4944 " --> pdb=" O PHE E4940 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP E4953 " --> pdb=" O GLN E4949 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET E4954 " --> pdb=" O VAL E4950 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU E4955 " --> pdb=" O LYS E4951 " (cutoff:3.500A) Processing helix chain 'E' and resid 4964 through 4968 removed outlier: 4.009A pdb=" N TYR E4967 " --> pdb=" O GLY E4964 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4981 Processing helix chain 'E' and resid 4986 through 4997 Processing helix chain 'E' and resid 5006 through 5017 Processing helix chain 'F' and resid 38 through 43 removed outlier: 3.761A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.986A pdb=" N GLY F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.815A 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 364 through 369 Processing helix chain 'G' and resid 395 through 412 removed outlier: 3.791A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET G 403 " --> pdb=" O GLN G 399 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.673A 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 450 removed outlier: 3.757A pdb=" N GLY G 450 " --> pdb=" O GLN G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 481 removed outlier: 3.614A pdb=" N GLN G 465 " --> pdb=" O HIS G 461 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE G 478 " --> pdb=" O ARG G 474 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU G 481 " --> pdb=" O LEU G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 removed outlier: 3.511A pdb=" N CYS G 490 " --> pdb=" O LEU G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 531 removed outlier: 4.141A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR G 523 " --> pdb=" O VAL G 519 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 524 " --> pdb=" O ASN G 520 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER G 528 " --> pdb=" O GLU G 524 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 529 " --> pdb=" O LEU G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 removed outlier: 3.647A pdb=" N SER G 541 " --> pdb=" O ALA G 538 " (cutoff:3.500A) removed outlier: 4.185A 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: 3.788A pdb=" N VAL G 548 " --> pdb=" O LEU G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 569 removed outlier: 3.777A pdb=" N TYR G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 577 removed outlier: 3.959A pdb=" N LEU G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 594 Processing helix chain 'G' and resid 596 through 608 removed outlier: 4.057A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G 603 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 625 removed outlier: 3.953A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP G 619 " --> pdb=" O ARG G 615 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR G 622 " --> pdb=" O GLN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 889 removed outlier: 3.540A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS G 873 " --> pdb=" O ARG G 869 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS G 879 " --> pdb=" O ALA G 875 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 887 " --> pdb=" O ALA G 883 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN G 889 " --> pdb=" O THR G 885 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 934 removed outlier: 3.771A pdb=" N ASN G 919 " --> pdb=" O GLU G 915 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 929 " --> pdb=" O SER G 925 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA G 934 " --> pdb=" O LYS G 930 " (cutoff:3.500A) Processing helix chain 'G' and resid 980 through 1001 removed outlier: 3.656A pdb=" N LEU G 984 " --> pdb=" O ALA G 980 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP G 986 " --> pdb=" O THR G 982 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 989 " --> pdb=" O VAL G 985 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN G 994 " --> pdb=" O GLU G 990 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1041 removed outlier: 4.226A pdb=" N GLN G1041 " --> pdb=" O ASP G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1042 through 1049 removed outlier: 3.756A pdb=" N LEU G1046 " --> pdb=" O ALA G1042 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G1047 " --> pdb=" O VAL G1043 " (cutoff:3.500A) Processing helix chain 'G' and resid 1078 through 1082 Processing helix chain 'G' and resid 1575 through 1579 removed outlier: 3.531A pdb=" N ALA G1578 " --> pdb=" O LEU G1575 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET G1579 " --> pdb=" O SER G1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1575 through 1579' Processing helix chain 'G' and resid 1652 through 1657 Processing helix chain 'G' and resid 1658 through 1674 removed outlier: 3.754A pdb=" N HIS G1665 " --> pdb=" O ARG G1661 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR G1670 " --> pdb=" O THR G1666 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG G1671 " --> pdb=" O LEU G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1686 removed outlier: 3.705A pdb=" N ALA G1684 " --> pdb=" O ARG G1680 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS G1686 " --> pdb=" O ALA G1682 " (cutoff:3.500A) Processing helix chain 'G' and resid 1692 through 1700 removed outlier: 4.139A pdb=" N LEU G1698 " --> pdb=" O LEU G1694 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G1699 " --> pdb=" O LEU G1695 " (cutoff:3.500A) Processing helix chain 'G' and resid 1710 through 1712 No H-bonds generated for 'chain 'G' and resid 1710 through 1712' Processing helix chain 'G' and resid 1713 through 1718 Processing helix chain 'G' and resid 1720 through 1730 removed outlier: 3.926A pdb=" N ARG G1725 " --> pdb=" O GLU G1721 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER G1726 " --> pdb=" O SER G1722 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 Processing helix chain 'G' and resid 1803 through 1824 removed outlier: 3.757A pdb=" N LEU G1807 " --> pdb=" O PRO G1803 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET G1814 " --> pdb=" O LYS G1810 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY G1816 " --> pdb=" O LEU G1812 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1838 Processing helix chain 'G' and resid 1840 through 1851 removed outlier: 3.533A pdb=" N MET G1851 " --> pdb=" O THR G1847 " (cutoff:3.500A) Processing helix chain 'G' and resid 1855 through 1863 Processing helix chain 'G' and resid 1866 through 1871 Processing helix chain 'G' and resid 1933 through 1982 removed outlier: 3.852A pdb=" N TYR G1945 " --> pdb=" O ASN G1941 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE G1946 " --> pdb=" O LEU G1942 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS G1947 " --> pdb=" O LEU G1943 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU G1963 " --> pdb=" O ALA G1959 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG G1964 " --> pdb=" O ALA G1960 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G1978 " --> pdb=" O ARG G1974 " (cutoff:3.500A) Processing helix chain 'G' and resid 1989 through 1994 removed outlier: 3.675A pdb=" N ARG G1994 " --> pdb=" O GLU G1990 " (cutoff:3.500A) Processing helix chain 'G' and resid 1995 through 1998 Processing helix chain 'G' and resid 2001 through 2011 removed outlier: 3.668A pdb=" N ILE G2006 " --> pdb=" O PRO G2002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN G2007 " --> pdb=" O GLN G2003 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) Processing helix chain 'G' and resid 2028 through 2042 removed outlier: 3.740A pdb=" N GLN G2032 " --> pdb=" O ARG G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2094 through 2108 removed outlier: 3.620A pdb=" N HIS G2100 " --> pdb=" O GLU G2096 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL G2103 " --> pdb=" O SER G2099 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2129 removed outlier: 3.683A pdb=" N TYR G2128 " --> pdb=" O LEU G2124 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2137 Processing helix chain 'G' and resid 2148 through 2165 removed outlier: 4.011A pdb=" N CYS G2158 " --> pdb=" O SER G2154 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN G2161 " --> pdb=" O GLU G2157 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G2165 " --> pdb=" O GLN G2161 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2187 removed outlier: 3.642A pdb=" N LEU G2177 " --> pdb=" O GLN G2173 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.824A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.567A pdb=" N VAL G2210 " --> pdb=" O THR G2206 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN G2213 " --> pdb=" O GLU G2209 " (cutoff:3.500A) Processing helix chain 'G' and resid 2228 through 2242 removed outlier: 3.654A pdb=" N CYS G2233 " --> pdb=" O VAL G2229 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR G2238 " --> pdb=" O ARG G2234 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2252 removed outlier: 3.572A pdb=" N ASP G2252 " --> pdb=" O ARG G2248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2262 removed outlier: 4.074A pdb=" N ASN G2260 " --> pdb=" O TYR G2256 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2279 Processing helix chain 'G' and resid 2294 through 2306 removed outlier: 3.520A pdb=" N VAL G2298 " --> pdb=" O ASP G2294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G2299 " --> pdb=" O LEU G2295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2315 removed outlier: 4.238A pdb=" N ALA G2315 " --> pdb=" O PRO G2311 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2331 removed outlier: 3.525A pdb=" N TYR G2331 " --> pdb=" O GLY G2327 " (cutoff:3.500A) Processing helix chain 'G' and resid 2335 through 2339 removed outlier: 4.266A pdb=" N ALA G2338 " --> pdb=" O LEU G2335 " (cutoff:3.500A) Processing helix chain 'G' and resid 2350 through 2358 removed outlier: 3.775A pdb=" N LEU G2356 " --> pdb=" O VAL G2352 " (cutoff:3.500A) Processing helix chain 'G' and resid 2360 through 2364 Processing helix chain 'G' and resid 2375 through 2388 Processing helix chain 'G' and resid 2389 through 2393 Processing helix chain 'G' and resid 2417 through 2436 removed outlier: 4.194A pdb=" N ALA G2421 " --> pdb=" O HIS G2417 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G2422 " --> pdb=" O LEU G2418 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET G2423 " --> pdb=" O GLY G2419 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA G2428 " --> pdb=" O SER G2424 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G2433 " --> pdb=" O LEU G2429 " (cutoff:3.500A) Processing helix chain 'G' and resid 2440 through 2445 Processing helix chain 'G' and resid 2448 through 2461 removed outlier: 3.731A pdb=" N ILE G2453 " --> pdb=" O GLU G2449 " (cutoff:3.500A) Processing helix chain 'G' and resid 2466 through 2471 Processing helix chain 'G' and resid 2500 through 2507 removed outlier: 3.537A pdb=" N UNK G2504 " --> pdb=" O UNK G2500 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N UNK G2505 " --> pdb=" O UNK G2501 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N UNK G2506 " --> pdb=" O UNK G2502 " (cutoff:3.500A) Processing helix chain 'G' and resid 2516 through 2522 Processing helix chain 'G' and resid 2525 through 2530 removed outlier: 3.583A pdb=" N UNK G2530 " --> pdb=" O UNK G2526 " (cutoff:3.500A) Processing helix chain 'G' and resid 2542 through 2548 removed outlier: 3.660A pdb=" N UNK G2546 " --> pdb=" O UNK G2542 " (cutoff:3.500A) Processing helix chain 'G' and resid 2551 through 2557 removed outlier: 3.768A pdb=" N UNK G2555 " --> pdb=" O UNK G2551 " (cutoff:3.500A) Processing helix chain 'G' and resid 2567 through 2581 removed outlier: 3.551A pdb=" N UNK G2578 " --> pdb=" O UNK G2574 " (cutoff:3.500A) Processing helix chain 'G' and resid 2587 through 2602 removed outlier: 3.615A pdb=" N UNK G2597 " --> pdb=" O UNK G2593 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N UNK G2602 " --> pdb=" O UNK G2598 " (cutoff:3.500A) Processing helix chain 'G' and resid 2610 through 2618 removed outlier: 3.798A pdb=" N UNK G2618 " --> pdb=" O UNK G2614 " (cutoff:3.500A) Processing helix chain 'G' and resid 2626 through 2640 removed outlier: 3.897A pdb=" N UNK G2630 " --> pdb=" O UNK G2626 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N UNK G2631 " --> pdb=" O UNK G2627 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNK G2634 " --> pdb=" O UNK G2630 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N UNK G2635 " --> pdb=" O UNK G2631 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK G2639 " --> pdb=" O UNK G2635 " (cutoff:3.500A) Processing helix chain 'G' and resid 2641 through 2643 No H-bonds generated for 'chain 'G' and resid 2641 through 2643' Processing helix chain 'G' and resid 2650 through 2666 Processing helix chain 'G' and resid 2677 through 2683 removed outlier: 4.139A pdb=" N UNK G2681 " --> pdb=" O UNK G2677 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N UNK G2683 " --> pdb=" O UNK G2679 " (cutoff:3.500A) Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 3.537A pdb=" N ASP G2752 " --> pdb=" O PRO G2748 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE G2768 " --> pdb=" O GLU G2764 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP G2769 " --> pdb=" O LYS G2765 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2797 removed outlier: 3.542A pdb=" N THR G2796 " --> pdb=" O PRO G2793 " (cutoff:3.500A) removed outlier: 3.704A 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: 4.065A pdb=" N ALA G2815 " --> pdb=" O GLU G2811 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET G2816 " --> pdb=" O SER G2812 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G2817 " --> pdb=" O LEU G2813 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2895 removed outlier: 4.021A pdb=" N MET G2874 " --> pdb=" O GLU G2870 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA G2875 " --> pdb=" O LEU G2871 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP G2886 " --> pdb=" O TYR G2882 " (cutoff:3.500A) Processing helix chain 'G' and resid 2907 through 2911 Processing helix chain 'G' and resid 2914 through 2932 removed outlier: 3.606A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG G2920 " --> pdb=" O LYS G2916 " (cutoff:3.500A) Processing helix chain 'G' and resid 2950 through 2976 removed outlier: 4.218A pdb=" N UNK G2956 " --> pdb=" O UNK G2952 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N UNK G2968 " --> pdb=" O UNK G2964 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK G2969 " --> pdb=" O UNK G2965 " (cutoff:3.500A) Processing helix chain 'G' and resid 2999 through 3015 removed outlier: 3.531A pdb=" N UNK G3004 " --> pdb=" O UNK G3000 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK G3006 " --> pdb=" O UNK G3002 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N UNK G3009 " --> pdb=" O UNK G3005 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK G3010 " --> pdb=" O UNK G3006 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.558A pdb=" N UNK G3037 " --> pdb=" O UNK G3033 " (cutoff:3.500A) Processing helix chain 'G' and resid 3052 through 3063 removed outlier: 4.309A pdb=" N UNK G3056 " --> pdb=" O UNK G3052 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK G3057 " --> pdb=" O UNK G3053 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N UNK G3061 " --> pdb=" O UNK G3057 " (cutoff:3.500A) removed outlier: 4.127A 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: 4.064A pdb=" N UNK G3154 " --> pdb=" O UNK G3150 " (cutoff:3.500A) Processing helix chain 'G' and resid 3175 through 3186 removed outlier: 3.704A pdb=" N UNK G3182 " --> pdb=" O UNK G3178 " (cutoff:3.500A) Processing helix chain 'G' and resid 3198 through 3212 Processing helix chain 'G' and resid 3213 through 3215 No H-bonds generated for 'chain 'G' and resid 3213 through 3215' Processing helix chain 'G' and resid 3224 through 3230 removed outlier: 3.889A pdb=" N UNK G3228 " --> pdb=" O UNK G3224 " (cutoff:3.500A) Processing helix chain 'G' and resid 3248 through 3254 removed outlier: 3.594A pdb=" N UNK G3252 " --> pdb=" O UNK G3248 " (cutoff:3.500A) Processing helix chain 'G' and resid 3271 through 3285 removed outlier: 3.520A pdb=" N UNK G3281 " --> pdb=" O UNK G3277 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N UNK G3282 " --> pdb=" O UNK G3278 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N UNK G3284 " --> pdb=" O UNK G3280 " (cutoff:3.500A) Processing helix chain 'G' and resid 3301 through 3304 Processing helix chain 'G' and resid 3305 through 3310 Processing helix chain 'G' and resid 3316 through 3321 removed outlier: 3.555A pdb=" N UNK G3321 " --> pdb=" O UNK G3317 " (cutoff:3.500A) Processing helix chain 'G' and resid 3321 through 3331 removed outlier: 3.559A pdb=" N UNK G3330 " --> pdb=" O UNK G3326 " (cutoff:3.500A) Processing helix chain 'G' and resid 3344 through 3349 removed outlier: 3.575A pdb=" N UNK G3348 " --> pdb=" O UNK G3344 " (cutoff:3.500A) Processing helix chain 'G' and resid 3361 through 3388 Processing helix chain 'G' and resid 3399 through 3407 removed outlier: 3.552A pdb=" N UNK G3403 " --> pdb=" O UNK G3399 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N UNK G3404 " --> pdb=" O UNK G3400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N UNK G3405 " --> pdb=" O UNK G3401 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK G3407 " --> pdb=" O UNK G3403 " (cutoff:3.500A) Processing helix chain 'G' and resid 3410 through 3425 removed outlier: 4.189A pdb=" N UNK G3416 " --> pdb=" O UNK G3412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK G3417 " --> pdb=" O UNK G3413 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N UNK G3420 " --> pdb=" O UNK G3416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N UNK G3421 " --> pdb=" O UNK G3417 " (cutoff:3.500A) Processing helix chain 'G' and resid 3437 through 3443 Processing helix chain 'G' and resid 3445 through 3450 Processing helix chain 'G' and resid 3461 through 3468 removed outlier: 3.572A pdb=" N UNK G3468 " --> pdb=" O UNK G3464 " (cutoff:3.500A) Processing helix chain 'G' and resid 3518 through 3521 removed outlier: 3.612A pdb=" N UNK G3521 " --> pdb=" O UNK G3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3518 through 3521' Processing helix chain 'G' and resid 3522 through 3527 Processing helix chain 'G' and resid 3541 through 3547 removed outlier: 3.633A pdb=" N UNK G3547 " --> pdb=" O UNK G3543 " (cutoff:3.500A) Processing helix chain 'G' and resid 3551 through 3560 Processing helix chain 'G' and resid 3574 through 3579 removed outlier: 3.567A pdb=" N UNK G3579 " --> pdb=" O UNK G3575 " (cutoff:3.500A) Processing helix chain 'G' and resid 3589 through 3611 removed outlier: 4.092A pdb=" N UNK G3595 " --> pdb=" O UNK G3591 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK G3598 " --> pdb=" O UNK G3594 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N UNK G3600 " --> pdb=" O UNK G3596 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N UNK G3601 " --> pdb=" O UNK G3597 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N UNK G3611 " --> pdb=" O UNK G3607 " (cutoff:3.500A) Processing helix chain 'G' and resid 3645 through 3656 removed outlier: 3.735A pdb=" N GLU G3655 " --> pdb=" O ASN G3651 " (cutoff:3.500A) Processing helix chain 'G' and resid 3657 through 3661 Processing helix chain 'G' and resid 3671 through 3680 removed outlier: 4.017A pdb=" N LEU G3677 " --> pdb=" O MET G3673 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER G3678 " --> pdb=" O ILE G3674 " (cutoff:3.500A) Processing helix chain 'G' and resid 3681 through 3683 No H-bonds generated for 'chain 'G' and resid 3681 through 3683' Processing helix chain 'G' and resid 3696 through 3708 Processing helix chain 'G' and resid 3719 through 3738 removed outlier: 3.805A pdb=" N GLU G3736 " --> pdb=" O SER G3732 " (cutoff:3.500A) Processing helix chain 'G' and resid 3752 through 3769 removed outlier: 4.013A pdb=" N LYS G3760 " --> pdb=" O LYS G3756 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN G3767 " --> pdb=" O LEU G3763 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER G3768 " --> pdb=" O LEU G3764 " (cutoff:3.500A) Processing helix chain 'G' and resid 3771 through 3784 removed outlier: 4.661A pdb=" N GLU G3777 " --> pdb=" O ARG G3773 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET G3778 " --> pdb=" O GLY G3774 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL G3779 " --> pdb=" O ALA G3775 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3803 removed outlier: 3.554A pdb=" N SER G3803 " --> pdb=" O LYS G3799 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3824 Processing helix chain 'G' and resid 3828 through 3838 removed outlier: 3.592A pdb=" N ILE G3832 " --> pdb=" O PHE G3828 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3856 Processing helix chain 'G' and resid 3877 through 3892 removed outlier: 3.689A pdb=" N GLN G3882 " --> pdb=" O ASP G3878 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP G3883 " --> pdb=" O GLU G3879 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G3885 " --> pdb=" O THR G3881 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS G3892 " --> pdb=" O LEU G3888 " (cutoff:3.500A) Processing helix chain 'G' and resid 3898 through 3903 Processing helix chain 'G' and resid 3914 through 3937 removed outlier: 4.031A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G3921 " --> pdb=" O ILE G3917 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER G3929 " --> pdb=" O ARG G3925 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR G3934 " --> pdb=" O ILE G3930 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP G3935 " --> pdb=" O SER G3931 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3967 removed outlier: 3.740A pdb=" N LYS G3953 " --> pdb=" O ARG G3949 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA G3954 " --> pdb=" O ASN G3950 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN G3960 " --> pdb=" O SER G3956 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G3967 " --> pdb=" O ASN G3963 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3983 removed outlier: 3.685A pdb=" N HIS G3982 " --> pdb=" O GLN G3978 " (cutoff:3.500A) Processing helix chain 'G' and resid 3984 through 4004 removed outlier: 4.138A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU G3993 " --> pdb=" O VAL G3989 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS G3994 " --> pdb=" O VAL G3990 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS G3998 " --> pdb=" O HIS G3994 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET G3999 " --> pdb=" O VAL G3995 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA G4004 " --> pdb=" O MET G4000 " (cutoff:3.500A) Processing helix chain 'G' and resid 4009 through 4030 removed outlier: 4.024A pdb=" N MET G4026 " --> pdb=" O ASP G4022 " (cutoff:3.500A) Processing helix chain 'G' and resid 4039 through 4051 removed outlier: 3.611A pdb=" N ASP G4046 " --> pdb=" O ARG G4042 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G4048 " --> pdb=" O MET G4044 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4063 removed outlier: 3.757A pdb=" N PHE G4061 " --> pdb=" O MET G4057 " (cutoff:3.500A) Processing helix chain 'G' and resid 4067 through 4072 Processing helix chain 'G' and resid 4074 through 4079 removed outlier: 3.547A pdb=" N GLN G4078 " --> pdb=" O SER G4074 " (cutoff:3.500A) Processing helix chain 'G' and resid 4090 through 4100 removed outlier: 3.623A pdb=" N ASP G4098 " --> pdb=" O GLN G4094 " (cutoff:3.500A) Processing helix chain 'G' and resid 4104 through 4115 Processing helix chain 'G' and resid 4124 through 4131 Processing helix chain 'G' and resid 4132 through 4154 removed outlier: 3.839A pdb=" N ALA G4136 " --> pdb=" O PHE G4132 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G4137 " --> pdb=" O GLN G4133 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASP G4138 " --> pdb=" O GLU G4134 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE G4139 " --> pdb=" O PRO G4135 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE G4141 " --> pdb=" O ARG G4137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU G4152 " --> pdb=" O THR G4148 " (cutoff:3.500A) removed outlier: 3.833A 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 4169 through 4174 removed outlier: 3.717A pdb=" N PHE G4174 " --> pdb=" O ILE G4170 " (cutoff:3.500A) Processing helix chain 'G' and resid 4198 through 4206 removed outlier: 3.953A pdb=" N ARG G4202 " --> pdb=" O SER G4198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G4203 " --> pdb=" O GLU G4199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN G4204 " --> pdb=" O THR G4200 " (cutoff:3.500A) Processing helix chain 'G' and resid 4207 through 4224 removed outlier: 4.003A pdb=" N VAL G4222 " --> pdb=" O ILE G4218 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4251 removed outlier: 3.764A pdb=" N PHE G4234 " --> pdb=" O LYS G4230 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE G4243 " --> pdb=" O GLU G4239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G4249 " --> pdb=" O MET G4245 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN G4250 " --> pdb=" O GLN G4246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G4251 " --> pdb=" O ILE G4247 " (cutoff:3.500A) Processing helix chain 'G' and resid 4542 through 4558 removed outlier: 3.541A pdb=" N VAL G4546 " --> pdb=" O GLY G4542 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR G4554 " --> pdb=" O LYS G4550 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN G4558 " --> pdb=" O TYR G4554 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4576 removed outlier: 3.586A pdb=" N ALA G4570 " --> pdb=" O ALA G4566 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE G4571 " --> pdb=" O LEU G4567 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G4572 " --> pdb=" O PHE G4568 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN G4574 " --> pdb=" O ALA G4570 " (cutoff:3.500A) Processing helix chain 'G' and resid 4641 through 4665 removed outlier: 3.594A pdb=" N ALA G4654 " --> pdb=" O HIS G4650 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE G4655 " --> pdb=" O THR G4651 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) Processing helix chain 'G' and resid 4667 through 4683 removed outlier: 3.512A pdb=" N GLU G4676 " --> pdb=" O LYS G4672 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA G4678 " --> pdb=" O GLU G4674 " (cutoff:3.500A) Processing helix chain 'G' and resid 4696 through 4702 removed outlier: 3.719A pdb=" N GLN G4700 " --> pdb=" O ASP G4696 " (cutoff:3.500A) Processing helix chain 'G' and resid 4703 through 4706 removed outlier: 3.565A pdb=" N LEU G4706 " --> pdb=" O ARG G4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4703 through 4706' 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 Processing helix chain 'G' and resid 4786 through 4802 removed outlier: 4.140A pdb=" N MET G4798 " --> pdb=" O TRP G4794 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU G4800 " --> pdb=" O MET G4796 " (cutoff:3.500A) Processing helix chain 'G' and resid 4812 through 4819 removed outlier: 3.507A pdb=" N ILE G4816 " --> pdb=" O HIS G4812 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G4817 " --> pdb=" O LEU G4813 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.676A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER G4829 " --> pdb=" O THR G4825 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 3.969A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY G4842 " --> pdb=" O VAL G4838 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G4843 " --> pdb=" O MET G4839 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU G4844 " --> pdb=" O THR G4840 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA G4845 " --> pdb=" O VAL G4841 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G4846 " --> pdb=" O GLY G4842 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL G4848 " --> pdb=" O LEU G4844 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL G4853 " --> pdb=" O TYR G4849 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL G4854 " --> pdb=" O LEU G4850 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4863 removed outlier: 3.574A pdb=" N PHE G4862 " --> pdb=" O PHE G4859 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR G4863 " --> pdb=" O ARG G4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4859 through 4863' Processing helix chain 'G' and resid 4878 through 4890 removed outlier: 3.663A pdb=" N PHE G4885 " --> pdb=" O THR G4881 " (cutoff:3.500A) Processing helix chain 'G' and resid 4896 through 4900 removed outlier: 3.919A pdb=" N ASP G4899 " --> pdb=" O GLY G4896 " (cutoff:3.500A) Processing helix chain 'G' and resid 4911 through 4925 removed outlier: 4.142A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE G4916 " --> pdb=" O TYR G4912 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP G4917 " --> pdb=" O ARG G4913 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE G4918 " --> pdb=" O VAL G4914 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE G4922 " --> pdb=" O ILE G4918 " (cutoff:3.500A) Processing helix chain 'G' and resid 4926 through 4957 removed outlier: 3.799A pdb=" N LEU G4935 " --> pdb=" O ILE G4931 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG G4944 " --> pdb=" O PHE G4940 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP G4953 " --> pdb=" O GLN G4949 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET G4954 " --> pdb=" O VAL G4950 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU G4955 " --> pdb=" O LYS G4951 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4968 removed outlier: 4.008A pdb=" N TYR G4967 " --> pdb=" O GLY G4964 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4981 Processing helix chain 'G' and resid 4986 through 4997 Processing helix chain 'G' and resid 5006 through 5017 Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.763A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 3.986A pdb=" N GLY H 62 " --> pdb=" O GLY H 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.814A 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 364 through 369 Processing helix chain 'I' and resid 395 through 412 removed outlier: 3.790A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET I 403 " --> pdb=" O GLN I 399 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS I 405 " --> pdb=" O ALA I 401 " (cutoff:3.500A) removed outlier: 3.673A 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 450 removed outlier: 3.757A pdb=" N GLY I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 481 removed outlier: 3.613A pdb=" N GLN I 465 " --> pdb=" O HIS I 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN I 479 " --> pdb=" O GLN I 475 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU I 480 " --> pdb=" O SER I 476 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU I 481 " --> pdb=" O LEU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 494 removed outlier: 3.512A pdb=" N CYS I 490 " --> pdb=" O LEU I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 531 removed outlier: 4.141A pdb=" N LYS I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU I 517 " --> pdb=" O GLU I 513 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR I 523 " --> pdb=" O VAL I 519 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU I 524 " --> pdb=" O ASN I 520 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER I 528 " --> pdb=" O GLU I 524 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU I 529 " --> pdb=" O LEU I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 538 through 542 removed outlier: 3.646A pdb=" N SER I 541 " --> pdb=" O ALA I 538 " (cutoff:3.500A) removed outlier: 4.186A 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: 3.788A pdb=" N VAL I 548 " --> pdb=" O LEU I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 569 removed outlier: 3.776A pdb=" N TYR I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 577 removed outlier: 3.959A pdb=" N LEU I 575 " --> pdb=" O SER I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 594 Processing helix chain 'I' and resid 596 through 608 removed outlier: 4.058A pdb=" N LEU I 600 " --> pdb=" O ASN I 596 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 603 " --> pdb=" O VAL I 599 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS I 607 " --> pdb=" O LEU I 603 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL I 608 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 625 removed outlier: 3.953A pdb=" N GLN I 618 " --> pdb=" O VAL I 614 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP I 619 " --> pdb=" O ARG I 615 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR I 622 " --> pdb=" O GLN I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 889 removed outlier: 3.541A pdb=" N ILE I 870 " --> pdb=" O HIS I 866 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU I 872 " --> pdb=" O GLU I 868 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS I 873 " --> pdb=" O ARG I 869 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS I 879 " --> pdb=" O ALA I 875 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG I 886 " --> pdb=" O TRP I 882 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE I 887 " --> pdb=" O ALA I 883 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN I 889 " --> pdb=" O THR I 885 " (cutoff:3.500A) Processing helix chain 'I' and resid 914 through 934 removed outlier: 3.771A pdb=" N ASN I 919 " --> pdb=" O GLU I 915 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU I 929 " --> pdb=" O SER I 925 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA I 934 " --> pdb=" O LYS I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 1001 removed outlier: 3.656A pdb=" N LEU I 984 " --> pdb=" O ALA I 980 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP I 986 " --> pdb=" O THR I 982 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA I 989 " --> pdb=" O VAL I 985 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN I 994 " --> pdb=" O GLU I 990 " (cutoff:3.500A) Processing helix chain 'I' and resid 1028 through 1041 removed outlier: 4.225A pdb=" N GLN I1041 " --> pdb=" O ASP I1037 " (cutoff:3.500A) Processing helix chain 'I' and resid 1042 through 1049 removed outlier: 3.755A pdb=" N LEU I1046 " --> pdb=" O ALA I1042 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU I1047 " --> pdb=" O VAL I1043 " (cutoff:3.500A) Processing helix chain 'I' and resid 1078 through 1082 Processing helix chain 'I' and resid 1575 through 1579 removed outlier: 3.530A pdb=" N ALA I1578 " --> pdb=" O LEU I1575 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET I1579 " --> pdb=" O SER I1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1575 through 1579' Processing helix chain 'I' and resid 1652 through 1657 Processing helix chain 'I' and resid 1658 through 1674 removed outlier: 3.753A pdb=" N HIS I1665 " --> pdb=" O ARG I1661 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR I1670 " --> pdb=" O THR I1666 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG I1671 " --> pdb=" O LEU I1667 " (cutoff:3.500A) Processing helix chain 'I' and resid 1678 through 1686 removed outlier: 3.706A pdb=" N ALA I1684 " --> pdb=" O ARG I1680 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS I1686 " --> pdb=" O ALA I1682 " (cutoff:3.500A) Processing helix chain 'I' and resid 1692 through 1700 removed outlier: 4.139A pdb=" N LEU I1698 " --> pdb=" O LEU I1694 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU I1699 " --> pdb=" O LEU I1695 " (cutoff:3.500A) Processing helix chain 'I' and resid 1710 through 1712 No H-bonds generated for 'chain 'I' and resid 1710 through 1712' Processing helix chain 'I' and resid 1713 through 1718 Processing helix chain 'I' and resid 1720 through 1730 removed outlier: 3.926A pdb=" N ARG I1725 " --> pdb=" O GLU I1721 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER I1726 " --> pdb=" O SER I1722 " (cutoff:3.500A) Processing helix chain 'I' and resid 1739 through 1744 Processing helix chain 'I' and resid 1803 through 1824 removed outlier: 3.755A pdb=" N LEU I1807 " --> pdb=" O PRO I1803 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET I1814 " --> pdb=" O LYS I1810 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY I1816 " --> pdb=" O LEU I1812 " (cutoff:3.500A) Processing helix chain 'I' and resid 1833 through 1838 Processing helix chain 'I' and resid 1840 through 1851 removed outlier: 3.532A pdb=" N MET I1851 " --> pdb=" O THR I1847 " (cutoff:3.500A) Processing helix chain 'I' and resid 1855 through 1863 Processing helix chain 'I' and resid 1866 through 1871 Processing helix chain 'I' and resid 1933 through 1982 removed outlier: 3.853A pdb=" N TYR I1945 " --> pdb=" O ASN I1941 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE I1946 " --> pdb=" O LEU I1942 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS I1947 " --> pdb=" O LEU I1943 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU I1963 " --> pdb=" O ALA I1959 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG I1964 " --> pdb=" O ALA I1960 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL I1966 " --> pdb=" O ALA I1962 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS I1968 " --> pdb=" O ARG I1964 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA I1978 " --> pdb=" O ARG I1974 " (cutoff:3.500A) Processing helix chain 'I' and resid 1989 through 1994 removed outlier: 3.675A pdb=" N ARG I1994 " --> pdb=" O GLU I1990 " (cutoff:3.500A) Processing helix chain 'I' and resid 1995 through 1998 Processing helix chain 'I' and resid 2001 through 2011 removed outlier: 3.669A pdb=" N ILE I2006 " --> pdb=" O PRO I2002 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN I2007 " --> pdb=" O GLN I2003 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS I2011 " --> pdb=" O ASN I2007 " (cutoff:3.500A) Processing helix chain 'I' and resid 2028 through 2042 removed outlier: 3.739A pdb=" N GLN I2032 " --> pdb=" O ARG I2028 " (cutoff:3.500A) Processing helix chain 'I' and resid 2094 through 2108 removed outlier: 3.620A pdb=" N HIS I2100 " --> pdb=" O GLU I2096 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL I2103 " --> pdb=" O SER I2099 " (cutoff:3.500A) Processing helix chain 'I' and resid 2113 through 2129 removed outlier: 3.683A pdb=" N TYR I2128 " --> pdb=" O LEU I2124 " (cutoff:3.500A) Processing helix chain 'I' and resid 2129 through 2137 Processing helix chain 'I' and resid 2148 through 2165 removed outlier: 4.010A pdb=" N CYS I2158 " --> pdb=" O SER I2154 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN I2161 " --> pdb=" O GLU I2157 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU I2165 " --> pdb=" O GLN I2161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2171 through 2187 removed outlier: 3.641A pdb=" N LEU I2177 " --> pdb=" O GLN I2173 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.824A pdb=" N MET I2198 " --> pdb=" O HIS I2194 " (cutoff:3.500A) Processing helix chain 'I' and resid 2202 through 2216 removed outlier: 3.567A pdb=" N VAL I2210 " --> pdb=" O THR I2206 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN I2213 " --> pdb=" O GLU I2209 " (cutoff:3.500A) Processing helix chain 'I' and resid 2228 through 2242 removed outlier: 3.655A pdb=" N CYS I2233 " --> pdb=" O VAL I2229 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR I2238 " --> pdb=" O ARG I2234 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2252 removed outlier: 3.572A pdb=" N ASP I2252 " --> pdb=" O ARG I2248 " (cutoff:3.500A) Processing helix chain 'I' and resid 2253 through 2262 removed outlier: 4.073A pdb=" N ASN I2260 " --> pdb=" O TYR I2256 " (cutoff:3.500A) Processing helix chain 'I' and resid 2271 through 2279 Processing helix chain 'I' and resid 2294 through 2306 removed outlier: 3.519A pdb=" N VAL I2298 " --> pdb=" O ASP I2294 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL I2299 " --> pdb=" O LEU I2295 " (cutoff:3.500A) Processing helix chain 'I' and resid 2310 through 2315 removed outlier: 4.239A pdb=" N ALA I2315 " --> pdb=" O PRO I2311 " (cutoff:3.500A) Processing helix chain 'I' and resid 2326 through 2331 removed outlier: 3.526A pdb=" N TYR I2331 " --> pdb=" O GLY I2327 " (cutoff:3.500A) Processing helix chain 'I' and resid 2335 through 2339 removed outlier: 4.265A pdb=" N ALA I2338 " --> pdb=" O LEU I2335 " (cutoff:3.500A) Processing helix chain 'I' and resid 2350 through 2358 removed outlier: 3.774A pdb=" N LEU I2356 " --> pdb=" O VAL I2352 " (cutoff:3.500A) Processing helix chain 'I' and resid 2360 through 2364 Processing helix chain 'I' and resid 2375 through 2388 Processing helix chain 'I' and resid 2389 through 2393 Processing helix chain 'I' and resid 2417 through 2436 removed outlier: 4.195A pdb=" N ALA I2421 " --> pdb=" O HIS I2417 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE I2422 " --> pdb=" O LEU I2418 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET I2423 " --> pdb=" O GLY I2419 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA I2428 " --> pdb=" O SER I2424 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I2433 " --> pdb=" O LEU I2429 " (cutoff:3.500A) Processing helix chain 'I' and resid 2440 through 2445 removed outlier: 3.500A pdb=" N ALA I2445 " --> pdb=" O HIS I2441 " (cutoff:3.500A) Processing helix chain 'I' and resid 2448 through 2461 removed outlier: 3.731A pdb=" N ILE I2453 " --> pdb=" O GLU I2449 " (cutoff:3.500A) Processing helix chain 'I' and resid 2466 through 2471 Processing helix chain 'I' and resid 2502 through 2507 removed outlier: 3.651A 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: 3.604A pdb=" N UNK I2530 " --> pdb=" O UNK I2526 " (cutoff:3.500A) Processing helix chain 'I' and resid 2542 through 2548 removed outlier: 3.661A pdb=" N UNK I2546 " --> pdb=" O UNK I2542 " (cutoff:3.500A) Processing helix chain 'I' and resid 2551 through 2556 removed outlier: 3.746A pdb=" N UNK I2555 " --> pdb=" O UNK I2551 " (cutoff:3.500A) Processing helix chain 'I' and resid 2567 through 2581 removed outlier: 3.566A pdb=" N UNK I2578 " --> pdb=" O UNK I2574 " (cutoff:3.500A) Processing helix chain 'I' and resid 2587 through 2602 removed outlier: 3.622A pdb=" N UNK I2597 " --> pdb=" O UNK I2593 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N UNK I2602 " --> pdb=" O UNK I2598 " (cutoff:3.500A) Processing helix chain 'I' and resid 2610 through 2618 removed outlier: 3.797A pdb=" N UNK I2618 " --> pdb=" O UNK I2614 " (cutoff:3.500A) Processing helix chain 'I' and resid 2626 through 2640 removed outlier: 3.901A pdb=" N UNK I2630 " --> pdb=" O UNK I2626 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N UNK I2631 " --> pdb=" O UNK I2627 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N UNK I2634 " --> pdb=" O UNK I2630 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK I2635 " --> pdb=" O UNK I2631 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N UNK I2639 " --> pdb=" O UNK I2635 " (cutoff:3.500A) Processing helix chain 'I' and resid 2641 through 2643 No H-bonds generated for 'chain 'I' and resid 2641 through 2643' Processing helix chain 'I' and resid 2650 through 2666 Processing helix chain 'I' and resid 2678 through 2683 removed outlier: 4.236A pdb=" N UNK I2683 " --> pdb=" O UNK I2679 " (cutoff:3.500A) Processing helix chain 'I' and resid 2748 through 2773 removed outlier: 3.537A pdb=" N ASP I2752 " --> pdb=" O PRO I2748 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER I2753 " --> pdb=" O GLU I2749 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE I2754 " --> pdb=" O LYS I2750 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE I2768 " --> pdb=" O GLU I2764 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP I2769 " --> pdb=" O LYS I2765 " (cutoff:3.500A) Processing helix chain 'I' and resid 2793 through 2797 removed outlier: 3.543A pdb=" N THR I2796 " --> pdb=" O PRO I2793 " (cutoff:3.500A) removed outlier: 3.705A 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 2800 through 2804 Processing helix chain 'I' and resid 2809 through 2820 removed outlier: 4.064A pdb=" N ALA I2815 " --> pdb=" O GLU I2811 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET I2816 " --> pdb=" O SER I2812 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I2817 " --> pdb=" O LEU I2813 " (cutoff:3.500A) Processing helix chain 'I' and resid 2868 through 2895 removed outlier: 4.022A pdb=" N MET I2874 " --> pdb=" O GLU I2870 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA I2875 " --> pdb=" O LEU I2871 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP I2886 " --> pdb=" O TYR I2882 " (cutoff:3.500A) Processing helix chain 'I' and resid 2907 through 2911 Processing helix chain 'I' and resid 2914 through 2932 removed outlier: 3.606A pdb=" N ASP I2919 " --> pdb=" O GLU I2915 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG I2920 " --> pdb=" O LYS I2916 " (cutoff:3.500A) Processing helix chain 'I' and resid 2950 through 2976 removed outlier: 4.200A pdb=" N UNK I2956 " --> pdb=" O UNK I2952 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N UNK I2968 " --> pdb=" O UNK I2964 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N UNK I2969 " --> pdb=" O UNK I2965 " (cutoff:3.500A) Processing helix chain 'I' and resid 2999 through 3015 removed outlier: 3.559A pdb=" N UNK I3004 " --> pdb=" O UNK I3000 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N UNK I3006 " --> pdb=" O UNK I3002 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK I3009 " --> pdb=" O UNK I3005 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N UNK I3010 " --> pdb=" O UNK I3006 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.561A pdb=" N UNK I3037 " --> pdb=" O UNK I3033 " (cutoff:3.500A) Processing helix chain 'I' and resid 3052 through 3063 removed outlier: 4.321A pdb=" N UNK I3056 " --> pdb=" O UNK I3052 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK I3057 " --> pdb=" O UNK I3053 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N UNK I3061 " --> pdb=" O UNK I3057 " (cutoff:3.500A) removed outlier: 4.123A 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: 4.065A pdb=" N UNK I3154 " --> pdb=" O UNK I3150 " (cutoff:3.500A) Processing helix chain 'I' and resid 3175 through 3186 removed outlier: 3.677A pdb=" N UNK I3182 " --> pdb=" O UNK I3178 " (cutoff:3.500A) Processing helix chain 'I' and resid 3198 through 3212 removed outlier: 3.510A pdb=" N UNK I3205 " --> pdb=" O UNK I3201 " (cutoff:3.500A) Processing helix chain 'I' and resid 3213 through 3215 No H-bonds generated for 'chain 'I' and resid 3213 through 3215' Processing helix chain 'I' and resid 3224 through 3230 removed outlier: 3.882A pdb=" N UNK I3228 " --> pdb=" O UNK I3224 " (cutoff:3.500A) Processing helix chain 'I' and resid 3248 through 3254 removed outlier: 3.588A pdb=" N UNK I3252 " --> pdb=" O UNK I3248 " (cutoff:3.500A) Processing helix chain 'I' and resid 3271 through 3285 removed outlier: 3.530A pdb=" N UNK I3281 " --> pdb=" O UNK I3277 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N UNK I3282 " --> pdb=" O UNK I3278 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNK I3284 " --> pdb=" O UNK I3280 " (cutoff:3.500A) Processing helix chain 'I' and resid 3301 through 3304 Processing helix chain 'I' and resid 3305 through 3310 Processing helix chain 'I' and resid 3316 through 3321 removed outlier: 3.566A pdb=" N UNK I3321 " --> pdb=" O UNK I3317 " (cutoff:3.500A) Processing helix chain 'I' and resid 3321 through 3331 removed outlier: 3.559A pdb=" N UNK I3330 " --> pdb=" O UNK I3326 " (cutoff:3.500A) Processing helix chain 'I' and resid 3344 through 3349 removed outlier: 3.561A pdb=" N UNK I3348 " --> pdb=" O UNK I3344 " (cutoff:3.500A) Processing helix chain 'I' and resid 3361 through 3388 Processing helix chain 'I' and resid 3399 through 3407 removed outlier: 3.545A pdb=" N UNK I3403 " --> pdb=" O UNK I3399 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N UNK I3404 " --> pdb=" O UNK I3400 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N UNK I3405 " --> pdb=" O UNK I3401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N UNK I3407 " --> pdb=" O UNK I3403 " (cutoff:3.500A) Processing helix chain 'I' and resid 3410 through 3425 removed outlier: 4.171A pdb=" N UNK I3416 " --> pdb=" O UNK I3412 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N UNK I3420 " --> pdb=" O UNK I3416 " (cutoff:3.500A) Processing helix chain 'I' and resid 3437 through 3443 Processing helix chain 'I' and resid 3445 through 3450 Processing helix chain 'I' and resid 3461 through 3468 removed outlier: 3.563A pdb=" N UNK I3468 " --> pdb=" O UNK I3464 " (cutoff:3.500A) Processing helix chain 'I' and resid 3518 through 3521 removed outlier: 3.616A pdb=" N UNK I3521 " --> pdb=" O UNK I3518 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3518 through 3521' Processing helix chain 'I' and resid 3522 through 3527 Processing helix chain 'I' and resid 3541 through 3547 removed outlier: 3.646A 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: 3.584A pdb=" N UNK I3579 " --> pdb=" O UNK I3575 " (cutoff:3.500A) Processing helix chain 'I' and resid 3589 through 3611 removed outlier: 4.081A pdb=" N UNK I3595 " --> pdb=" O UNK I3591 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK I3598 " --> pdb=" O UNK I3594 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N UNK I3600 " --> pdb=" O UNK I3596 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N UNK I3601 " --> pdb=" O UNK I3597 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N UNK I3611 " --> pdb=" O UNK I3607 " (cutoff:3.500A) Processing helix chain 'I' and resid 3645 through 3656 removed outlier: 3.736A pdb=" N GLU I3655 " --> pdb=" O ASN I3651 " (cutoff:3.500A) Processing helix chain 'I' and resid 3657 through 3661 Processing helix chain 'I' and resid 3671 through 3680 removed outlier: 4.017A pdb=" N LEU I3677 " --> pdb=" O MET I3673 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER I3678 " --> pdb=" O ILE I3674 " (cutoff:3.500A) Processing helix chain 'I' and resid 3681 through 3683 No H-bonds generated for 'chain 'I' and resid 3681 through 3683' Processing helix chain 'I' and resid 3696 through 3708 Processing helix chain 'I' and resid 3719 through 3738 removed outlier: 3.806A pdb=" N GLU I3736 " --> pdb=" O SER I3732 " (cutoff:3.500A) Processing helix chain 'I' and resid 3752 through 3769 removed outlier: 4.013A pdb=" N LYS I3760 " --> pdb=" O LYS I3756 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN I3767 " --> pdb=" O LEU I3763 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER I3768 " --> pdb=" O LEU I3764 " (cutoff:3.500A) Processing helix chain 'I' and resid 3771 through 3784 removed outlier: 4.661A pdb=" N GLU I3777 " --> pdb=" O ARG I3773 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET I3778 " --> pdb=" O GLY I3774 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL I3779 " --> pdb=" O ALA I3775 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU I3780 " --> pdb=" O ALA I3776 " (cutoff:3.500A) Processing helix chain 'I' and resid 3791 through 3803 removed outlier: 3.555A pdb=" N SER I3803 " --> pdb=" O LYS I3799 " (cutoff:3.500A) Processing helix chain 'I' and resid 3809 through 3824 Processing helix chain 'I' and resid 3828 through 3838 removed outlier: 3.592A pdb=" N ILE I3832 " --> pdb=" O PHE I3828 " (cutoff:3.500A) Processing helix chain 'I' and resid 3843 through 3856 Processing helix chain 'I' and resid 3877 through 3892 removed outlier: 3.690A pdb=" N GLN I3882 " --> pdb=" O ASP I3878 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP I3883 " --> pdb=" O GLU I3879 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE I3885 " --> pdb=" O THR I3881 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS I3892 " --> pdb=" O LEU I3888 " (cutoff:3.500A) Processing helix chain 'I' and resid 3898 through 3903 Processing helix chain 'I' and resid 3914 through 3937 removed outlier: 4.033A pdb=" N CYS I3918 " --> pdb=" O ASN I3914 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP I3921 " --> pdb=" O ILE I3917 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER I3929 " --> pdb=" O ARG I3925 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR I3934 " --> pdb=" O ILE I3930 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP I3935 " --> pdb=" O SER I3931 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR I3936 " --> pdb=" O ASP I3932 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR I3937 " --> pdb=" O PHE I3933 " (cutoff:3.500A) Processing helix chain 'I' and resid 3944 through 3967 removed outlier: 3.741A pdb=" N LYS I3953 " --> pdb=" O ARG I3949 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA I3954 " --> pdb=" O ASN I3950 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN I3960 " --> pdb=" O SER I3956 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU I3967 " --> pdb=" O ASN I3963 " (cutoff:3.500A) Processing helix chain 'I' and resid 3973 through 3983 removed outlier: 3.686A pdb=" N HIS I3982 " --> pdb=" O GLN I3978 " (cutoff:3.500A) Processing helix chain 'I' and resid 3984 through 4004 removed outlier: 4.138A pdb=" N GLY I3991 " --> pdb=" O ASP I3987 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE I3992 " --> pdb=" O ALA I3988 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU I3993 " --> pdb=" O VAL I3989 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS I3994 " --> pdb=" O VAL I3990 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS I3998 " --> pdb=" O HIS I3994 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET I3999 " --> pdb=" O VAL I3995 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET I4000 " --> pdb=" O PHE I3996 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA I4004 " --> pdb=" O MET I4000 " (cutoff:3.500A) Processing helix chain 'I' and resid 4009 through 4030 removed outlier: 4.023A pdb=" N MET I4026 " --> pdb=" O ASP I4022 " (cutoff:3.500A) Processing helix chain 'I' and resid 4039 through 4051 removed outlier: 3.611A pdb=" N ASP I4046 " --> pdb=" O ARG I4042 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU I4048 " --> pdb=" O MET I4044 " (cutoff:3.500A) Processing helix chain 'I' and resid 4051 through 4063 removed outlier: 3.757A pdb=" N PHE I4061 " --> pdb=" O MET I4057 " (cutoff:3.500A) Processing helix chain 'I' and resid 4067 through 4072 Processing helix chain 'I' and resid 4074 through 4079 removed outlier: 3.546A pdb=" N GLN I4078 " --> pdb=" O SER I4074 " (cutoff:3.500A) Processing helix chain 'I' and resid 4090 through 4100 removed outlier: 3.622A pdb=" N ASP I4098 " --> pdb=" O GLN I4094 " (cutoff:3.500A) Processing helix chain 'I' and resid 4104 through 4115 Processing helix chain 'I' and resid 4124 through 4131 Processing helix chain 'I' and resid 4132 through 4154 removed outlier: 3.837A pdb=" N ALA I4136 " --> pdb=" O PHE I4132 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG I4137 " --> pdb=" O GLN I4133 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP I4138 " --> pdb=" O GLU I4134 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE I4139 " --> pdb=" O PRO I4135 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE I4141 " --> pdb=" O ARG I4137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU I4152 " --> pdb=" O THR I4148 " (cutoff:3.500A) removed outlier: 3.833A 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 4169 through 4174 removed outlier: 3.716A pdb=" N PHE I4174 " --> pdb=" O ILE I4170 " (cutoff:3.500A) Processing helix chain 'I' and resid 4198 through 4206 removed outlier: 3.951A pdb=" N ARG I4202 " --> pdb=" O SER I4198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I4203 " --> pdb=" O GLU I4199 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN I4204 " --> pdb=" O THR I4200 " (cutoff:3.500A) Processing helix chain 'I' and resid 4207 through 4224 removed outlier: 4.001A pdb=" N VAL I4222 " --> pdb=" O ILE I4218 " (cutoff:3.500A) Processing helix chain 'I' and resid 4228 through 4251 removed outlier: 3.765A pdb=" N PHE I4234 " --> pdb=" O LYS I4230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE I4243 " --> pdb=" O GLU I4239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I4249 " --> pdb=" O MET I4245 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN I4250 " --> pdb=" O GLN I4246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE I4251 " --> pdb=" O ILE I4247 " (cutoff:3.500A) Processing helix chain 'I' and resid 4542 through 4558 removed outlier: 3.541A pdb=" N VAL I4546 " --> pdb=" O GLY I4542 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR I4554 " --> pdb=" O LYS I4550 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN I4558 " --> pdb=" O TYR I4554 " (cutoff:3.500A) Processing helix chain 'I' and resid 4558 through 4576 removed outlier: 3.587A pdb=" N ALA I4570 " --> pdb=" O ALA I4566 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE I4571 " --> pdb=" O LEU I4567 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA I4572 " --> pdb=" O PHE I4568 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN I4574 " --> pdb=" O ALA I4570 " (cutoff:3.500A) Processing helix chain 'I' and resid 4641 through 4665 removed outlier: 3.594A pdb=" N ALA I4654 " --> pdb=" O HIS I4650 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE I4655 " --> pdb=" O THR I4651 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE I4659 " --> pdb=" O PHE I4655 " (cutoff:3.500A) Processing helix chain 'I' and resid 4667 through 4683 removed outlier: 3.513A pdb=" N GLU I4676 " --> pdb=" O LYS I4672 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA I4678 " --> pdb=" O GLU I4674 " (cutoff:3.500A) Processing helix chain 'I' and resid 4696 through 4702 removed outlier: 3.720A pdb=" N GLN I4700 " --> pdb=" O ASP I4696 " (cutoff:3.500A) Processing helix chain 'I' and resid 4703 through 4706 removed outlier: 3.566A pdb=" N LEU I4706 " --> pdb=" O ARG I4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4703 through 4706' 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 Processing helix chain 'I' and resid 4786 through 4802 removed outlier: 4.140A pdb=" N MET I4798 " --> pdb=" O TRP I4794 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER I4799 " --> pdb=" O TYR I4795 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU I4800 " --> pdb=" O MET I4796 " (cutoff:3.500A) Processing helix chain 'I' and resid 4812 through 4819 removed outlier: 3.508A pdb=" N ILE I4816 " --> pdb=" O HIS I4812 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA I4817 " --> pdb=" O LEU I4813 " (cutoff:3.500A) Processing helix chain 'I' and resid 4820 through 4833 removed outlier: 3.676A pdb=" N ILE I4826 " --> pdb=" O THR I4822 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I4829 " --> pdb=" O THR I4825 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL I4830 " --> pdb=" O ILE I4826 " (cutoff:3.500A) Processing helix chain 'I' and resid 4833 through 4858 removed outlier: 3.970A pdb=" N MET I4839 " --> pdb=" O LYS I4835 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY I4842 " --> pdb=" O VAL I4838 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU I4843 " --> pdb=" O MET I4839 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU I4844 " --> pdb=" O THR I4840 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA I4845 " --> pdb=" O VAL I4841 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I4846 " --> pdb=" O GLY I4842 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL I4848 " --> pdb=" O LEU I4844 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL I4853 " --> pdb=" O TYR I4849 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL I4854 " --> pdb=" O LEU I4850 " (cutoff:3.500A) Processing helix chain 'I' and resid 4859 through 4863 removed outlier: 3.573A pdb=" N PHE I4862 " --> pdb=" O PHE I4859 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR I4863 " --> pdb=" O ARG I4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4859 through 4863' Processing helix chain 'I' and resid 4878 through 4890 removed outlier: 3.663A pdb=" N PHE I4885 " --> pdb=" O THR I4881 " (cutoff:3.500A) Processing helix chain 'I' and resid 4896 through 4900 removed outlier: 3.919A pdb=" N ASP I4899 " --> pdb=" O GLY I4896 " (cutoff:3.500A) Processing helix chain 'I' and resid 4911 through 4925 removed outlier: 4.141A pdb=" N VAL I4915 " --> pdb=" O LEU I4911 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE I4916 " --> pdb=" O TYR I4912 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP I4917 " --> pdb=" O ARG I4913 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE I4918 " --> pdb=" O VAL I4914 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE I4922 " --> pdb=" O ILE I4918 " (cutoff:3.500A) Processing helix chain 'I' and resid 4926 through 4957 removed outlier: 3.800A pdb=" N LEU I4935 " --> pdb=" O ILE I4931 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG I4944 " --> pdb=" O PHE I4940 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP I4953 " --> pdb=" O GLN I4949 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET I4954 " --> pdb=" O VAL I4950 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU I4955 " --> pdb=" O LYS I4951 " (cutoff:3.500A) Processing helix chain 'I' and resid 4964 through 4968 removed outlier: 4.011A pdb=" N TYR I4967 " --> pdb=" O GLY I4964 " (cutoff:3.500A) Processing helix chain 'I' and resid 4973 through 4981 Processing helix chain 'I' and resid 4986 through 4997 Processing helix chain 'I' and resid 5006 through 5017 Processing helix chain 'J' and resid 38 through 43 removed outlier: 3.762A pdb=" N ARG J 42 " --> pdb=" O SER J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.986A pdb=" N GLY J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.815A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.863A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG B 110 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU B 69 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 21 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 27 Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 152 removed outlier: 3.779A pdb=" N TRP B 200 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AA7, first strand: chain 'B' and resid 280 through 284 removed outlier: 3.628A pdb=" N PHE B 223 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 389 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 233 removed outlier: 5.762A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS B 374 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.715A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 314 through 316 Processing sheet with id=AB2, first strand: chain 'B' and resid 634 through 639 removed outlier: 3.928A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 644 through 646 Processing sheet with id=AB4, first strand: chain 'B' and resid 661 through 663 Processing sheet with id=AB5, first strand: chain 'B' and resid 742 through 744 removed outlier: 3.563A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 713 through 714 Processing sheet with id=AB7, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AB8, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AB9, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.372A pdb=" N THR B 892 " --> pdb=" O HIS B 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 940 through 941 Processing sheet with id=AC2, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 5.598A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1255 through 1259 removed outlier: 3.589A pdb=" N GLU B1256 " --> pdb=" O ALA B1273 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1459 through 1463 removed outlier: 3.818A pdb=" N UNK B1287 " --> pdb=" O UNK B1460 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1293 through 1294 Processing sheet with id=AC6, first strand: chain 'B' and resid 1515 through 1516 Processing sheet with id=AC7, first strand: chain 'B' and resid 1734 through 1736 Processing sheet with id=AC8, first strand: chain 'B' and resid 4178 through 4183 Processing sheet with id=AC9, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AD1, first strand: chain 'E' and resid 116 through 117 removed outlier: 3.864A pdb=" N GLN E 71 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG E 110 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU E 69 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL E 21 " --> pdb=" O PRO E 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 23 through 27 Processing sheet with id=AD3, first strand: chain 'E' and resid 148 through 152 removed outlier: 3.778A pdb=" N TRP E 200 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AD5, first strand: chain 'E' and resid 280 through 284 removed outlier: 3.629A pdb=" N PHE E 223 " --> pdb=" O PHE E 389 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE E 389 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 230 through 233 removed outlier: 5.760A pdb=" N VAL E 245 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS E 374 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 290 through 292 removed outlier: 3.715A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 314 through 316 Processing sheet with id=AD9, first strand: chain 'E' and resid 634 through 639 removed outlier: 3.928A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG E1646 " --> pdb=" O ILE E1641 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 644 through 646 Processing sheet with id=AE2, first strand: chain 'E' and resid 661 through 663 Processing sheet with id=AE3, first strand: chain 'E' and resid 742 through 744 removed outlier: 3.562A pdb=" N VAL E 666 " --> pdb=" O VAL E 744 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 713 through 714 Processing sheet with id=AE5, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AE6, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AE7, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.373A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 940 through 941 Processing sheet with id=AE9, first strand: chain 'E' and resid 1136 through 1138 removed outlier: 5.597A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 1255 through 1259 removed outlier: 3.589A pdb=" N GLU E1256 " --> pdb=" O ALA E1273 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 1459 through 1462 removed outlier: 3.749A pdb=" N UNK E1287 " --> pdb=" O UNK E1460 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK E1462 " --> pdb=" O UNK E1285 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 1293 through 1294 Processing sheet with id=AF4, first strand: chain 'E' and resid 1734 through 1736 Processing sheet with id=AF5, first strand: chain 'E' and resid 4178 through 4183 Processing sheet with id=AF6, first strand: chain 'E' and resid 4580 through 4583 Processing sheet with id=AF7, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AF8, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AF9, first strand: chain 'G' and resid 116 through 117 removed outlier: 3.864A pdb=" N GLN G 71 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG G 110 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU G 69 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL G 21 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 23 through 27 Processing sheet with id=AG2, first strand: chain 'G' and resid 148 through 152 removed outlier: 3.779A pdb=" N TRP G 200 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 181 through 184 Processing sheet with id=AG4, first strand: chain 'G' and resid 280 through 284 removed outlier: 3.629A pdb=" N PHE G 223 " --> pdb=" O PHE G 389 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE G 389 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 230 through 233 removed outlier: 5.761A pdb=" N VAL G 245 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS G 374 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 290 through 292 removed outlier: 3.715A pdb=" N VAL G 300 " --> pdb=" O ALA G 292 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 314 through 316 Processing sheet with id=AG8, first strand: chain 'G' and resid 634 through 639 removed outlier: 3.929A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG G1646 " --> pdb=" O ILE G1641 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 644 through 646 Processing sheet with id=AH1, first strand: chain 'G' and resid 661 through 663 Processing sheet with id=AH2, first strand: chain 'G' and resid 742 through 744 removed outlier: 3.563A pdb=" N VAL G 666 " --> pdb=" O VAL G 744 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 713 through 714 Processing sheet with id=AH4, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AH5, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AH6, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.372A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'G' and resid 940 through 941 Processing sheet with id=AH8, first strand: chain 'G' and resid 1136 through 1138 removed outlier: 5.598A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 1255 through 1259 removed outlier: 3.588A pdb=" N GLU G1256 " --> pdb=" O ALA G1273 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 1459 through 1462 removed outlier: 3.726A pdb=" N UNK G1287 " --> pdb=" O UNK G1460 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 1293 through 1294 Processing sheet with id=AI3, first strand: chain 'G' and resid 1734 through 1736 Processing sheet with id=AI4, first strand: chain 'G' and resid 4178 through 4183 Processing sheet with id=AI5, first strand: chain 'G' and resid 4580 through 4583 Processing sheet with id=AI6, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AI7, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AI8, first strand: chain 'I' and resid 116 through 117 removed outlier: 3.863A pdb=" N GLN I 71 " --> pdb=" O LEU I 108 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG I 110 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU I 69 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL I 21 " --> pdb=" O PRO I 204 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 23 through 27 Processing sheet with id=AJ1, first strand: chain 'I' and resid 148 through 152 removed outlier: 3.779A pdb=" N TRP I 200 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 181 through 184 Processing sheet with id=AJ3, first strand: chain 'I' and resid 280 through 284 removed outlier: 3.629A pdb=" N PHE I 223 " --> pdb=" O PHE I 389 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE I 389 " --> pdb=" O PHE I 223 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'I' and resid 230 through 233 removed outlier: 5.761A pdb=" N VAL I 245 " --> pdb=" O ALA I 376 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS I 374 " --> pdb=" O TYR I 247 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'I' and resid 290 through 292 removed outlier: 3.716A pdb=" N VAL I 300 " --> pdb=" O ALA I 292 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 314 through 316 Processing sheet with id=AJ7, first strand: chain 'I' and resid 634 through 639 removed outlier: 3.927A pdb=" N GLN I 634 " --> pdb=" O HIS I1640 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG I1646 " --> pdb=" O ILE I1641 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'I' and resid 644 through 646 Processing sheet with id=AJ9, first strand: chain 'I' and resid 661 through 663 Processing sheet with id=AK1, first strand: chain 'I' and resid 742 through 744 removed outlier: 3.562A pdb=" N VAL I 666 " --> pdb=" O VAL I 744 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 713 through 714 Processing sheet with id=AK3, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AK4, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AK5, first strand: chain 'I' and resid 892 through 893 removed outlier: 6.371A pdb=" N THR I 892 " --> pdb=" O HIS I 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'I' and resid 940 through 941 Processing sheet with id=AK7, first strand: chain 'I' and resid 1136 through 1138 removed outlier: 5.598A pdb=" N ILE I1074 " --> pdb=" O SER I1239 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'I' and resid 1255 through 1259 removed outlier: 3.589A pdb=" N GLU I1256 " --> pdb=" O ALA I1273 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'I' and resid 1459 through 1462 removed outlier: 3.817A pdb=" N UNK I1287 " --> pdb=" O UNK I1460 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'I' and resid 1293 through 1294 Processing sheet with id=AL2, first strand: chain 'I' and resid 1515 through 1516 Processing sheet with id=AL3, first strand: chain 'I' and resid 1734 through 1736 Processing sheet with id=AL4, first strand: chain 'I' and resid 4178 through 4183 Processing sheet with id=AL5, first strand: chain 'I' and resid 4580 through 4583 Processing sheet with id=AL6, first strand: chain 'J' and resid 21 through 23 Processing sheet with id=AL7, first strand: chain 'J' and resid 28 through 30 5015 hydrogen bonds defined for protein. 14430 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: 92.82 Time building geometry restraints manager: 35.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 39201 1.34 - 1.46: 20374 1.46 - 1.58: 62417 1.58 - 1.70: 0 1.70 - 1.82: 1020 Bond restraints: 123012 Sorted by residual: bond pdb=" C ARG B4175 " pdb=" N PRO B4176 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.25e-02 6.40e+03 1.89e+01 bond pdb=" C ARG G4175 " pdb=" N PRO G4176 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.25e-02 6.40e+03 1.84e+01 bond pdb=" C ARG E4175 " pdb=" N PRO E4176 " ideal model delta sigma weight residual 1.336 1.389 -0.054 1.25e-02 6.40e+03 1.84e+01 bond pdb=" C ARG I4175 " pdb=" N PRO I4176 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.25e-02 6.40e+03 1.83e+01 bond pdb=" N GLU B4871 " pdb=" CA GLU B4871 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.05e-02 9.07e+03 5.75e+00 ... (remaining 123007 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.99: 2848 105.99 - 114.16: 70930 114.16 - 122.32: 72118 122.32 - 130.49: 21237 130.49 - 138.66: 587 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 113.53 103.66 9.87 1.39e+00 5.18e-01 5.04e+01 angle pdb=" N PRO I4872 " pdb=" CA PRO I4872 " pdb=" C PRO I4872 " ideal model delta sigma weight residual 113.53 103.66 9.87 1.39e+00 5.18e-01 5.04e+01 angle pdb=" N PRO E4872 " pdb=" CA PRO E4872 " pdb=" C PRO E4872 " ideal model delta sigma weight residual 113.53 103.73 9.80 1.39e+00 5.18e-01 4.97e+01 angle pdb=" N PRO B4872 " pdb=" CA PRO B4872 " pdb=" C PRO B4872 " ideal model delta sigma weight residual 113.53 103.75 9.78 1.39e+00 5.18e-01 4.95e+01 angle pdb=" N SER H 8 " pdb=" CA SER H 8 " pdb=" C SER H 8 " ideal model delta sigma weight residual 113.25 120.73 -7.48 1.30e+00 5.92e-01 3.31e+01 ... (remaining 167715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 69941 15.37 - 30.75: 2591 30.75 - 46.12: 732 46.12 - 61.49: 64 61.49 - 76.87: 96 Dihedral angle restraints: 73424 sinusoidal: 23656 harmonic: 49768 Sorted by residual: 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 -121.26 -58.74 0 5.00e+00 4.00e-02 1.38e+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 -121.26 -58.74 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA GLY G2343 " pdb=" C GLY G2343 " pdb=" N GLU G2344 " pdb=" CA GLU G2344 " ideal model delta harmonic sigma weight residual -180.00 -121.30 -58.70 0 5.00e+00 4.00e-02 1.38e+02 ... (remaining 73421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 16885 0.066 - 0.133: 2403 0.133 - 0.199: 256 0.199 - 0.265: 42 0.265 - 0.332: 14 Chirality restraints: 19600 Sorted by residual: 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 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 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 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE I 826 " pdb=" CA ILE I 826 " pdb=" CG1 ILE I 826 " pdb=" CG2 ILE I 826 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 19597 not shown) Planarity restraints: 22092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B4666 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B4667 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B4667 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B4667 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I4666 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO I4667 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO I4667 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO I4667 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G4666 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO G4667 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO G4667 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO G4667 " -0.056 5.00e-02 4.00e+02 ... (remaining 22089 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 12 2.08 - 2.78: 29716 2.78 - 3.49: 161137 3.49 - 4.19: 280259 4.19 - 4.90: 460655 Nonbonded interactions: 931779 Sorted by model distance: nonbonded pdb=" O UNK G3557 " pdb=" CB UNK G3561 " model vdw 1.373 3.440 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 B3557 " pdb=" CB UNK B3561 " model vdw 1.373 3.440 nonbonded pdb=" O UNK B1487 " pdb=" CB UNK B1551 " model vdw 1.374 3.440 ... (remaining 931774 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 17.070 Check model and map are aligned: 1.270 Set scattering table: 0.870 Process input model: 296.840 Find NCS groups from input model: 6.310 Set up NCS constraints: 0.580 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:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 327.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3596 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 : 0.004 0.058 123012 Z= 0.269 Angle : 0.919 12.998 167720 Z= 0.503 Chirality : 0.047 0.332 19600 Planarity : 0.007 0.102 22092 Dihedral : 10.074 76.868 41064 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.29 % Rotamer: Outliers : 0.31 % Allowed : 2.62 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.34 % 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: -4.79 (0.06), residues: 13356 helix: -3.48 (0.04), residues: 5504 sheet: -2.43 (0.15), residues: 1116 loop : -3.03 (0.07), residues: 6736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G5019 HIS 0.010 0.002 HIS B2125 PHE 0.027 0.003 PHE I1748 TYR 0.027 0.002 TYR B4863 ARG 0.017 0.001 ARG E 281 *********************** 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 8 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.3591 time to fit residues: 3.0363 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.072 Evaluate side-chains 467 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 459 time to evaluate : 2.169 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 131 LEU cc_start: 0.2047 (OUTLIER) cc_final: 0.1519 (mt) REVERT: B 3920 VAL cc_start: 0.8227 (t) cc_final: 0.7824 (t) REVERT: B 4058 ILE cc_start: 0.7665 (mt) cc_final: 0.7065 (tp) REVERT: B 4146 LEU cc_start: 0.6942 (tp) cc_final: 0.6604 (tt) REVERT: B 4769 MET cc_start: 0.5714 (ptm) cc_final: 0.4903 (pmm) REVERT: B 4936 ILE cc_start: 0.7440 (mm) cc_final: 0.6828 (tp) outliers start: 8 outliers final: 1 residues processed: 467 average time/residue: 0.3704 time to fit residues: 264.2650 Evaluate side-chains 248 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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: 0.2980 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 50.0000 chunk 20 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 overall best weight: 5.9386 ------------------------------------------------------------------------------- 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 23 GLN B 44 ASN B 57 ASN B 105 HIS B 111 HIS B 113 HIS B 203 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 460 GLN B 461 HIS B 465 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN B 797 HIS ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 ASN B1598 GLN B1660 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1691 GLN B1693 GLN B1719 HIS B1972 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2036 GLN B2100 HIS B2127 GLN B2884 ASN B2931 GLN ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3830 GLN ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3982 HIS B3994 HIS B4054 ASN B4142 ASN B4714 ASN B4728 HIS B4806 ASN ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3842 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 123012 Z= 0.251 Angle : 0.731 14.400 167720 Z= 0.382 Chirality : 0.040 0.379 19600 Planarity : 0.006 0.083 22092 Dihedral : 6.009 53.503 18056 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.67 % Favored : 90.24 % Rotamer: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % 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: -3.33 (0.07), residues: 13356 helix: -1.77 (0.06), residues: 5724 sheet: -2.08 (0.16), residues: 1012 loop : -2.64 (0.07), residues: 6620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E3935 HIS 0.009 0.001 HIS B4973 PHE 0.039 0.002 PHE B4093 TYR 0.034 0.002 TYR B5009 ARG 0.010 0.001 ARG G 469 *********************** 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 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3482 time to fit residues: 1.8917 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.072 Evaluate side-chains 306 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 304 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1100 MET cc_start: -0.3564 (mtm) cc_final: -0.3979 (mtt) REVERT: B 2790 MET cc_start: -0.2822 (ttt) cc_final: -0.3613 (ttm) REVERT: B 2816 MET cc_start: 0.2664 (tpp) cc_final: 0.2296 (tpp) REVERT: B 3965 LEU cc_start: 0.8434 (mt) cc_final: 0.8213 (mm) REVERT: B 4000 MET cc_start: 0.4978 (ttp) cc_final: 0.4460 (ttt) REVERT: B 4048 LEU cc_start: 0.7423 (mt) cc_final: 0.7000 (mt) REVERT: B 4059 LEU cc_start: 0.7900 (tt) cc_final: 0.7592 (tp) REVERT: B 4097 MET cc_start: 0.1501 (mtm) cc_final: 0.1039 (mtt) REVERT: B 4769 MET cc_start: 0.5643 (ptm) cc_final: 0.5003 (pmm) REVERT: B 4814 LEU cc_start: 0.7189 (pp) cc_final: 0.6861 (pp) REVERT: B 4839 MET cc_start: 0.5052 (ttt) cc_final: 0.4850 (ttt) REVERT: B 5020 ASP cc_start: 0.5198 (p0) cc_final: 0.4632 (p0) outliers start: 2 outliers final: 0 residues processed: 305 average time/residue: 0.3363 time to fit residues: 164.4045 Evaluate side-chains 216 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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: 30.0000 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN 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 201 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 479 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** B1702 HIS B1775 HIS B1941 ASN ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3950 ASN B3978 GLN ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4714 ASN B4832 HIS ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3871 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.209 123012 Z= 0.292 Angle : 0.914 22.769 167720 Z= 0.460 Chirality : 0.050 0.819 19600 Planarity : 0.009 0.274 22092 Dihedral : 6.253 48.818 18056 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.63 % Favored : 89.19 % Rotamer: Outliers : 0.35 % Allowed : 2.94 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.06), residues: 13356 helix: -1.83 (0.06), residues: 5776 sheet: -1.99 (0.16), residues: 968 loop : -2.72 (0.07), residues: 6612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.005 TRP G3935 HIS 0.046 0.004 HIS I4832 PHE 0.061 0.004 PHE A 46 TYR 0.089 0.005 TYR G4883 ARG 0.066 0.002 ARG G1110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3606 time to fit residues: 1.9547 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.072 Evaluate side-chains 291 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 282 time to evaluate : 2.196 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: B 924 MET cc_start: -0.0879 (ptt) cc_final: -0.1803 (ptt) REVERT: B 961 MET cc_start: -0.1339 (OUTLIER) cc_final: -0.3108 (mtt) REVERT: B 1100 MET cc_start: -0.3307 (mtm) cc_final: -0.3753 (mtt) REVERT: B 2790 MET cc_start: -0.2707 (ttt) cc_final: -0.2914 (ttm) REVERT: B 4000 MET cc_start: 0.4915 (ttp) cc_final: 0.4222 (ttp) REVERT: B 4059 LEU cc_start: 0.7741 (tt) cc_final: 0.7418 (tp) REVERT: B 4097 MET cc_start: 0.2580 (mtm) cc_final: 0.2328 (mtt) REVERT: B 4769 MET cc_start: 0.5730 (ptm) cc_final: 0.4999 (pmm) REVERT: B 4796 MET cc_start: 0.5811 (tpt) cc_final: 0.5504 (tpt) REVERT: B 4816 ILE cc_start: 0.6104 (OUTLIER) cc_final: 0.5511 (mt) outliers start: 9 outliers final: 2 residues processed: 286 average time/residue: 0.3247 time to fit residues: 149.8015 Evaluate side-chains 209 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 0.0980 chunk 24 optimal weight: 0.0870 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.0000 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 0.2980 chunk 10 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.1962 ------------------------------------------------------------------------------- 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 138 GLN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 479 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** ** B1775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3878 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.209 123012 Z= 0.292 Angle : 0.914 22.768 167720 Z= 0.460 Chirality : 0.050 0.819 19600 Planarity : 0.009 0.274 22092 Dihedral : 6.253 48.818 18056 Min Nonbonded Distance : 0.908 Molprobity Statistics. All-atom Clashscore : 29.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.63 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.06), residues: 13356 helix: -1.83 (0.06), residues: 5776 sheet: -1.99 (0.16), residues: 968 loop : -2.72 (0.07), residues: 6612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.005 TRP E3935 HIS 0.046 0.004 HIS E4832 PHE 0.061 0.004 PHE H 46 TYR 0.089 0.005 TYR G4883 ARG 0.066 0.002 ARG G1110 *********************** 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 : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3455 time to fit residues: 1.8862 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.065 Evaluate side-chains 265 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.965 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: B 924 MET cc_start: -0.0886 (ptt) cc_final: -0.1798 (ptt) REVERT: B 961 MET cc_start: -0.0896 (mtt) cc_final: -0.2497 (mtt) REVERT: B 1100 MET cc_start: -0.3285 (mtm) cc_final: -0.3733 (mtt) REVERT: B 2267 MET cc_start: 0.0148 (ptt) cc_final: -0.0199 (ptt) REVERT: B 4000 MET cc_start: 0.4588 (ttp) cc_final: 0.4108 (ttp) REVERT: B 4097 MET cc_start: 0.2552 (mtm) cc_final: 0.2321 (mtt) REVERT: B 4769 MET cc_start: 0.5752 (ptm) cc_final: 0.4997 (pmm) REVERT: B 4796 MET cc_start: 0.5813 (tpt) cc_final: 0.5501 (tpt) REVERT: B 4816 ILE cc_start: 0.6381 (mt) cc_final: 0.6079 (mt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3213 time to fit residues: 138.6107 Evaluate side-chains 203 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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: 3.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 0.0970 chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 479 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** ** B1775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3879 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.209 123012 Z= 0.292 Angle : 0.914 22.762 167720 Z= 0.460 Chirality : 0.050 0.819 19600 Planarity : 0.009 0.274 22092 Dihedral : 6.253 48.817 18056 Min Nonbonded Distance : 0.895 Molprobity Statistics. All-atom Clashscore : 29.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.63 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.06), residues: 13356 helix: -1.83 (0.06), residues: 5776 sheet: -1.99 (0.16), residues: 968 loop : -2.72 (0.07), residues: 6612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.005 TRP E3935 HIS 0.046 0.004 HIS E4832 PHE 0.061 0.004 PHE H 46 TYR 0.088 0.005 TYR I4883 ARG 0.065 0.002 ARG E1110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3678 time to fit residues: 2.0085 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.074 Evaluate side-chains 261 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.231 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: B 924 MET cc_start: -0.0885 (ptt) cc_final: -0.1800 (ptt) REVERT: B 961 MET cc_start: -0.0896 (mtt) cc_final: -0.2496 (mtt) REVERT: B 1100 MET cc_start: -0.3282 (mtm) cc_final: -0.3735 (mtt) REVERT: B 2790 MET cc_start: -0.2447 (ttt) cc_final: -0.2995 (ttm) REVERT: B 4000 MET cc_start: 0.4573 (ttp) cc_final: 0.4101 (ttp) REVERT: B 4097 MET cc_start: 0.2555 (mtm) cc_final: 0.2325 (mtt) REVERT: B 4769 MET cc_start: 0.5758 (ptm) cc_final: 0.4999 (pmm) REVERT: B 4796 MET cc_start: 0.5806 (tpt) cc_final: 0.5498 (tpt) REVERT: B 4816 ILE cc_start: 0.6364 (mt) cc_final: 0.6082 (mt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3178 time to fit residues: 135.4857 Evaluate side-chains 204 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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: 6.9990 chunk 38 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 0.0050 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 40.0000 chunk 37 optimal weight: 0.0060 chunk 4 optimal weight: 40.0000 chunk 22 optimal weight: 0.0070 chunk 28 optimal weight: 0.0970 overall best weight: 0.1026 ------------------------------------------------------------------------------- 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN ** B 765 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** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2005 GLN B2291 GLN ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3950 ASN B4691 GLN B4714 ASN ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3785 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 123012 Z= 0.212 Angle : 0.827 13.136 167720 Z= 0.416 Chirality : 0.047 0.701 19600 Planarity : 0.008 0.120 22092 Dihedral : 6.145 49.855 18056 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.99 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -3.49 (0.06), residues: 13356 helix: -1.89 (0.06), residues: 5848 sheet: -1.92 (0.15), residues: 1072 loop : -2.80 (0.07), residues: 6436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.005 TRP I3935 HIS 0.031 0.003 HIS E 736 PHE 0.049 0.004 PHE G2235 TYR 0.051 0.004 TYR B4909 ARG 0.048 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 6 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.4411 time to fit residues: 2.8556 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.075 Evaluate side-chains 292 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.447 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: -0.0035 (ptt) cc_final: -0.1123 (ptt) REVERT: B 961 MET cc_start: -0.0417 (mtt) cc_final: -0.1615 (mtt) REVERT: B 2790 MET cc_start: -0.3611 (ttt) cc_final: -0.4348 (ttm) REVERT: B 3793 MET cc_start: 0.6894 (pmm) cc_final: 0.6584 (pmm) REVERT: B 3898 ASP cc_start: 0.5677 (p0) cc_final: 0.5429 (p0) REVERT: B 4000 MET cc_start: 0.4589 (ttp) cc_final: 0.3641 (ttp) REVERT: B 4097 MET cc_start: 0.2364 (mtm) cc_final: 0.1904 (mtm) REVERT: B 4730 ASP cc_start: 0.6121 (p0) cc_final: 0.5724 (p0) REVERT: B 4769 MET cc_start: 0.6558 (ptm) cc_final: 0.4707 (pmm) REVERT: B 4816 ILE cc_start: 0.6287 (mt) cc_final: 0.6074 (mt) REVERT: B 4839 MET cc_start: 0.4265 (ttt) cc_final: 0.4051 (ttt) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.3224 time to fit residues: 152.0377 Evaluate side-chains 205 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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: 8.9990 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.0570 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 765 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** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4037 ASN ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4714 ASN ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3796 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 123012 Z= 0.238 Angle : 0.866 15.442 167720 Z= 0.435 Chirality : 0.048 0.645 19600 Planarity : 0.009 0.168 22092 Dihedral : 6.195 49.756 18056 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.32 % Favored : 88.56 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.19 % 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: -3.55 (0.06), residues: 13356 helix: -1.93 (0.06), residues: 5860 sheet: -1.86 (0.15), residues: 1164 loop : -2.86 (0.07), residues: 6332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP B3935 HIS 0.031 0.003 HIS E 736 PHE 0.049 0.004 PHE B2235 TYR 0.051 0.004 TYR E 117 ARG 0.047 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 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3817 time to fit residues: 2.0749 Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.073 Evaluate side-chains 273 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.240 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 116 MET cc_start: 0.4688 (ttp) cc_final: 0.4447 (ptm) REVERT: B 924 MET cc_start: 0.0077 (ptt) cc_final: -0.0994 (ptt) REVERT: B 961 MET cc_start: -0.0231 (mtt) cc_final: -0.1579 (mtt) REVERT: B 2790 MET cc_start: -0.3710 (ttt) cc_final: -0.4349 (ttm) REVERT: B 3920 VAL cc_start: 0.8059 (t) cc_final: 0.7684 (t) REVERT: B 4000 MET cc_start: 0.4581 (ttp) cc_final: 0.3784 (ttp) REVERT: B 4097 MET cc_start: 0.2454 (mtm) cc_final: 0.1909 (mtm) REVERT: B 4730 ASP cc_start: 0.6117 (p0) cc_final: 0.5697 (p0) REVERT: B 4769 MET cc_start: 0.6546 (ptm) cc_final: 0.4711 (pmm) REVERT: B 5020 ASP cc_start: 0.5897 (p0) cc_final: 0.5115 (p0) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3182 time to fit residues: 141.8426 Evaluate side-chains 206 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 23 optimal weight: 0.3980 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 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** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3771 HIS ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3813 GLN ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3809 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 123012 Z= 0.226 Angle : 0.854 17.682 167720 Z= 0.430 Chirality : 0.050 0.800 19600 Planarity : 0.008 0.192 22092 Dihedral : 6.152 49.185 18056 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.62 % Favored : 88.23 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 3.05 % Twisted General : 0.19 % 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: -3.50 (0.07), residues: 13356 helix: -1.90 (0.06), residues: 5840 sheet: -1.79 (0.15), residues: 1188 loop : -2.85 (0.07), residues: 6328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP G1626 HIS 0.056 0.003 HIS E4156 PHE 0.050 0.004 PHE B2235 TYR 0.053 0.004 TYR E 117 ARG 0.047 0.001 ARG B4734 *********************** 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 5 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.3895 time to fit residues: 2.1207 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.072 Evaluate side-chains 267 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.241 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: B 924 MET cc_start: 0.0053 (ptt) cc_final: -0.1018 (ptt) REVERT: B 961 MET cc_start: -0.0673 (mtt) cc_final: -0.1983 (mtt) REVERT: B 2790 MET cc_start: -0.3194 (ttt) cc_final: -0.3771 (ttm) REVERT: B 2932 MET cc_start: -0.1319 (ptt) cc_final: -0.2657 (ptt) REVERT: B 4000 MET cc_start: 0.3916 (ttp) cc_final: 0.3425 (ttp) REVERT: B 4024 VAL cc_start: 0.7981 (m) cc_final: 0.7577 (p) REVERT: B 4057 MET cc_start: 0.6773 (pmm) cc_final: 0.6467 (pmm) REVERT: B 4097 MET cc_start: 0.2448 (mtm) cc_final: 0.1874 (mtm) REVERT: B 4730 ASP cc_start: 0.6095 (p0) cc_final: 0.5793 (p0) REVERT: B 4769 MET cc_start: 0.6403 (ptm) cc_final: 0.4566 (pmm) REVERT: B 4796 MET cc_start: 0.5454 (tpt) cc_final: 0.4786 (tpt) REVERT: B 5020 ASP cc_start: 0.5858 (p0) cc_final: 0.5075 (p0) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3553 time to fit residues: 154.5397 Evaluate side-chains 200 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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: 0.0570 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 0.0370 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 30.0000 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 overall best weight: 1.8778 ------------------------------------------------------------------------------- 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 765 GLN ** 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** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2188 ASN ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4714 ASN ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3809 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 123012 Z= 0.232 Angle : 0.870 16.819 167720 Z= 0.436 Chirality : 0.050 0.714 19600 Planarity : 0.009 0.172 22092 Dihedral : 6.156 49.306 18056 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.80 % Favored : 88.02 % Rotamer: Outliers : 0.04 % Allowed : 0.81 % Favored : 99.15 % 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: -3.51 (0.06), residues: 13356 helix: -1.91 (0.06), residues: 5840 sheet: -1.72 (0.15), residues: 1188 loop : -2.86 (0.07), residues: 6328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP G1626 HIS 0.030 0.003 HIS E 736 PHE 0.050 0.004 PHE B3996 TYR 0.053 0.004 TYR I 117 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 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2880 time to fit residues: 1.3077 Evaluate side-chains 3 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.075 Evaluate side-chains 267 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 924 MET cc_start: -0.0013 (ptt) cc_final: -0.1056 (ptt) REVERT: B 961 MET cc_start: -0.0700 (mtt) cc_final: -0.2054 (mtt) REVERT: B 1637 MET cc_start: 0.0621 (mtt) cc_final: -0.0765 (mtt) REVERT: B 2790 MET cc_start: -0.3225 (ttt) cc_final: -0.3755 (ttm) REVERT: B 2816 MET cc_start: 0.2100 (tpt) cc_final: 0.1797 (tpt) REVERT: B 2932 MET cc_start: -0.1328 (ptt) cc_final: -0.2728 (ptt) REVERT: B 4000 MET cc_start: 0.3872 (ttp) cc_final: 0.3406 (ttp) REVERT: B 4024 VAL cc_start: 0.7711 (m) cc_final: 0.7453 (p) REVERT: B 4057 MET cc_start: 0.6756 (pmm) cc_final: 0.6449 (pmm) REVERT: B 4097 MET cc_start: 0.2456 (mtm) cc_final: 0.1811 (mtm) REVERT: B 4730 ASP cc_start: 0.6088 (p0) cc_final: 0.5698 (p0) REVERT: B 4769 MET cc_start: 0.6401 (ptm) cc_final: 0.4555 (pmm) REVERT: B 4796 MET cc_start: 0.5465 (tpt) cc_final: 0.4927 (tpt) REVERT: B 5020 ASP cc_start: 0.5761 (p0) cc_final: 0.4969 (p0) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.3128 time to fit residues: 137.2472 Evaluate side-chains 200 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0040 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 40.0000 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 13 optimal weight: 0.0570 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.0060 overall best weight: 0.7128 ------------------------------------------------------------------------------- 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** 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** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3810 moved from start: 0.3888 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= 0.232 Angle : 0.870 16.819 167720 Z= 0.436 Chirality : 0.050 0.714 19600 Planarity : 0.009 0.172 22092 Dihedral : 6.156 49.306 18056 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.80 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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: -3.51 (0.06), residues: 13356 helix: -1.91 (0.06), residues: 5840 sheet: -1.72 (0.15), residues: 1188 loop : -2.86 (0.07), residues: 6328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP B1626 HIS 0.030 0.003 HIS E 736 PHE 0.050 0.004 PHE I3996 TYR 0.053 0.004 TYR I 117 ARG 0.046 0.002 ARG B4734 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26712 Ramachandran restraints generated. 13356 Oldfield, 0 Emsley, 13356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2911 time to fit residues: 1.3204 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 259 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 924 MET cc_start: -0.0014 (ptt) cc_final: -0.1056 (ptt) REVERT: B 961 MET cc_start: -0.0712 (mtt) cc_final: -0.2054 (mtt) REVERT: B 1637 MET cc_start: 0.0597 (mtt) cc_final: -0.0762 (mtt) REVERT: B 2790 MET cc_start: -0.3227 (ttt) cc_final: -0.3755 (ttm) REVERT: B 2816 MET cc_start: 0.2102 (tpt) cc_final: 0.1799 (tpt) REVERT: B 2932 MET cc_start: -0.1328 (ptt) cc_final: -0.2729 (ptt) REVERT: B 4000 MET cc_start: 0.3924 (ttp) cc_final: 0.3407 (ttp) REVERT: B 4057 MET cc_start: 0.6776 (pmm) cc_final: 0.6441 (pmm) REVERT: B 4097 MET cc_start: 0.2395 (mtm) cc_final: 0.1821 (mtm) REVERT: B 4730 ASP cc_start: 0.6070 (p0) cc_final: 0.5693 (p0) REVERT: B 4769 MET cc_start: 0.6425 (ptm) cc_final: 0.4578 (pmm) REVERT: B 4796 MET cc_start: 0.5456 (tpt) cc_final: 0.4926 (tpt) REVERT: B 5020 ASP cc_start: 0.5764 (p0) cc_final: 0.4981 (p0) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3095 time to fit residues: 131.3749 Evaluate side-chains 198 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.0060 chunk 25 optimal weight: 0.0020 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 overall best weight: 0.6544 ------------------------------------------------------------------------------- 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 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** 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** ** B1972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.023918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.021384 restraints weight = 26622.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.021375 restraints weight = 29415.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.021375 restraints weight = 29615.356| |-----------------------------------------------------------------------------| r_work (final): 0.3006 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.050023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.038114 restraints weight = 470325.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.038482 restraints weight = 352965.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.038827 restraints weight = 288422.249| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3887 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= 0.232 Angle : 0.870 16.818 167720 Z= 0.436 Chirality : 0.050 0.714 19600 Planarity : 0.009 0.172 22092 Dihedral : 6.156 49.306 18056 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.80 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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: -3.51 (0.06), residues: 13356 helix: -1.91 (0.06), residues: 5840 sheet: -1.72 (0.15), residues: 1188 loop : -2.86 (0.07), residues: 6328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP G1626 HIS 0.030 0.003 HIS E 736 PHE 0.050 0.004 PHE I3996 TYR 0.053 0.004 TYR I 117 ARG 0.046 0.002 ARG E4734 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13048.00 seconds wall clock time: 208 minutes 38.98 seconds (12518.98 seconds total)