Starting phenix.real_space_refine on Thu Mar 14 11:06:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tay_8389/03_2024/5tay_8389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tay_8389/03_2024/5tay_8389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tay_8389/03_2024/5tay_8389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tay_8389/03_2024/5tay_8389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tay_8389/03_2024/5tay_8389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tay_8389/03_2024/5tay_8389.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. 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 76808 2.51 5 N 21488 2.21 5 O 22328 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 PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 1271": "NH1" <-> "NH2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B ARG 1607": "NH1" <-> "NH2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1743": "NH1" <-> "NH2" Residue "B ARG 1797": "NH1" <-> "NH2" Residue "B ARG 1827": "NH1" <-> "NH2" Residue "B ARG 1996": "NH1" <-> "NH2" Residue "B ARG 2140": "NH1" <-> "NH2" Residue "B ARG 2355": "NH1" <-> "NH2" Residue "B ARG 2452": "NH1" <-> "NH2" Residue "B ARG 3648": "NH1" <-> "NH2" Residue "B ARG 3886": "NH1" <-> "NH2" Residue "B ARG 3904": "NH1" <-> "NH2" Residue "B ARG 3949": "NH1" <-> "NH2" Residue "B ARG 3984": "NH1" <-> "NH2" Residue "B ARG 4042": "NH1" <-> "NH2" Residue "B ARG 4137": "NH1" <-> "NH2" Residue "B ARG 4159": "NH1" <-> "NH2" Residue "B ARG 4175": "NH1" <-> "NH2" Residue "B ARG 4192": "NH1" <-> "NH2" Residue "B ARG 4548": "NH1" <-> "NH2" Residue "B ARG 4557": "NH1" <-> "NH2" Residue "B ARG 4563": "NH1" <-> "NH2" Residue "B ARG 4673": "NH1" <-> "NH2" Residue "B ARG 4703": "NH1" <-> "NH2" Residue "B ARG 4722": "NH1" <-> "NH2" Residue "B ARG 4734": "NH1" <-> "NH2" Residue "B ARG 4736": "NH1" <-> "NH2" Residue "B ARG 4824": "NH1" <-> "NH2" Residue "B ARG 4860": "NH1" <-> "NH2" Residue "B ARG 4892": "NH1" <-> "NH2" Residue "B ARG 4913": "NH1" <-> "NH2" Residue "B ARG 5017": "NH1" <-> "NH2" Residue "B ARG 5029": "NH1" <-> "NH2" Residue "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 PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 553": "NH1" <-> "NH2" Residue "G ARG 1271": "NH1" <-> "NH2" Residue "G ARG 1594": "NH1" <-> "NH2" Residue "G ARG 1607": "NH1" <-> "NH2" Residue "G ARG 1656": "NH1" <-> "NH2" Residue "G ARG 1725": "NH1" <-> "NH2" Residue "G ARG 1743": "NH1" <-> "NH2" Residue "G ARG 1797": "NH1" <-> "NH2" Residue "G ARG 1827": "NH1" <-> "NH2" Residue "G ARG 1996": "NH1" <-> "NH2" Residue "G ARG 2140": "NH1" <-> "NH2" Residue "G ARG 2355": "NH1" <-> "NH2" Residue "G ARG 2452": "NH1" <-> "NH2" Residue "G ARG 3648": "NH1" <-> "NH2" Residue "G ARG 3886": "NH1" <-> "NH2" Residue "G ARG 3904": "NH1" <-> "NH2" Residue "G ARG 3949": "NH1" <-> "NH2" Residue "G ARG 3984": "NH1" <-> "NH2" Residue "G ARG 4042": "NH1" <-> "NH2" Residue "G ARG 4137": "NH1" <-> "NH2" Residue "G ARG 4159": "NH1" <-> "NH2" Residue "G ARG 4175": "NH1" <-> "NH2" Residue "G ARG 4192": "NH1" <-> "NH2" Residue "G ARG 4548": "NH1" <-> "NH2" Residue "G ARG 4557": "NH1" <-> "NH2" Residue "G ARG 4563": "NH1" <-> "NH2" Residue "G ARG 4673": "NH1" <-> "NH2" Residue "G ARG 4703": "NH1" <-> "NH2" Residue "G ARG 4722": "NH1" <-> "NH2" Residue "G ARG 4734": "NH1" <-> "NH2" Residue "G ARG 4736": "NH1" <-> "NH2" Residue "G ARG 4824": "NH1" <-> "NH2" Residue "G ARG 4860": "NH1" <-> "NH2" Residue "G ARG 4892": "NH1" <-> "NH2" Residue "G ARG 4913": "NH1" <-> "NH2" Residue "G ARG 5017": "NH1" <-> "NH2" Residue "G ARG 5029": "NH1" <-> "NH2" 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 PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 553": "NH1" <-> "NH2" Residue "I ARG 1271": "NH1" <-> "NH2" Residue "I ARG 1594": "NH1" <-> "NH2" Residue "I ARG 1607": "NH1" <-> "NH2" Residue "I ARG 1656": "NH1" <-> "NH2" Residue "I ARG 1725": "NH1" <-> "NH2" Residue "I ARG 1743": "NH1" <-> "NH2" Residue "I ARG 1797": "NH1" <-> "NH2" Residue "I ARG 1827": "NH1" <-> "NH2" Residue "I ARG 1996": "NH1" <-> "NH2" Residue "I ARG 2140": "NH1" <-> "NH2" Residue "I ARG 2355": "NH1" <-> "NH2" Residue "I ARG 2452": "NH1" <-> "NH2" Residue "I ARG 3648": "NH1" <-> "NH2" Residue "I ARG 3886": "NH1" <-> "NH2" Residue "I ARG 3904": "NH1" <-> "NH2" Residue "I ARG 3949": "NH1" <-> "NH2" Residue "I ARG 3984": "NH1" <-> "NH2" Residue "I ARG 4042": "NH1" <-> "NH2" Residue "I ARG 4137": "NH1" <-> "NH2" Residue "I ARG 4159": "NH1" <-> "NH2" Residue "I ARG 4175": "NH1" <-> "NH2" Residue "I ARG 4192": "NH1" <-> "NH2" Residue "I ARG 4548": "NH1" <-> "NH2" Residue "I ARG 4557": "NH1" <-> "NH2" Residue "I ARG 4563": "NH1" <-> "NH2" Residue "I ARG 4673": "NH1" <-> "NH2" Residue "I ARG 4703": "NH1" <-> "NH2" Residue "I ARG 4722": "NH1" <-> "NH2" Residue "I ARG 4734": "NH1" <-> "NH2" Residue "I ARG 4736": "NH1" <-> "NH2" Residue "I ARG 4824": "NH1" <-> "NH2" Residue "I ARG 4860": "NH1" <-> "NH2" Residue "I ARG 4892": "NH1" <-> "NH2" Residue "I ARG 4913": "NH1" <-> "NH2" Residue "I ARG 5017": "NH1" <-> "NH2" Residue "I ARG 5029": "NH1" <-> "NH2" Residue "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 PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E ARG 1271": "NH1" <-> "NH2" Residue "E ARG 1594": "NH1" <-> "NH2" Residue "E ARG 1607": "NH1" <-> "NH2" Residue "E ARG 1656": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1743": "NH1" <-> "NH2" Residue "E ARG 1797": "NH1" <-> "NH2" Residue "E ARG 1827": "NH1" <-> "NH2" Residue "E ARG 1996": "NH1" <-> "NH2" Residue "E ARG 2140": "NH1" <-> "NH2" Residue "E ARG 2355": "NH1" <-> "NH2" Residue "E ARG 2452": "NH1" <-> "NH2" Residue "E ARG 3648": "NH1" <-> "NH2" Residue "E ARG 3886": "NH1" <-> "NH2" Residue "E ARG 3904": "NH1" <-> "NH2" Residue "E ARG 3949": "NH1" <-> "NH2" Residue "E ARG 3984": "NH1" <-> "NH2" Residue "E ARG 4042": "NH1" <-> "NH2" Residue "E ARG 4137": "NH1" <-> "NH2" Residue "E ARG 4159": "NH1" <-> "NH2" Residue "E ARG 4175": "NH1" <-> "NH2" Residue "E ARG 4192": "NH1" <-> "NH2" Residue "E ARG 4548": "NH1" <-> "NH2" Residue "E ARG 4557": "NH1" <-> "NH2" Residue "E ARG 4563": "NH1" <-> "NH2" Residue "E ARG 4673": "NH1" <-> "NH2" Residue "E ARG 4703": "NH1" <-> "NH2" Residue "E ARG 4722": "NH1" <-> "NH2" Residue "E ARG 4734": "NH1" <-> "NH2" Residue "E ARG 4736": "NH1" <-> "NH2" Residue "E ARG 4824": "NH1" <-> "NH2" Residue "E ARG 4860": "NH1" <-> "NH2" Residue "E ARG 4892": "NH1" <-> "NH2" Residue "E ARG 4913": "NH1" <-> "NH2" Residue "E ARG 5017": "NH1" <-> "NH2" Residue "E ARG 5029": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 121276 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 Chain: "G" Number of atoms: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 Chain: "I" Number of atoms: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 Chain: "E" Number of atoms: 29499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4194, 29499 Classifications: {'peptide': 4194} Incomplete info: {'truncation_to_alanine': 1272} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4036} Chain breaks: 26 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3079 Unresolved non-hydrogen angles: 4307 Unresolved non-hydrogen dihedrals: 1905 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 926, '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: 1786 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: "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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32100 SG CYS B4958 178.077 204.799 87.513 1.00187.16 S ATOM 32125 SG CYS B4961 178.759 205.749 89.190 1.00188.49 S ATOM 61599 SG CYS G4958 211.133 184.177 87.556 1.00187.16 S ATOM 61624 SG CYS G4961 210.456 183.232 89.238 1.00188.49 S ATOM 91098 SG CYS I4958 184.177 177.745 87.585 1.00187.16 S ATOM 91123 SG CYS I4961 183.237 178.419 89.271 1.00188.49 S ATOM A0FW5 SG CYS E4958 204.925 211.339 87.490 1.00187.16 S ATOM A0FWU SG CYS E4961 205.865 210.664 89.175 1.00188.49 S Time building chain proxies: 45.20, per 1000 atoms: 0.37 Number of scatterers: 121276 At special positions: 0 Unit cell: (390.305, 390.305, 205.82, 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 22328 8.00 N 21488 7.00 C 76808 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: 31.66 Conformation dependent library (CDL) restraints added in 13.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" NE2 HIS E4983 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4958 " pdb="ZN ZN E5101 " - pdb=" NE2 HIS E4978 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4961 " pdb=" ZN G5101 " pdb="ZN ZN G5101 " - pdb=" NE2 HIS G4983 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4958 " pdb="ZN ZN G5101 " - pdb=" NE2 HIS G4978 " pdb="ZN ZN G5101 " - pdb=" SG CYS G4961 " pdb=" ZN I5101 " pdb="ZN ZN I5101 " - pdb=" NE2 HIS I4983 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4958 " pdb="ZN ZN I5101 " - pdb=" NE2 HIS I4978 " pdb="ZN ZN I5101 " - pdb=" SG CYS I4961 " 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: 32568 Finding SS restraints... Secondary structure from input PDB file: 724 helices and 96 sheets defined 62.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.62 Creating SS restraints... Processing helix chain 'F' and resid 38 through 43 removed outlier: 4.106A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.803A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.650A pdb=" N VAL F 80 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F 81 " --> pdb=" O PRO F 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 77 through 81' Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.105A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.803A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.649A pdb=" N VAL A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 81' Processing helix chain 'H' and resid 38 through 43 removed outlier: 4.105A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 3.803A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.649A pdb=" N VAL H 80 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA H 81 " --> pdb=" O PRO H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 81' Processing helix chain 'J' and resid 38 through 43 removed outlier: 4.105A pdb=" N ARG J 42 " --> pdb=" O SER J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.803A pdb=" N ALA J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.649A pdb=" N VAL J 80 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA J 81 " --> pdb=" O PRO J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 81' Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.890A pdb=" N ILE B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.748A pdb=" N GLN B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.964A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 395 through 420 removed outlier: 4.050A pdb=" N GLN B 399 " --> pdb=" O GLN B 395 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 418 " --> pdb=" O PHE B 414 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.505A pdb=" N ASP B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 477 removed outlier: 3.913A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.583A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.503A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.513A pdb=" N ALA B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 539' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.697A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 568 removed outlier: 3.521A pdb=" N LEU B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.517A pdb=" N ILE B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 578' Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 597 through 608 removed outlier: 3.753A pdb=" N LEU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 4.130A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 622 " --> pdb=" O GLN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 889 removed outlier: 3.581A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 932 removed outlier: 3.802A pdb=" N ASN B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 920 " --> pdb=" O PRO B 916 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN B 921 " --> pdb=" O GLU B 917 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 928 " --> pdb=" O MET B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.096A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 991 " --> pdb=" O ARG B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1039 removed outlier: 3.509A pdb=" N LYS B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.892A pdb=" N LEU B1046 " --> pdb=" O ALA B1042 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B1047 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B1048 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B1049 " --> pdb=" O THR B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1042 through 1049' Processing helix chain 'B' and resid 1078 through 1082 Processing helix chain 'B' and resid 1575 through 1580 removed outlier: 4.028A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1575 through 1580' Processing helix chain 'B' and resid 1623 through 1627 Processing helix chain 'B' and resid 1652 through 1657 removed outlier: 3.665A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1674 removed outlier: 3.757A pdb=" N HIS B1665 " --> pdb=" O ARG B1661 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B1666 " --> pdb=" O PHE B1662 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B1670 " --> pdb=" O THR B1666 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG B1671 " --> pdb=" O LEU B1667 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1686 removed outlier: 3.639A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) Processing helix chain 'B' and resid 1692 through 1697 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 1720 Processing helix chain 'B' and resid 1720 through 1730 removed outlier: 3.582A pdb=" N ARG B1725 " --> pdb=" O GLU B1721 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1823 removed outlier: 3.612A pdb=" N MET B1814 " --> pdb=" O LYS B1810 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B1815 " --> pdb=" O ALA B1811 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B1817 " --> pdb=" O ARG B1813 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1838 Processing helix chain 'B' and resid 1840 through 1851 removed outlier: 3.570A pdb=" N LEU B1848 " --> pdb=" O LEU B1844 " (cutoff:3.500A) removed outlier: 3.522A 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 1934 through 1977 removed outlier: 3.707A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B1948 " --> pdb=" O GLU B1944 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B1966 " --> pdb=" O ALA B1962 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1980 No H-bonds generated for 'chain 'B' and resid 1978 through 1980' Processing helix chain 'B' and resid 1989 through 1994 removed outlier: 3.543A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2014 removed outlier: 3.682A pdb=" N ILE B2006 " --> pdb=" O PRO B2002 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE B2012 " --> pdb=" O MET B2008 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B2013 " --> pdb=" O LEU B2009 " (cutoff:3.500A) Processing helix chain 'B' and resid 2028 through 2042 removed outlier: 3.897A pdb=" N LEU B2039 " --> pdb=" O HIS B2035 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2107 removed outlier: 4.011A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B2106 " --> pdb=" O VAL B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2126 removed outlier: 3.743A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B2126 " --> pdb=" O SER B2122 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2138 removed outlier: 3.797A pdb=" N ALA B2137 " --> pdb=" O GLU B2133 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2166 removed outlier: 3.911A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS B2158 " --> pdb=" O SER B2154 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B2159 " --> pdb=" O LEU B2155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B2160 " --> pdb=" O LEU B2156 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2187 removed outlier: 3.599A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2201 removed outlier: 3.854A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2216 removed outlier: 3.666A pdb=" N THR B2206 " --> pdb=" O GLY B2202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B2207 " --> pdb=" O MET B2203 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2228 through 2242 removed outlier: 4.019A pdb=" N TYR B2238 " --> pdb=" O ARG B2234 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2252 removed outlier: 3.710A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2261 removed outlier: 3.704A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2262 through 2264 No H-bonds generated for 'chain 'B' and resid 2262 through 2264' Processing helix chain 'B' and resid 2271 through 2279 Processing helix chain 'B' and resid 2294 through 2304 removed outlier: 3.703A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 3.830A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2331 Processing helix chain 'B' and resid 2335 through 2339 removed outlier: 3.550A pdb=" N ALA B2338 " --> pdb=" O LEU B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2358 removed outlier: 3.619A pdb=" N ALA B2350 " --> pdb=" O VAL B2346 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL B2353 " --> pdb=" O ASN B2349 " (cutoff:3.500A) removed outlier: 3.561A 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 2389 removed outlier: 3.703A pdb=" N ILE B2380 " --> pdb=" O LEU B2376 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B2385 " --> pdb=" O GLU B2381 " (cutoff:3.500A) Processing helix chain 'B' and resid 2390 through 2393 removed outlier: 3.552A pdb=" N ASP B2393 " --> pdb=" O PRO B2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2390 through 2393' Processing helix chain 'B' and resid 2419 through 2436 removed outlier: 3.615A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B2433 " --> pdb=" O LEU B2429 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2445 removed outlier: 4.072A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2461 removed outlier: 4.030A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 2464 through 2471 removed outlier: 3.607A pdb=" N ILE B2469 " --> pdb=" O ASP B2465 " (cutoff:3.500A) Processing helix chain 'B' and resid 2496 through 2500 Processing helix chain 'B' and resid 2502 through 2509 removed outlier: 3.769A pdb=" N UNK B2506 " --> pdb=" O UNK B2502 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2530 removed outlier: 4.334A pdb=" N UNK B2523 " --> pdb=" O UNK B2519 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N UNK B2526 " --> pdb=" O UNK B2522 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N UNK B2527 " --> pdb=" O UNK B2523 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N UNK B2528 " --> pdb=" O UNK B2524 " (cutoff:3.500A) Processing helix chain 'B' and resid 2542 through 2548 removed outlier: 3.546A pdb=" N UNK B2546 " --> pdb=" O UNK B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2557 removed outlier: 3.634A pdb=" N UNK B2555 " --> pdb=" O UNK B2551 " (cutoff:3.500A) Processing helix chain 'B' and resid 2566 through 2581 removed outlier: 4.125A pdb=" N UNK B2570 " --> pdb=" O UNK B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2601 removed outlier: 3.553A pdb=" N UNK B2597 " --> pdb=" O UNK B2593 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2604 No H-bonds generated for 'chain 'B' and resid 2602 through 2604' Processing helix chain 'B' and resid 2610 through 2618 removed outlier: 3.763A pdb=" N UNK B2617 " --> pdb=" O UNK B2613 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK B2618 " --> pdb=" O UNK B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2640 removed outlier: 3.502A pdb=" N UNK B2632 " --> pdb=" O UNK B2628 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N UNK B2634 " --> pdb=" O UNK B2630 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK B2635 " --> pdb=" O UNK B2631 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK B2639 " --> pdb=" O UNK B2635 " (cutoff:3.500A) Processing helix chain 'B' and resid 2641 through 2643 No H-bonds generated for 'chain 'B' and resid 2641 through 2643' Processing helix chain 'B' and resid 2650 through 2666 removed outlier: 3.554A pdb=" N UNK B2654 " --> pdb=" O UNK B2650 " (cutoff:3.500A) Processing helix chain 'B' and resid 2675 through 2680 removed outlier: 3.502A pdb=" N UNK B2680 " --> pdb=" O UNK B2676 " (cutoff:3.500A) Processing helix chain 'B' and resid 2683 through 2687 removed outlier: 3.888A pdb=" N UNK B2686 " --> pdb=" O UNK B2683 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N UNK B2687 " --> pdb=" O UNK B2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2683 through 2687' Processing helix chain 'B' and resid 2741 through 2745 removed outlier: 3.949A pdb=" N ASN B2744 " --> pdb=" O GLU B2741 " (cutoff:3.500A) Processing helix chain 'B' and resid 2748 through 2773 removed outlier: 3.524A pdb=" N ASP B2752 " --> pdb=" O PRO B2748 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.909A pdb=" N THR B2796 " --> pdb=" O PRO B2793 " (cutoff:3.500A) Processing helix chain 'B' and resid 2800 through 2805 removed outlier: 3.957A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2800 through 2805' Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 3.905A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.462A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B2875 " --> pdb=" O LEU B2871 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP B2886 " --> pdb=" O TYR B2882 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B2895 " --> pdb=" O LYS B2891 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2911 removed outlier: 3.587A pdb=" N THR B2910 " --> pdb=" O PRO B2907 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B2911 " --> pdb=" O TYR B2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2907 through 2911' Processing helix chain 'B' and resid 2917 through 2932 removed outlier: 3.788A pdb=" N GLU B2921 " --> pdb=" O ALA B2917 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B2926 " --> pdb=" O LYS B2922 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2976 removed outlier: 3.959A pdb=" N UNK B2956 " --> pdb=" O UNK B2952 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK B2968 " --> pdb=" O UNK B2964 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N UNK B2969 " --> pdb=" O UNK B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3015 removed outlier: 3.745A pdb=" N UNK B3002 " --> pdb=" O UNK B2998 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK B3004 " --> pdb=" O UNK B3000 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N UNK B3006 " --> pdb=" O UNK B3002 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) Processing helix chain 'B' and resid 3017 through 3022 Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.188A pdb=" N UNK B3028 " --> pdb=" O UNK B3024 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK B3032 " --> pdb=" O UNK B3028 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK B3040 " --> pdb=" O UNK B3036 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3060 removed outlier: 4.090A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) Processing helix chain 'B' and resid 3141 through 3146 Processing helix chain 'B' and resid 3146 through 3162 removed outlier: 3.922A pdb=" N UNK B3154 " --> pdb=" O UNK B3150 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3187 Processing helix chain 'B' and resid 3188 through 3190 No H-bonds generated for 'chain 'B' and resid 3188 through 3190' Processing helix chain 'B' and resid 3198 through 3212 removed outlier: 3.723A pdb=" N UNK B3205 " --> pdb=" O UNK B3201 " (cutoff:3.500A) Processing helix chain 'B' and resid 3224 through 3230 removed outlier: 3.959A pdb=" N UNK B3228 " --> pdb=" O UNK B3224 " (cutoff:3.500A) Processing helix chain 'B' and resid 3248 through 3254 Processing helix chain 'B' and resid 3271 through 3285 removed outlier: 4.022A pdb=" N UNK B3282 " --> pdb=" O UNK B3278 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK B3284 " --> pdb=" O UNK B3280 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N UNK B3285 " --> pdb=" O UNK B3281 " (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 3315 through 3321 removed outlier: 3.874A pdb=" N UNK B3319 " --> pdb=" O UNK B3315 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3331 removed outlier: 3.504A pdb=" N UNK B3330 " --> pdb=" O UNK B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3349 removed outlier: 3.618A pdb=" N UNK B3348 " --> pdb=" O UNK B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3350 through 3354 Processing helix chain 'B' and resid 3361 through 3388 Processing helix chain 'B' and resid 3399 through 3407 removed outlier: 3.603A pdb=" N UNK B3403 " --> pdb=" O UNK B3399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK B3405 " --> pdb=" O UNK B3401 " (cutoff:3.500A) Processing helix chain 'B' and resid 3407 through 3425 removed outlier: 3.837A pdb=" N UNK B3413 " --> pdb=" O UNK B3409 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK B3416 " --> pdb=" O UNK B3412 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N UNK B3417 " --> pdb=" O UNK B3413 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N UNK B3420 " --> pdb=" O UNK B3416 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N UNK B3421 " --> pdb=" O UNK B3417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N UNK B3425 " --> pdb=" O UNK B3421 " (cutoff:3.500A) Processing helix chain 'B' and resid 3426 through 3431 Processing helix chain 'B' and resid 3437 through 3443 Processing helix chain 'B' and resid 3445 through 3450 Processing helix chain 'B' and resid 3457 through 3460 Processing helix chain 'B' and resid 3461 through 3468 Processing helix chain 'B' and resid 3522 through 3527 Processing helix chain 'B' and resid 3541 through 3547 removed outlier: 3.501A pdb=" N UNK B3545 " --> pdb=" O UNK B3541 " (cutoff:3.500A) Processing helix chain 'B' and resid 3551 through 3560 Processing helix chain 'B' and resid 3574 through 3583 removed outlier: 4.331A pdb=" N UNK B3580 " --> pdb=" O UNK B3576 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N UNK B3583 " --> pdb=" O UNK B3579 " (cutoff:3.500A) Processing helix chain 'B' and resid 3590 through 3608 removed outlier: 3.522A pdb=" N UNK B3595 " --> pdb=" O UNK B3591 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK B3596 " --> pdb=" O UNK B3592 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N UNK B3598 " --> pdb=" O UNK B3594 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N UNK B3600 " --> pdb=" O UNK B3596 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK B3601 " --> pdb=" O UNK B3597 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 removed outlier: 3.726A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) Processing helix chain 'B' and resid 3671 through 3680 removed outlier: 3.655A pdb=" N ASP B3676 " --> pdb=" O ARG B3672 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B3680 " --> pdb=" O ASP B3676 " (cutoff:3.500A) Processing helix chain 'B' and resid 3681 through 3687 removed outlier: 6.854A pdb=" N GLU B3684 " --> pdb=" O GLY B3681 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B3685 " --> pdb=" O GLU B3682 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3708 removed outlier: 3.600A pdb=" N LEU B3701 " --> pdb=" O PRO B3697 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3738 removed outlier: 3.817A pdb=" N TYR B3725 " --> pdb=" O LEU B3721 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B3727 " --> pdb=" O MET B3723 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B3737 " --> pdb=" O CYS B3733 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 3.724A pdb=" N GLU B3757 " --> pdb=" O PHE B3753 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B3758 " --> pdb=" O GLU B3754 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B3759 " --> pdb=" O GLU B3755 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN B3766 " --> pdb=" O ARG B3762 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN B3767 " --> pdb=" O LEU B3763 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B3768 " --> pdb=" O LEU B3764 " (cutoff:3.500A) Processing helix chain 'B' and resid 3771 through 3782 removed outlier: 3.696A pdb=" N ALA B3775 " --> pdb=" O HIS B3771 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B3776 " --> pdb=" O THR B3772 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B3777 " --> pdb=" O ARG B3773 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B3781 " --> pdb=" O GLU B3777 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3805 removed outlier: 4.208A pdb=" N LYS B3799 " --> pdb=" O SER B3795 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B3800 " --> pdb=" O SER B3796 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B3803 " --> pdb=" O LYS B3799 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B3805 " --> pdb=" O GLY B3801 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 removed outlier: 3.538A pdb=" N GLN B3814 " --> pdb=" O ALA B3810 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B3815 " --> pdb=" O GLU B3811 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B3824 " --> pdb=" O LEU B3820 " (cutoff:3.500A) Processing helix chain 'B' and resid 3827 through 3838 removed outlier: 3.618A pdb=" N ILE B3832 " --> pdb=" O PHE B3828 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3854 Processing helix chain 'B' and resid 3880 through 3891 Processing helix chain 'B' and resid 3898 through 3905 Processing helix chain 'B' and resid 3914 through 3937 removed outlier: 3.803A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B3920 " --> pdb=" O ILE B3916 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B3929 " --> pdb=" O ARG B3925 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3967 removed outlier: 4.025A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.530A pdb=" N GLN B3977 " --> pdb=" O CYS B3973 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 4003 removed outlier: 3.740A pdb=" N VAL B3990 " --> pdb=" O TRP B3986 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B3992 " --> pdb=" O ALA B3988 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4004 through 4006 No H-bonds generated for 'chain 'B' and resid 4004 through 4006' Processing helix chain 'B' and resid 4009 through 4030 Processing helix chain 'B' and resid 4039 through 4051 removed outlier: 3.610A pdb=" N VAL B4049 " --> pdb=" O VAL B4045 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4065 removed outlier: 3.548A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B4064 " --> pdb=" O LYS B4060 " (cutoff:3.500A) Processing helix chain 'B' and resid 4066 through 4072 removed outlier: 3.911A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B4072 " --> pdb=" O LEU B4068 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4079 removed outlier: 3.776A pdb=" N GLN B4078 " --> pdb=" O SER B4074 " (cutoff:3.500A) Processing helix chain 'B' and resid 4090 through 4100 removed outlier: 3.513A pdb=" N MET B4097 " --> pdb=" O PHE B4093 " (cutoff:3.500A) removed outlier: 3.917A 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 4132 removed outlier: 4.412A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) Processing helix chain 'B' and resid 4132 through 4154 removed outlier: 3.593A pdb=" N ALA B4136 " --> pdb=" O PHE B4132 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B4151 " --> pdb=" O LEU B4147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B4152 " --> pdb=" O THR B4148 " (cutoff:3.500A) removed outlier: 3.726A 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 4168 through 4175 removed outlier: 3.545A pdb=" N TYR B4173 " --> pdb=" O SER B4169 " (cutoff:3.500A) Processing helix chain 'B' and resid 4199 through 4206 removed outlier: 3.824A pdb=" N ALA B4203 " --> pdb=" O GLU B4199 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 4.106A pdb=" N SER B4213 " --> pdb=" O GLN B4209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B4223 " --> pdb=" O PHE B4219 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4248 removed outlier: 4.024A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B4242 " --> pdb=" O CYS B4238 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B4243 " --> pdb=" O GLU B4239 " (cutoff:3.500A) Processing helix chain 'B' and resid 4321 through 4337 removed outlier: 3.537A pdb=" N UNK B4327 " --> pdb=" O UNK B4323 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK B4332 " --> pdb=" O UNK B4328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4543 through 4556 removed outlier: 3.964A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4576 removed outlier: 3.535A pdb=" N ALA B4566 " --> pdb=" O LEU B4562 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B4574 " --> pdb=" O ALA B4570 " (cutoff:3.500A) Processing helix chain 'B' and resid 4577 through 4580 removed outlier: 3.928A pdb=" N TYR B4580 " --> pdb=" O LEU B4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4577 through 4580' Processing helix chain 'B' and resid 4641 through 4665 removed outlier: 3.618A pdb=" N LEU B4648 " --> pdb=" O TRP B4644 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B4649 " --> pdb=" O CYS B4645 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B4654 " --> pdb=" O HIS B4650 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B4658 " --> pdb=" O ALA B4654 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B4660 " --> pdb=" O LEU B4656 " (cutoff:3.500A) Processing helix chain 'B' and resid 4665 through 4683 removed outlier: 3.539A pdb=" N LYS B4672 " --> pdb=" O LEU B4668 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B4677 " --> pdb=" O ARG B4673 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B4678 " --> pdb=" O GLU B4674 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B4683 " --> pdb=" O ARG B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4697 through 4702 removed outlier: 3.577A pdb=" N ASP B4702 " --> pdb=" O LYS B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4710 through 4714 removed outlier: 3.515A pdb=" N SER B4713 " --> pdb=" O SER B4710 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN B4714 " --> pdb=" O PHE B4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4710 through 4714' Processing helix chain 'B' and resid 4719 through 4728 removed outlier: 3.526A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4741 removed outlier: 3.553A pdb=" N LEU B4741 " --> pdb=" O ILE B4737 " (cutoff:3.500A) Processing helix chain 'B' and resid 4745 through 4750 Processing helix chain 'B' and resid 4751 through 4755 removed outlier: 4.040A pdb=" N GLU B4755 " --> pdb=" O ALA B4752 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.654A pdb=" N THR B4785 " --> pdb=" O GLY B4781 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4802 removed outlier: 3.534A pdb=" N SER B4799 " --> pdb=" O TYR B4795 " (cutoff:3.500A) Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 3.853A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.748A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B4831 " --> pdb=" O LEU B4827 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 removed outlier: 3.964A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B4842 " --> pdb=" O VAL B4838 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B4843 " --> pdb=" O MET B4839 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B4844 " --> pdb=" O THR B4840 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B4853 " --> pdb=" O TYR B4849 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B4854 " --> pdb=" O LEU B4850 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B4855 " --> pdb=" O TYR B4851 " (cutoff:3.500A) Processing helix chain 'B' and resid 4859 through 4863 removed outlier: 3.957A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4890 removed outlier: 3.654A pdb=" N MET B4887 " --> pdb=" O TYR B4883 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4925 removed outlier: 3.682A pdb=" N ARG B4913 " --> pdb=" O TYR B4909 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B4918 " --> pdb=" O VAL B4914 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B4923 " --> pdb=" O THR B4919 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) Processing helix chain 'B' and resid 4927 through 4957 removed outlier: 3.640A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B4942 " --> pdb=" O ASP B4938 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B4943 " --> pdb=" O ALA B4939 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B4947 " --> pdb=" O LEU B4943 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B4957 " --> pdb=" O ASP B4953 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4971 removed outlier: 4.318A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR B4971 " --> pdb=" O TYR B4967 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4979 removed outlier: 3.761A pdb=" N THR B4977 " --> pdb=" O HIS B4973 " (cutoff:3.500A) Processing helix chain 'B' and resid 4986 through 4997 removed outlier: 4.009A pdb=" N PHE B4990 " --> pdb=" O ALA B4986 " (cutoff:3.500A) Processing helix chain 'B' and resid 5006 through 5017 removed outlier: 3.639A pdb=" N TRP B5011 " --> pdb=" O GLU B5007 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B5012 " --> pdb=" O SER B5008 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B5013 " --> pdb=" O TYR B5009 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.890A pdb=" N ILE G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 removed outlier: 3.747A pdb=" N GLN G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 255 removed outlier: 3.965A pdb=" N THR G 254 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 369 Processing helix chain 'G' and resid 395 through 420 removed outlier: 4.050A pdb=" N GLN G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 401 " --> pdb=" O GLU G 397 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG G 402 " --> pdb=" O SER G 398 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN G 413 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 416 " --> pdb=" O ASN G 412 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY G 417 " --> pdb=" O GLN G 413 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 418 " --> pdb=" O PHE G 414 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP G 419 " --> pdb=" O ILE G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 452 removed outlier: 3.505A pdb=" N ASP G 447 " --> pdb=" O LEU G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 477 removed outlier: 3.913A pdb=" N SER G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG G 474 " --> pdb=" O SER G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 removed outlier: 3.584A pdb=" N CYS G 490 " --> pdb=" O LEU G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 513 No H-bonds generated for 'chain 'G' and resid 511 through 513' Processing helix chain 'G' and resid 514 through 529 removed outlier: 3.503A pdb=" N ILE G 518 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 521 " --> pdb=" O GLU G 517 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR G 523 " --> pdb=" O VAL G 519 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU G 529 " --> pdb=" O LEU G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 539 removed outlier: 3.512A pdb=" N ALA G 538 " --> pdb=" O ARG G 534 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 539 " --> pdb=" O ALA G 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 534 through 539' Processing helix chain 'G' and resid 543 through 551 removed outlier: 3.697A pdb=" N VAL G 548 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER G 549 " --> pdb=" O ASP G 545 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G 550 " --> pdb=" O TRP G 546 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G 551 " --> pdb=" O VAL G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 568 removed outlier: 3.521A pdb=" N LEU G 564 " --> pdb=" O ILE G 560 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 578 removed outlier: 3.517A pdb=" N ILE G 577 " --> pdb=" O VAL G 574 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE G 578 " --> pdb=" O LEU G 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 574 through 578' Processing helix chain 'G' and resid 581 through 593 Processing helix chain 'G' and resid 597 through 608 removed outlier: 3.753A pdb=" N LEU G 603 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 625 removed outlier: 4.130A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR G 622 " --> pdb=" O GLN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 889 removed outlier: 3.580A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS G 873 " --> pdb=" O ARG G 869 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 875 " --> pdb=" O ARG G 871 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN G 877 " --> pdb=" O LYS G 873 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG G 886 " --> pdb=" O TRP G 882 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 887 " --> pdb=" O ALA G 883 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 932 removed outlier: 3.803A pdb=" N ASN G 919 " --> pdb=" O GLU G 915 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR G 920 " --> pdb=" O PRO G 916 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN G 921 " --> pdb=" O GLU G 917 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 927 " --> pdb=" O GLN G 923 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR G 928 " --> pdb=" O MET G 924 " (cutoff:3.500A) Processing helix chain 'G' and resid 980 through 1001 removed outlier: 4.098A pdb=" N LEU G 984 " --> pdb=" O ALA G 980 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP G 986 " --> pdb=" O THR G 982 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN G 991 " --> pdb=" O ARG G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1039 removed outlier: 3.509A pdb=" N LYS G1032 " --> pdb=" O ASP G1028 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU G1039 " --> pdb=" O ASN G1035 " (cutoff:3.500A) Processing helix chain 'G' and resid 1042 through 1049 removed outlier: 3.892A pdb=" N LEU G1046 " --> pdb=" O ALA G1042 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G1047 " --> pdb=" O VAL G1043 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY G1048 " --> pdb=" O ARG G1044 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR G1049 " --> pdb=" O THR G1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1042 through 1049' Processing helix chain 'G' and resid 1078 through 1082 Processing helix chain 'G' and resid 1575 through 1580 removed outlier: 4.028A pdb=" N MET G1579 " --> pdb=" O LEU G1575 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G1580 " --> pdb=" O SER G1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1575 through 1580' Processing helix chain 'G' and resid 1623 through 1627 Processing helix chain 'G' and resid 1652 through 1657 removed outlier: 3.665A pdb=" N LEU G1657 " --> pdb=" O LEU G1653 " (cutoff:3.500A) Processing helix chain 'G' and resid 1658 through 1674 removed outlier: 3.757A pdb=" N HIS G1665 " --> pdb=" O ARG G1661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR G1666 " --> pdb=" O PHE G1662 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR G1670 " --> pdb=" O THR G1666 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG G1671 " --> pdb=" O LEU G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1686 removed outlier: 3.640A pdb=" N ALA G1684 " --> pdb=" O ARG G1680 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS G1686 " --> pdb=" O ALA G1682 " (cutoff:3.500A) Processing helix chain 'G' and resid 1692 through 1697 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 1720 Processing helix chain 'G' and resid 1720 through 1730 removed outlier: 3.583A pdb=" N ARG G1725 " --> pdb=" O GLU G1721 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N SER G1726 " --> pdb=" O SER G1722 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET G1730 " --> pdb=" O SER G1726 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1744 Processing helix chain 'G' and resid 1803 through 1823 removed outlier: 3.612A pdb=" N MET G1814 " --> pdb=" O LYS G1810 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU G1815 " --> pdb=" O ALA G1811 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU G1817 " --> pdb=" O ARG G1813 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1838 Processing helix chain 'G' and resid 1840 through 1851 removed outlier: 3.570A pdb=" N LEU G1848 " --> pdb=" O LEU G1844 " (cutoff:3.500A) removed outlier: 3.522A 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 1934 through 1977 removed outlier: 3.707A pdb=" N GLN G1938 " --> pdb=" O SER G1934 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR G1945 " --> pdb=" O ASN G1941 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE G1946 " --> pdb=" O LEU G1942 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP G1948 " --> pdb=" O GLU G1944 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU G1963 " --> pdb=" O ALA G1959 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG G1964 " --> pdb=" O ALA G1960 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G1966 " --> pdb=" O ALA G1962 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) Processing helix chain 'G' and resid 1978 through 1980 No H-bonds generated for 'chain 'G' and resid 1978 through 1980' Processing helix chain 'G' and resid 1989 through 1994 removed outlier: 3.542A pdb=" N ARG G1994 " --> pdb=" O GLU G1990 " (cutoff:3.500A) Processing helix chain 'G' and resid 2001 through 2014 removed outlier: 3.681A pdb=" N ILE G2006 " --> pdb=" O PRO G2002 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE G2012 " --> pdb=" O MET G2008 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G2013 " --> pdb=" O LEU G2009 " (cutoff:3.500A) Processing helix chain 'G' and resid 2028 through 2042 removed outlier: 3.897A pdb=" N LEU G2039 " --> pdb=" O HIS G2035 " (cutoff:3.500A) Processing helix chain 'G' and resid 2093 through 2107 removed outlier: 4.011A pdb=" N VAL G2103 " --> pdb=" O SER G2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA G2106 " --> pdb=" O VAL G2102 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2126 removed outlier: 3.743A pdb=" N VAL G2117 " --> pdb=" O SER G2113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG G2126 " --> pdb=" O SER G2122 " (cutoff:3.500A) Processing helix chain 'G' and resid 2129 through 2138 removed outlier: 3.797A pdb=" N ALA G2137 " --> pdb=" O GLU G2133 " (cutoff:3.500A) Processing helix chain 'G' and resid 2148 through 2166 removed outlier: 3.912A pdb=" N SER G2154 " --> pdb=" O GLU G2150 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS G2158 " --> pdb=" O SER G2154 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU G2159 " --> pdb=" O LEU G2155 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY G2160 " --> pdb=" O LEU G2156 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN G2161 " --> pdb=" O GLU G2157 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2187 removed outlier: 3.598A pdb=" N LEU G2177 " --> pdb=" O GLN G2173 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G2185 " --> pdb=" O SER G2181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN G2187 " --> pdb=" O GLY G2183 " (cutoff:3.500A) Processing helix chain 'G' and resid 2194 through 2201 removed outlier: 3.854A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2202 through 2216 removed outlier: 3.666A pdb=" N THR G2206 " --> pdb=" O GLY G2202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G2207 " --> pdb=" O MET G2203 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN G2213 " --> pdb=" O GLU G2209 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G2214 " --> pdb=" O VAL G2210 " (cutoff:3.500A) Processing helix chain 'G' and resid 2228 through 2242 removed outlier: 4.019A pdb=" N TYR G2238 " --> pdb=" O ARG G2234 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2252 removed outlier: 3.710A pdb=" N ASP G2252 " --> pdb=" O ARG G2248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2253 through 2261 removed outlier: 3.704A pdb=" N ASN G2260 " --> pdb=" O TYR G2256 " (cutoff:3.500A) Processing helix chain 'G' and resid 2262 through 2264 No H-bonds generated for 'chain 'G' and resid 2262 through 2264' Processing helix chain 'G' and resid 2271 through 2279 Processing helix chain 'G' and resid 2294 through 2304 removed outlier: 3.702A pdb=" N VAL G2299 " --> pdb=" O LEU G2295 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER G2300 " --> pdb=" O GLU G2296 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2315 removed outlier: 3.830A pdb=" N ALA G2315 " --> pdb=" O PRO G2311 " (cutoff:3.500A) Processing helix chain 'G' and resid 2326 through 2331 Processing helix chain 'G' and resid 2335 through 2339 removed outlier: 3.550A pdb=" N ALA G2338 " --> pdb=" O LEU G2335 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2358 removed outlier: 3.619A pdb=" N ALA G2350 " --> pdb=" O VAL G2346 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL G2353 " --> pdb=" O ASN G2349 " (cutoff:3.500A) removed outlier: 3.561A 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 2389 removed outlier: 3.702A pdb=" N ILE G2380 " --> pdb=" O LEU G2376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG G2385 " --> pdb=" O GLU G2381 " (cutoff:3.500A) Processing helix chain 'G' and resid 2390 through 2393 removed outlier: 3.551A pdb=" N ASP G2393 " --> pdb=" O PRO G2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2390 through 2393' Processing helix chain 'G' and resid 2419 through 2436 removed outlier: 3.615A pdb=" N MET G2423 " --> pdb=" O GLY G2419 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU G2433 " --> pdb=" O LEU G2429 " (cutoff:3.500A) Processing helix chain 'G' and resid 2440 through 2445 removed outlier: 4.072A pdb=" N ALA G2445 " --> pdb=" O HIS G2441 " (cutoff:3.500A) Processing helix chain 'G' and resid 2448 through 2461 removed outlier: 4.030A pdb=" N ILE G2453 " --> pdb=" O GLU G2449 " (cutoff:3.500A) Processing helix chain 'G' and resid 2464 through 2471 removed outlier: 3.607A pdb=" N ILE G2469 " --> pdb=" O ASP G2465 " (cutoff:3.500A) Processing helix chain 'G' and resid 2496 through 2500 Processing helix chain 'G' and resid 2502 through 2509 removed outlier: 3.769A pdb=" N UNK G2506 " --> pdb=" O UNK G2502 " (cutoff:3.500A) Processing helix chain 'G' and resid 2516 through 2530 removed outlier: 4.334A pdb=" N UNK G2523 " --> pdb=" O UNK G2519 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N UNK G2526 " --> pdb=" O UNK G2522 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N UNK G2527 " --> pdb=" O UNK G2523 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK G2528 " --> pdb=" O UNK G2524 " (cutoff:3.500A) Processing helix chain 'G' and resid 2542 through 2548 removed outlier: 3.546A pdb=" N UNK G2546 " --> pdb=" O UNK G2542 " (cutoff:3.500A) Processing helix chain 'G' and resid 2551 through 2557 removed outlier: 3.633A pdb=" N UNK G2555 " --> pdb=" O UNK G2551 " (cutoff:3.500A) Processing helix chain 'G' and resid 2566 through 2581 removed outlier: 4.125A pdb=" N UNK G2570 " --> pdb=" O UNK G2566 " (cutoff:3.500A) Processing helix chain 'G' and resid 2587 through 2601 removed outlier: 3.553A pdb=" N UNK G2597 " --> pdb=" O UNK G2593 " (cutoff:3.500A) Processing helix chain 'G' and resid 2602 through 2604 No H-bonds generated for 'chain 'G' and resid 2602 through 2604' Processing helix chain 'G' and resid 2610 through 2618 removed outlier: 3.763A pdb=" N UNK G2617 " --> pdb=" O UNK G2613 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK G2618 " --> pdb=" O UNK G2614 " (cutoff:3.500A) Processing helix chain 'G' and resid 2628 through 2640 removed outlier: 3.502A pdb=" N UNK G2632 " --> pdb=" O UNK G2628 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N UNK G2634 " --> pdb=" O UNK G2630 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK G2635 " --> pdb=" O UNK G2631 " (cutoff:3.500A) removed outlier: 3.586A 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 removed outlier: 3.553A pdb=" N UNK G2654 " --> pdb=" O UNK G2650 " (cutoff:3.500A) Processing helix chain 'G' and resid 2675 through 2680 removed outlier: 3.502A pdb=" N UNK G2680 " --> pdb=" O UNK G2676 " (cutoff:3.500A) Processing helix chain 'G' and resid 2683 through 2687 removed outlier: 3.888A pdb=" N UNK G2686 " --> pdb=" O UNK G2683 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N UNK G2687 " --> pdb=" O UNK G2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2683 through 2687' Processing helix chain 'G' and resid 2741 through 2745 removed outlier: 3.949A pdb=" N ASN G2744 " --> pdb=" O GLU G2741 " (cutoff:3.500A) Processing helix chain 'G' and resid 2748 through 2773 removed outlier: 3.524A pdb=" N ASP G2752 " --> pdb=" O PRO G2748 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE G2768 " --> pdb=" O GLU G2764 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2797 removed outlier: 3.909A pdb=" N THR G2796 " --> pdb=" O PRO G2793 " (cutoff:3.500A) Processing helix chain 'G' and resid 2800 through 2805 removed outlier: 3.957A pdb=" N ILE G2804 " --> pdb=" O LYS G2800 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR G2805 " --> pdb=" O ASP G2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2800 through 2805' Processing helix chain 'G' and resid 2809 through 2820 removed outlier: 3.905A pdb=" N ALA G2815 " --> pdb=" O GLU G2811 " (cutoff:3.500A) Processing helix chain 'G' and resid 2868 through 2895 removed outlier: 4.461A pdb=" N MET G2874 " --> pdb=" O GLU G2870 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA G2875 " --> pdb=" O LEU G2871 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP G2886 " --> pdb=" O TYR G2882 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU G2895 " --> pdb=" O LYS G2891 " (cutoff:3.500A) Processing helix chain 'G' and resid 2907 through 2911 removed outlier: 3.587A pdb=" N THR G2910 " --> pdb=" O PRO G2907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU G2911 " --> pdb=" O TYR G2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2907 through 2911' Processing helix chain 'G' and resid 2917 through 2932 removed outlier: 3.788A pdb=" N GLU G2921 " --> pdb=" O ALA G2917 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU G2926 " --> pdb=" O LYS G2922 " (cutoff:3.500A) Processing helix chain 'G' and resid 2950 through 2976 removed outlier: 3.959A pdb=" N UNK G2956 " --> pdb=" O UNK G2952 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK G2968 " --> pdb=" O UNK G2964 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N UNK G2969 " --> pdb=" O UNK G2965 " (cutoff:3.500A) Processing helix chain 'G' and resid 2997 through 3015 removed outlier: 3.745A pdb=" N UNK G3002 " --> pdb=" O UNK G2998 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK G3004 " --> pdb=" O UNK G3000 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N UNK G3006 " --> pdb=" O UNK G3002 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNK G3009 " --> pdb=" O UNK G3005 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK G3010 " --> pdb=" O UNK G3006 " (cutoff:3.500A) Processing helix chain 'G' and resid 3017 through 3022 Processing helix chain 'G' and resid 3024 through 3040 removed outlier: 4.187A pdb=" N UNK G3028 " --> pdb=" O UNK G3024 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N UNK G3032 " --> pdb=" O UNK G3028 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N UNK G3040 " --> pdb=" O UNK G3036 " (cutoff:3.500A) Processing helix chain 'G' and resid 3050 through 3060 removed outlier: 4.091A pdb=" N UNK G3056 " --> pdb=" O UNK G3052 " (cutoff:3.500A) Processing helix chain 'G' and resid 3141 through 3146 Processing helix chain 'G' and resid 3146 through 3162 removed outlier: 3.922A pdb=" N UNK G3154 " --> pdb=" O UNK G3150 " (cutoff:3.500A) Processing helix chain 'G' and resid 3175 through 3187 Processing helix chain 'G' and resid 3188 through 3190 No H-bonds generated for 'chain 'G' and resid 3188 through 3190' Processing helix chain 'G' and resid 3198 through 3212 removed outlier: 3.723A pdb=" N UNK G3205 " --> pdb=" O UNK G3201 " (cutoff:3.500A) Processing helix chain 'G' and resid 3224 through 3230 removed outlier: 3.959A pdb=" N UNK G3228 " --> pdb=" O UNK G3224 " (cutoff:3.500A) Processing helix chain 'G' and resid 3248 through 3254 Processing helix chain 'G' and resid 3271 through 3285 removed outlier: 4.023A pdb=" N UNK G3282 " --> pdb=" O UNK G3278 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK G3284 " --> pdb=" O UNK G3280 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK G3285 " --> pdb=" O UNK G3281 " (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 3315 through 3321 removed outlier: 3.874A pdb=" N UNK G3319 " --> pdb=" O UNK G3315 " (cutoff:3.500A) Processing helix chain 'G' and resid 3321 through 3331 removed outlier: 3.504A pdb=" N UNK G3330 " --> pdb=" O UNK G3326 " (cutoff:3.500A) Processing helix chain 'G' and resid 3344 through 3349 removed outlier: 3.618A pdb=" N UNK G3348 " --> pdb=" O UNK G3344 " (cutoff:3.500A) Processing helix chain 'G' and resid 3350 through 3354 Processing helix chain 'G' and resid 3361 through 3388 Processing helix chain 'G' and resid 3399 through 3407 removed outlier: 3.602A pdb=" N UNK G3403 " --> pdb=" O UNK G3399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK G3405 " --> pdb=" O UNK G3401 " (cutoff:3.500A) Processing helix chain 'G' and resid 3407 through 3425 removed outlier: 3.837A pdb=" N UNK G3413 " --> pdb=" O UNK G3409 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK G3416 " --> pdb=" O UNK G3412 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N UNK G3417 " --> pdb=" O UNK G3413 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N UNK G3420 " --> pdb=" O UNK G3416 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N UNK G3421 " --> pdb=" O UNK G3417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N UNK G3425 " --> pdb=" O UNK G3421 " (cutoff:3.500A) Processing helix chain 'G' and resid 3426 through 3431 Processing helix chain 'G' and resid 3437 through 3443 Processing helix chain 'G' and resid 3445 through 3450 Processing helix chain 'G' and resid 3457 through 3460 Processing helix chain 'G' and resid 3461 through 3468 Processing helix chain 'G' and resid 3522 through 3527 Processing helix chain 'G' and resid 3541 through 3547 removed outlier: 3.501A pdb=" N UNK G3545 " --> pdb=" O UNK G3541 " (cutoff:3.500A) Processing helix chain 'G' and resid 3551 through 3560 Processing helix chain 'G' and resid 3574 through 3583 removed outlier: 4.331A pdb=" N UNK G3580 " --> pdb=" O UNK G3576 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N UNK G3583 " --> pdb=" O UNK G3579 " (cutoff:3.500A) Processing helix chain 'G' and resid 3590 through 3608 removed outlier: 3.521A pdb=" N UNK G3595 " --> pdb=" O UNK G3591 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK G3596 " --> pdb=" O UNK G3592 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N UNK G3598 " --> pdb=" O UNK G3594 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N UNK G3600 " --> pdb=" O UNK G3596 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK G3601 " --> pdb=" O UNK G3597 " (cutoff:3.500A) Processing helix chain 'G' and resid 3645 through 3656 removed outlier: 3.726A pdb=" N GLU G3655 " --> pdb=" O ASN G3651 " (cutoff:3.500A) Processing helix chain 'G' and resid 3671 through 3680 removed outlier: 3.656A pdb=" N ASP G3676 " --> pdb=" O ARG G3672 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU G3677 " --> pdb=" O MET G3673 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER G3678 " --> pdb=" O ILE G3674 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA G3680 " --> pdb=" O ASP G3676 " (cutoff:3.500A) Processing helix chain 'G' and resid 3681 through 3687 removed outlier: 6.855A pdb=" N GLU G3684 " --> pdb=" O GLY G3681 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU G3685 " --> pdb=" O GLU G3682 " (cutoff:3.500A) Processing helix chain 'G' and resid 3696 through 3708 removed outlier: 3.601A pdb=" N LEU G3701 " --> pdb=" O PRO G3697 " (cutoff:3.500A) Processing helix chain 'G' and resid 3719 through 3738 removed outlier: 3.817A pdb=" N TYR G3725 " --> pdb=" O LEU G3721 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP G3727 " --> pdb=" O MET G3723 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS G3733 " --> pdb=" O MET G3729 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS G3734 " --> pdb=" O ALA G3730 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU G3736 " --> pdb=" O SER G3732 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU G3737 " --> pdb=" O CYS G3733 " (cutoff:3.500A) Processing helix chain 'G' and resid 3752 through 3771 removed outlier: 3.724A pdb=" N GLU G3757 " --> pdb=" O PHE G3753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET G3758 " --> pdb=" O GLU G3754 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU G3759 " --> pdb=" O GLU G3755 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS G3760 " --> pdb=" O LYS G3756 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR G3765 " --> pdb=" O GLN G3761 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN G3766 " --> pdb=" O ARG G3762 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN G3767 " --> pdb=" O LEU G3763 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER G3768 " --> pdb=" O LEU G3764 " (cutoff:3.500A) Processing helix chain 'G' and resid 3771 through 3782 removed outlier: 3.696A pdb=" N ALA G3775 " --> pdb=" O HIS G3771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA G3776 " --> pdb=" O THR G3772 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU G3777 " --> pdb=" O ARG G3773 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET G3778 " --> pdb=" O GLY G3774 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU G3780 " --> pdb=" O ALA G3776 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN G3781 " --> pdb=" O GLU G3777 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3805 removed outlier: 4.208A pdb=" N LYS G3799 " --> pdb=" O SER G3795 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU G3800 " --> pdb=" O SER G3796 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G3803 " --> pdb=" O LYS G3799 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G3805 " --> pdb=" O GLY G3801 " (cutoff:3.500A) Processing helix chain 'G' and resid 3809 through 3824 removed outlier: 3.537A pdb=" N GLN G3814 " --> pdb=" O ALA G3810 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G3815 " --> pdb=" O GLU G3811 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS G3824 " --> pdb=" O LEU G3820 " (cutoff:3.500A) Processing helix chain 'G' and resid 3827 through 3838 removed outlier: 3.619A pdb=" N ILE G3832 " --> pdb=" O PHE G3828 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3854 Processing helix chain 'G' and resid 3880 through 3891 Processing helix chain 'G' and resid 3898 through 3905 Processing helix chain 'G' and resid 3914 through 3937 removed outlier: 3.803A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G3920 " --> pdb=" O ILE G3916 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER G3929 " --> pdb=" O ARG G3925 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP G3935 " --> pdb=" O SER G3931 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR G3936 " --> pdb=" O ASP G3932 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR G3937 " --> pdb=" O PHE G3933 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3967 removed outlier: 4.025A pdb=" N ALA G3954 " --> pdb=" O ASN G3950 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G3960 " --> pdb=" O SER G3956 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G3967 " --> pdb=" O ASN G3963 " (cutoff:3.500A) Processing helix chain 'G' and resid 3973 through 3983 removed outlier: 3.530A pdb=" N GLN G3977 " --> pdb=" O CYS G3973 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS G3982 " --> pdb=" O GLN G3978 " (cutoff:3.500A) Processing helix chain 'G' and resid 3984 through 4003 removed outlier: 3.740A pdb=" N VAL G3990 " --> pdb=" O TRP G3986 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY G3991 " --> pdb=" O ASP G3987 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE G3992 " --> pdb=" O ALA G3988 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS G3998 " --> pdb=" O HIS G3994 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET G4000 " --> pdb=" O PHE G3996 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET G4001 " --> pdb=" O ALA G3997 " (cutoff:3.500A) Processing helix chain 'G' and resid 4004 through 4006 No H-bonds generated for 'chain 'G' and resid 4004 through 4006' Processing helix chain 'G' and resid 4009 through 4030 Processing helix chain 'G' and resid 4039 through 4051 removed outlier: 3.610A pdb=" N VAL G4049 " --> pdb=" O VAL G4045 " (cutoff:3.500A) Processing helix chain 'G' and resid 4051 through 4065 removed outlier: 3.548A pdb=" N MET G4057 " --> pdb=" O SER G4053 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET G4064 " --> pdb=" O LYS G4060 " (cutoff:3.500A) Processing helix chain 'G' and resid 4066 through 4072 removed outlier: 3.913A pdb=" N ASP G4070 " --> pdb=" O LEU G4066 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL G4072 " --> pdb=" O LEU G4068 " (cutoff:3.500A) Processing helix chain 'G' and resid 4074 through 4079 removed outlier: 3.776A pdb=" N GLN G4078 " --> pdb=" O SER G4074 " (cutoff:3.500A) Processing helix chain 'G' and resid 4090 through 4100 removed outlier: 3.513A pdb=" N MET G4097 " --> pdb=" O PHE G4093 " (cutoff:3.500A) removed outlier: 3.917A 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 4132 removed outlier: 4.412A pdb=" N PHE G4132 " --> pdb=" O PHE G4128 " (cutoff:3.500A) Processing helix chain 'G' and resid 4132 through 4154 removed outlier: 3.593A pdb=" N ALA G4136 " --> pdb=" O PHE G4132 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP G4138 " --> pdb=" O GLU G4134 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE G4139 " --> pdb=" O PRO G4135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER G4151 " --> pdb=" O LEU G4147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU G4152 " --> pdb=" O THR G4148 " (cutoff:3.500A) removed outlier: 3.726A 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 4168 through 4175 removed outlier: 3.544A pdb=" N TYR G4173 " --> pdb=" O SER G4169 " (cutoff:3.500A) Processing helix chain 'G' and resid 4199 through 4206 removed outlier: 3.823A pdb=" N ALA G4203 " --> pdb=" O GLU G4199 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU G4206 " --> pdb=" O ARG G4202 " (cutoff:3.500A) Processing helix chain 'G' and resid 4207 through 4224 removed outlier: 4.105A pdb=" N SER G4213 " --> pdb=" O GLN G4209 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G4222 " --> pdb=" O ILE G4218 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN G4223 " --> pdb=" O PHE G4219 " (cutoff:3.500A) Processing helix chain 'G' and resid 4228 through 4248 removed outlier: 4.024A pdb=" N PHE G4234 " --> pdb=" O LYS G4230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE G4242 " --> pdb=" O CYS G4238 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE G4243 " --> pdb=" O GLU G4239 " (cutoff:3.500A) Processing helix chain 'G' and resid 4321 through 4337 removed outlier: 3.537A pdb=" N UNK G4327 " --> pdb=" O UNK G4323 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK G4332 " --> pdb=" O UNK G4328 " (cutoff:3.500A) Processing helix chain 'G' and resid 4543 through 4556 removed outlier: 3.964A pdb=" N TYR G4554 " --> pdb=" O LYS G4550 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4576 removed outlier: 3.535A pdb=" N ALA G4566 " --> pdb=" O LEU G4562 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE G4571 " --> pdb=" O LEU G4567 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA G4572 " --> pdb=" O PHE G4568 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE G4573 " --> pdb=" O LEU G4569 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G4574 " --> pdb=" O ALA G4570 " (cutoff:3.500A) Processing helix chain 'G' and resid 4577 through 4580 removed outlier: 3.927A pdb=" N TYR G4580 " --> pdb=" O LEU G4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4577 through 4580' Processing helix chain 'G' and resid 4641 through 4665 removed outlier: 3.618A pdb=" N LEU G4648 " --> pdb=" O TRP G4644 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G4649 " --> pdb=" O CYS G4645 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA G4654 " --> pdb=" O HIS G4650 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G4658 " --> pdb=" O ALA G4654 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE G4659 " --> pdb=" O PHE G4655 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY G4660 " --> pdb=" O LEU G4656 " (cutoff:3.500A) Processing helix chain 'G' and resid 4665 through 4683 removed outlier: 3.539A pdb=" N LYS G4672 " --> pdb=" O LEU G4668 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G4677 " --> pdb=" O ARG G4673 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA G4678 " --> pdb=" O GLU G4674 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE G4683 " --> pdb=" O ARG G4679 " (cutoff:3.500A) Processing helix chain 'G' and resid 4697 through 4702 removed outlier: 3.577A pdb=" N ASP G4702 " --> pdb=" O LYS G4698 " (cutoff:3.500A) Processing helix chain 'G' and resid 4710 through 4714 removed outlier: 3.515A pdb=" N SER G4713 " --> pdb=" O SER G4710 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN G4714 " --> pdb=" O PHE G4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4710 through 4714' Processing helix chain 'G' and resid 4719 through 4728 removed outlier: 3.526A pdb=" N LEU G4725 " --> pdb=" O LYS G4721 " (cutoff:3.500A) Processing helix chain 'G' and resid 4733 through 4741 removed outlier: 3.553A pdb=" N LEU G4741 " --> pdb=" O ILE G4737 " (cutoff:3.500A) Processing helix chain 'G' and resid 4745 through 4750 Processing helix chain 'G' and resid 4751 through 4755 removed outlier: 4.039A pdb=" N GLU G4755 " --> pdb=" O ALA G4752 " (cutoff:3.500A) Processing helix chain 'G' and resid 4772 through 4786 removed outlier: 3.654A pdb=" N THR G4785 " --> pdb=" O GLY G4781 " (cutoff:3.500A) Processing helix chain 'G' and resid 4786 through 4802 removed outlier: 3.535A pdb=" N SER G4799 " --> pdb=" O TYR G4795 " (cutoff:3.500A) Processing helix chain 'G' and resid 4814 through 4820 removed outlier: 3.852A pdb=" N MET G4818 " --> pdb=" O LEU G4814 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G4820 " --> pdb=" O ILE G4816 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.748A pdb=" N ILE G4826 " --> pdb=" O THR G4822 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR G4831 " --> pdb=" O LEU G4827 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 removed outlier: 3.964A pdb=" N MET G4839 " --> pdb=" O LYS G4835 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY G4842 " --> pdb=" O VAL G4838 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G4843 " --> pdb=" O MET G4839 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G4844 " --> pdb=" O THR G4840 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G4853 " --> pdb=" O TYR G4849 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G4854 " --> pdb=" O LEU G4850 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA G4855 " --> pdb=" O TYR G4851 " (cutoff:3.500A) Processing helix chain 'G' and resid 4859 through 4863 removed outlier: 3.957A pdb=" N TYR G4863 " --> pdb=" O ARG G4860 " (cutoff:3.500A) Processing helix chain 'G' and resid 4878 through 4890 removed outlier: 3.655A pdb=" N MET G4887 " --> pdb=" O TYR G4883 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4925 removed outlier: 3.681A pdb=" N ARG G4913 " --> pdb=" O TYR G4909 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G4914 " --> pdb=" O GLU G4910 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G4915 " --> pdb=" O LEU G4911 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G4918 " --> pdb=" O VAL G4914 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE G4923 " --> pdb=" O THR G4919 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE G4925 " --> pdb=" O PHE G4921 " (cutoff:3.500A) Processing helix chain 'G' and resid 4927 through 4957 removed outlier: 3.640A pdb=" N ILE G4932 " --> pdb=" O LEU G4928 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE G4936 " --> pdb=" O ILE G4932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G4942 " --> pdb=" O ASP G4938 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G4943 " --> pdb=" O ALA G4939 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN G4947 " --> pdb=" O LEU G4943 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS G4951 " --> pdb=" O GLN G4947 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G4957 " --> pdb=" O ASP G4953 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4971 removed outlier: 4.317A pdb=" N PHE G4968 " --> pdb=" O GLY G4964 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR G4971 " --> pdb=" O TYR G4967 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4979 removed outlier: 3.761A pdb=" N THR G4977 " --> pdb=" O HIS G4973 " (cutoff:3.500A) Processing helix chain 'G' and resid 4986 through 4997 removed outlier: 4.009A pdb=" N PHE G4990 " --> pdb=" O ALA G4986 " (cutoff:3.500A) Processing helix chain 'G' and resid 5006 through 5017 removed outlier: 3.639A pdb=" N TRP G5011 " --> pdb=" O GLU G5007 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS G5012 " --> pdb=" O SER G5008 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET G5013 " --> pdb=" O TYR G5009 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.890A pdb=" N ILE I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 removed outlier: 3.749A pdb=" N GLN I 79 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 255 removed outlier: 3.964A pdb=" N THR I 254 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 369 Processing helix chain 'I' and resid 395 through 420 removed outlier: 4.050A pdb=" N GLN I 399 " --> pdb=" O GLN I 395 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN I 413 " --> pdb=" O GLY I 409 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE I 414 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS I 416 " --> pdb=" O ASN I 412 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY I 417 " --> pdb=" O GLN I 413 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU I 418 " --> pdb=" O PHE I 414 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP I 419 " --> pdb=" O ILE I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 452 removed outlier: 3.504A pdb=" N ASP I 447 " --> pdb=" O LEU I 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 477 removed outlier: 3.913A pdb=" N SER I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG I 474 " --> pdb=" O SER I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 494 removed outlier: 3.583A pdb=" N CYS I 490 " --> pdb=" O LEU I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 513 No H-bonds generated for 'chain 'I' and resid 511 through 513' Processing helix chain 'I' and resid 514 through 529 removed outlier: 3.504A pdb=" N ILE I 518 " --> pdb=" O SER I 514 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I 521 " --> pdb=" O GLU I 517 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR I 523 " --> pdb=" O VAL I 519 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 529 " --> pdb=" O LEU I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 534 through 539 removed outlier: 3.513A pdb=" N ALA I 538 " --> pdb=" O ARG I 534 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 539 " --> pdb=" O ALA I 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 534 through 539' Processing helix chain 'I' and resid 543 through 551 removed outlier: 3.697A pdb=" N VAL I 548 " --> pdb=" O LEU I 544 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER I 549 " --> pdb=" O ASP I 545 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS I 550 " --> pdb=" O TRP I 546 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU I 551 " --> pdb=" O VAL I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 568 removed outlier: 3.521A pdb=" N LEU I 564 " --> pdb=" O ILE I 560 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 578 removed outlier: 3.516A pdb=" N ILE I 577 " --> pdb=" O VAL I 574 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE I 578 " --> pdb=" O LEU I 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 574 through 578' Processing helix chain 'I' and resid 581 through 593 Processing helix chain 'I' and resid 597 through 608 removed outlier: 3.753A pdb=" N LEU I 603 " --> pdb=" O VAL I 599 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS I 607 " --> pdb=" O LEU I 603 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL I 608 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 625 removed outlier: 4.130A pdb=" N GLN I 618 " --> pdb=" O VAL I 614 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR I 622 " --> pdb=" O GLN I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 889 removed outlier: 3.580A pdb=" N ILE I 870 " --> pdb=" O HIS I 866 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU I 872 " --> pdb=" O GLU I 868 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS I 873 " --> pdb=" O ARG I 869 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA I 875 " --> pdb=" O ARG I 871 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN I 877 " --> pdb=" O LYS I 873 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG I 886 " --> pdb=" O TRP I 882 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 887 " --> pdb=" O ALA I 883 " (cutoff:3.500A) Processing helix chain 'I' and resid 914 through 932 removed outlier: 3.802A pdb=" N ASN I 919 " --> pdb=" O GLU I 915 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR I 920 " --> pdb=" O PRO I 916 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN I 921 " --> pdb=" O GLU I 917 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU I 927 " --> pdb=" O GLN I 923 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR I 928 " --> pdb=" O MET I 924 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 1001 removed outlier: 4.096A pdb=" N LEU I 984 " --> pdb=" O ALA I 980 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP I 986 " --> pdb=" O THR I 982 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN I 991 " --> pdb=" O ARG I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1028 through 1039 removed outlier: 3.508A pdb=" N LYS I1032 " --> pdb=" O ASP I1028 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU I1039 " --> pdb=" O ASN I1035 " (cutoff:3.500A) Processing helix chain 'I' and resid 1042 through 1049 removed outlier: 3.892A pdb=" N LEU I1046 " --> pdb=" O ALA I1042 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I1047 " --> pdb=" O VAL I1043 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY I1048 " --> pdb=" O ARG I1044 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR I1049 " --> pdb=" O THR I1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1042 through 1049' Processing helix chain 'I' and resid 1078 through 1082 Processing helix chain 'I' and resid 1575 through 1580 removed outlier: 4.028A pdb=" N MET I1579 " --> pdb=" O LEU I1575 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE I1580 " --> pdb=" O SER I1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1575 through 1580' Processing helix chain 'I' and resid 1623 through 1627 Processing helix chain 'I' and resid 1652 through 1657 removed outlier: 3.665A pdb=" N LEU I1657 " --> pdb=" O LEU I1653 " (cutoff:3.500A) Processing helix chain 'I' and resid 1658 through 1674 removed outlier: 3.757A pdb=" N HIS I1665 " --> pdb=" O ARG I1661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR I1666 " --> pdb=" O PHE I1662 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR I1670 " --> pdb=" O THR I1666 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG I1671 " --> pdb=" O LEU I1667 " (cutoff:3.500A) Processing helix chain 'I' and resid 1678 through 1686 removed outlier: 3.639A pdb=" N ALA I1684 " --> pdb=" O ARG I1680 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS I1686 " --> pdb=" O ALA I1682 " (cutoff:3.500A) Processing helix chain 'I' and resid 1692 through 1697 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 1720 Processing helix chain 'I' and resid 1720 through 1730 removed outlier: 3.583A pdb=" N ARG I1725 " --> pdb=" O GLU I1721 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N SER I1726 " --> pdb=" O SER I1722 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET I1730 " --> pdb=" O SER I1726 " (cutoff:3.500A) Processing helix chain 'I' and resid 1739 through 1744 Processing helix chain 'I' and resid 1803 through 1823 removed outlier: 3.612A pdb=" N MET I1814 " --> pdb=" O LYS I1810 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU I1815 " --> pdb=" O ALA I1811 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU I1817 " --> pdb=" O ARG I1813 " (cutoff:3.500A) Processing helix chain 'I' and resid 1833 through 1838 Processing helix chain 'I' and resid 1840 through 1851 removed outlier: 3.569A pdb=" N LEU I1848 " --> pdb=" O LEU I1844 " (cutoff:3.500A) removed outlier: 3.522A 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 1934 through 1977 removed outlier: 3.707A pdb=" N GLN I1938 " --> pdb=" O SER I1934 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR I1945 " --> pdb=" O ASN I1941 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE I1946 " --> pdb=" O LEU I1942 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP I1948 " --> pdb=" O GLU I1944 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU I1963 " --> pdb=" O ALA I1959 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG I1964 " --> pdb=" O ALA I1960 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL I1966 " --> pdb=" O ALA I1962 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS I1968 " --> pdb=" O ARG I1964 " (cutoff:3.500A) Processing helix chain 'I' and resid 1978 through 1980 No H-bonds generated for 'chain 'I' and resid 1978 through 1980' Processing helix chain 'I' and resid 1989 through 1994 removed outlier: 3.543A pdb=" N ARG I1994 " --> pdb=" O GLU I1990 " (cutoff:3.500A) Processing helix chain 'I' and resid 2001 through 2014 removed outlier: 3.681A pdb=" N ILE I2006 " --> pdb=" O PRO I2002 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS I2011 " --> pdb=" O ASN I2007 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE I2012 " --> pdb=" O MET I2008 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS I2013 " --> pdb=" O LEU I2009 " (cutoff:3.500A) Processing helix chain 'I' and resid 2028 through 2042 removed outlier: 3.896A pdb=" N LEU I2039 " --> pdb=" O HIS I2035 " (cutoff:3.500A) Processing helix chain 'I' and resid 2093 through 2107 removed outlier: 4.011A pdb=" N VAL I2103 " --> pdb=" O SER I2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA I2106 " --> pdb=" O VAL I2102 " (cutoff:3.500A) Processing helix chain 'I' and resid 2113 through 2126 removed outlier: 3.743A pdb=" N VAL I2117 " --> pdb=" O SER I2113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG I2126 " --> pdb=" O SER I2122 " (cutoff:3.500A) Processing helix chain 'I' and resid 2129 through 2138 removed outlier: 3.797A pdb=" N ALA I2137 " --> pdb=" O GLU I2133 " (cutoff:3.500A) Processing helix chain 'I' and resid 2148 through 2166 removed outlier: 3.911A pdb=" N SER I2154 " --> pdb=" O GLU I2150 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS I2158 " --> pdb=" O SER I2154 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU I2159 " --> pdb=" O LEU I2155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY I2160 " --> pdb=" O LEU I2156 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN I2161 " --> pdb=" O GLU I2157 " (cutoff:3.500A) Processing helix chain 'I' and resid 2171 through 2187 removed outlier: 3.598A pdb=" N LEU I2177 " --> pdb=" O GLN I2173 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I2185 " --> pdb=" O SER I2181 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN I2187 " --> pdb=" O GLY I2183 " (cutoff:3.500A) Processing helix chain 'I' and resid 2194 through 2201 removed outlier: 3.855A pdb=" N MET I2198 " --> pdb=" O HIS I2194 " (cutoff:3.500A) Processing helix chain 'I' and resid 2202 through 2216 removed outlier: 3.665A pdb=" N THR I2206 " --> pdb=" O GLY I2202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I2207 " --> pdb=" O MET I2203 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN I2213 " --> pdb=" O GLU I2209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL I2214 " --> pdb=" O VAL I2210 " (cutoff:3.500A) Processing helix chain 'I' and resid 2228 through 2242 removed outlier: 4.019A pdb=" N TYR I2238 " --> pdb=" O ARG I2234 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2252 removed outlier: 3.709A pdb=" N ASP I2252 " --> pdb=" O ARG I2248 " (cutoff:3.500A) Processing helix chain 'I' and resid 2253 through 2261 removed outlier: 3.704A pdb=" N ASN I2260 " --> pdb=" O TYR I2256 " (cutoff:3.500A) Processing helix chain 'I' and resid 2262 through 2264 No H-bonds generated for 'chain 'I' and resid 2262 through 2264' Processing helix chain 'I' and resid 2271 through 2279 Processing helix chain 'I' and resid 2294 through 2304 removed outlier: 3.702A pdb=" N VAL I2299 " --> pdb=" O LEU I2295 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER I2300 " --> pdb=" O GLU I2296 " (cutoff:3.500A) Processing helix chain 'I' and resid 2310 through 2315 removed outlier: 3.830A pdb=" N ALA I2315 " --> pdb=" O PRO I2311 " (cutoff:3.500A) Processing helix chain 'I' and resid 2326 through 2331 Processing helix chain 'I' and resid 2335 through 2339 removed outlier: 3.551A pdb=" N ALA I2338 " --> pdb=" O LEU I2335 " (cutoff:3.500A) Processing helix chain 'I' and resid 2346 through 2358 removed outlier: 3.619A pdb=" N ALA I2350 " --> pdb=" O VAL I2346 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL I2352 " --> pdb=" O GLU I2348 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL I2353 " --> pdb=" O ASN I2349 " (cutoff:3.500A) removed outlier: 3.562A 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 2389 removed outlier: 3.702A pdb=" N ILE I2380 " --> pdb=" O LEU I2376 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG I2385 " --> pdb=" O GLU I2381 " (cutoff:3.500A) Processing helix chain 'I' and resid 2390 through 2393 removed outlier: 3.552A pdb=" N ASP I2393 " --> pdb=" O PRO I2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2390 through 2393' Processing helix chain 'I' and resid 2419 through 2436 removed outlier: 3.615A pdb=" N MET I2423 " --> pdb=" O GLY I2419 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU I2433 " --> pdb=" O LEU I2429 " (cutoff:3.500A) Processing helix chain 'I' and resid 2440 through 2445 removed outlier: 4.071A pdb=" N ALA I2445 " --> pdb=" O HIS I2441 " (cutoff:3.500A) Processing helix chain 'I' and resid 2448 through 2461 removed outlier: 4.030A pdb=" N ILE I2453 " --> pdb=" O GLU I2449 " (cutoff:3.500A) Processing helix chain 'I' and resid 2464 through 2471 removed outlier: 3.607A pdb=" N ILE I2469 " --> pdb=" O ASP I2465 " (cutoff:3.500A) Processing helix chain 'I' and resid 2496 through 2500 Processing helix chain 'I' and resid 2502 through 2509 removed outlier: 3.770A pdb=" N UNK I2506 " --> pdb=" O UNK I2502 " (cutoff:3.500A) Processing helix chain 'I' and resid 2516 through 2530 removed outlier: 4.333A pdb=" N UNK I2523 " --> pdb=" O UNK I2519 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N UNK I2526 " --> pdb=" O UNK I2522 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N UNK I2527 " --> pdb=" O UNK I2523 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK I2528 " --> pdb=" O UNK I2524 " (cutoff:3.500A) Processing helix chain 'I' and resid 2542 through 2548 removed outlier: 3.546A pdb=" N UNK I2546 " --> pdb=" O UNK I2542 " (cutoff:3.500A) Processing helix chain 'I' and resid 2551 through 2557 removed outlier: 3.633A pdb=" N UNK I2555 " --> pdb=" O UNK I2551 " (cutoff:3.500A) Processing helix chain 'I' and resid 2566 through 2581 removed outlier: 4.125A pdb=" N UNK I2570 " --> pdb=" O UNK I2566 " (cutoff:3.500A) Processing helix chain 'I' and resid 2587 through 2601 removed outlier: 3.553A pdb=" N UNK I2597 " --> pdb=" O UNK I2593 " (cutoff:3.500A) Processing helix chain 'I' and resid 2602 through 2604 No H-bonds generated for 'chain 'I' and resid 2602 through 2604' Processing helix chain 'I' and resid 2610 through 2618 removed outlier: 3.763A pdb=" N UNK I2617 " --> pdb=" O UNK I2613 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK I2618 " --> pdb=" O UNK I2614 " (cutoff:3.500A) Processing helix chain 'I' and resid 2628 through 2640 removed outlier: 3.502A pdb=" N UNK I2632 " --> pdb=" O UNK I2628 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N UNK I2634 " --> pdb=" O UNK I2630 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK I2635 " --> pdb=" O UNK I2631 " (cutoff:3.500A) removed outlier: 3.586A 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 removed outlier: 3.554A pdb=" N UNK I2654 " --> pdb=" O UNK I2650 " (cutoff:3.500A) Processing helix chain 'I' and resid 2675 through 2680 removed outlier: 3.502A pdb=" N UNK I2680 " --> pdb=" O UNK I2676 " (cutoff:3.500A) Processing helix chain 'I' and resid 2683 through 2687 removed outlier: 3.888A pdb=" N UNK I2686 " --> pdb=" O UNK I2683 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK I2687 " --> pdb=" O UNK I2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2683 through 2687' Processing helix chain 'I' and resid 2741 through 2745 removed outlier: 3.949A pdb=" N ASN I2744 " --> pdb=" O GLU I2741 " (cutoff:3.500A) Processing helix chain 'I' and resid 2748 through 2773 removed outlier: 3.524A pdb=" N ASP I2752 " --> pdb=" O PRO I2748 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER I2753 " --> pdb=" O GLU I2749 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE I2754 " --> pdb=" O LYS I2750 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE I2768 " --> pdb=" O GLU I2764 " (cutoff:3.500A) Processing helix chain 'I' and resid 2793 through 2797 removed outlier: 3.910A pdb=" N THR I2796 " --> pdb=" O PRO I2793 " (cutoff:3.500A) Processing helix chain 'I' and resid 2800 through 2805 removed outlier: 3.956A pdb=" N ILE I2804 " --> pdb=" O LYS I2800 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR I2805 " --> pdb=" O ASP I2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2800 through 2805' Processing helix chain 'I' and resid 2809 through 2820 removed outlier: 3.905A pdb=" N ALA I2815 " --> pdb=" O GLU I2811 " (cutoff:3.500A) Processing helix chain 'I' and resid 2868 through 2895 removed outlier: 4.462A pdb=" N MET I2874 " --> pdb=" O GLU I2870 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA I2875 " --> pdb=" O LEU I2871 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP I2886 " --> pdb=" O TYR I2882 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU I2895 " --> pdb=" O LYS I2891 " (cutoff:3.500A) Processing helix chain 'I' and resid 2907 through 2911 removed outlier: 3.587A pdb=" N THR I2910 " --> pdb=" O PRO I2907 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU I2911 " --> pdb=" O TYR I2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2907 through 2911' Processing helix chain 'I' and resid 2917 through 2932 removed outlier: 3.788A pdb=" N GLU I2921 " --> pdb=" O ALA I2917 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU I2926 " --> pdb=" O LYS I2922 " (cutoff:3.500A) Processing helix chain 'I' and resid 2950 through 2976 removed outlier: 3.958A pdb=" N UNK I2956 " --> pdb=" O UNK I2952 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK I2968 " --> pdb=" O UNK I2964 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N UNK I2969 " --> pdb=" O UNK I2965 " (cutoff:3.500A) Processing helix chain 'I' and resid 2997 through 3015 removed outlier: 3.744A pdb=" N UNK I3002 " --> pdb=" O UNK I2998 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK I3004 " --> pdb=" O UNK I3000 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N UNK I3006 " --> pdb=" O UNK I3002 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N UNK I3009 " --> pdb=" O UNK I3005 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK I3010 " --> pdb=" O UNK I3006 " (cutoff:3.500A) Processing helix chain 'I' and resid 3017 through 3022 Processing helix chain 'I' and resid 3024 through 3040 removed outlier: 4.188A pdb=" N UNK I3028 " --> pdb=" O UNK I3024 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK I3032 " --> pdb=" O UNK I3028 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N UNK I3040 " --> pdb=" O UNK I3036 " (cutoff:3.500A) Processing helix chain 'I' and resid 3050 through 3060 removed outlier: 4.090A pdb=" N UNK I3056 " --> pdb=" O UNK I3052 " (cutoff:3.500A) Processing helix chain 'I' and resid 3141 through 3146 Processing helix chain 'I' and resid 3146 through 3162 removed outlier: 3.922A pdb=" N UNK I3154 " --> pdb=" O UNK I3150 " (cutoff:3.500A) Processing helix chain 'I' and resid 3175 through 3187 Processing helix chain 'I' and resid 3188 through 3190 No H-bonds generated for 'chain 'I' and resid 3188 through 3190' Processing helix chain 'I' and resid 3198 through 3212 removed outlier: 3.723A pdb=" N UNK I3205 " --> pdb=" O UNK I3201 " (cutoff:3.500A) Processing helix chain 'I' and resid 3224 through 3230 removed outlier: 3.959A pdb=" N UNK I3228 " --> pdb=" O UNK I3224 " (cutoff:3.500A) Processing helix chain 'I' and resid 3248 through 3254 Processing helix chain 'I' and resid 3271 through 3285 removed outlier: 4.023A pdb=" N UNK I3282 " --> pdb=" O UNK I3278 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK I3284 " --> pdb=" O UNK I3280 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK I3285 " --> pdb=" O UNK I3281 " (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 3315 through 3321 removed outlier: 3.873A pdb=" N UNK I3319 " --> pdb=" O UNK I3315 " (cutoff:3.500A) Processing helix chain 'I' and resid 3321 through 3331 removed outlier: 3.504A pdb=" N UNK I3330 " --> pdb=" O UNK I3326 " (cutoff:3.500A) Processing helix chain 'I' and resid 3344 through 3349 removed outlier: 3.618A pdb=" N UNK I3348 " --> pdb=" O UNK I3344 " (cutoff:3.500A) Processing helix chain 'I' and resid 3350 through 3354 Processing helix chain 'I' and resid 3361 through 3388 Processing helix chain 'I' and resid 3399 through 3407 removed outlier: 3.604A pdb=" N UNK I3403 " --> pdb=" O UNK I3399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK I3405 " --> pdb=" O UNK I3401 " (cutoff:3.500A) Processing helix chain 'I' and resid 3407 through 3425 removed outlier: 3.837A pdb=" N UNK I3413 " --> pdb=" O UNK I3409 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK I3416 " --> pdb=" O UNK I3412 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N UNK I3417 " --> pdb=" O UNK I3413 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N UNK I3420 " --> pdb=" O UNK I3416 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N UNK I3421 " --> pdb=" O UNK I3417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N UNK I3425 " --> pdb=" O UNK I3421 " (cutoff:3.500A) Processing helix chain 'I' and resid 3426 through 3431 Processing helix chain 'I' and resid 3437 through 3443 Processing helix chain 'I' and resid 3445 through 3450 Processing helix chain 'I' and resid 3457 through 3460 Processing helix chain 'I' and resid 3461 through 3468 Processing helix chain 'I' and resid 3522 through 3527 Processing helix chain 'I' and resid 3541 through 3547 removed outlier: 3.501A pdb=" N UNK I3545 " --> pdb=" O UNK I3541 " (cutoff:3.500A) Processing helix chain 'I' and resid 3551 through 3560 Processing helix chain 'I' and resid 3574 through 3583 removed outlier: 4.331A pdb=" N UNK I3580 " --> pdb=" O UNK I3576 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N UNK I3583 " --> pdb=" O UNK I3579 " (cutoff:3.500A) Processing helix chain 'I' and resid 3590 through 3608 removed outlier: 3.522A pdb=" N UNK I3595 " --> pdb=" O UNK I3591 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK I3596 " --> pdb=" O UNK I3592 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N UNK I3598 " --> pdb=" O UNK I3594 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N UNK I3600 " --> pdb=" O UNK I3596 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK I3601 " --> pdb=" O UNK I3597 " (cutoff:3.500A) Processing helix chain 'I' and resid 3645 through 3656 removed outlier: 3.725A pdb=" N GLU I3655 " --> pdb=" O ASN I3651 " (cutoff:3.500A) Processing helix chain 'I' and resid 3671 through 3680 removed outlier: 3.656A pdb=" N ASP I3676 " --> pdb=" O ARG I3672 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU I3677 " --> pdb=" O MET I3673 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER I3678 " --> pdb=" O ILE I3674 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I3680 " --> pdb=" O ASP I3676 " (cutoff:3.500A) Processing helix chain 'I' and resid 3681 through 3687 removed outlier: 6.855A pdb=" N GLU I3684 " --> pdb=" O GLY I3681 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU I3685 " --> pdb=" O GLU I3682 " (cutoff:3.500A) Processing helix chain 'I' and resid 3696 through 3708 removed outlier: 3.600A pdb=" N LEU I3701 " --> pdb=" O PRO I3697 " (cutoff:3.500A) Processing helix chain 'I' and resid 3719 through 3738 removed outlier: 3.817A pdb=" N TYR I3725 " --> pdb=" O LEU I3721 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP I3727 " --> pdb=" O MET I3723 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS I3733 " --> pdb=" O MET I3729 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS I3734 " --> pdb=" O ALA I3730 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU I3736 " --> pdb=" O SER I3732 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU I3737 " --> pdb=" O CYS I3733 " (cutoff:3.500A) Processing helix chain 'I' and resid 3752 through 3771 removed outlier: 3.724A pdb=" N GLU I3757 " --> pdb=" O PHE I3753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET I3758 " --> pdb=" O GLU I3754 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU I3759 " --> pdb=" O GLU I3755 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS I3760 " --> pdb=" O LYS I3756 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I3765 " --> pdb=" O GLN I3761 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN I3766 " --> pdb=" O ARG I3762 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN I3767 " --> pdb=" O LEU I3763 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER I3768 " --> pdb=" O LEU I3764 " (cutoff:3.500A) Processing helix chain 'I' and resid 3771 through 3782 removed outlier: 3.695A pdb=" N ALA I3775 " --> pdb=" O HIS I3771 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA I3776 " --> pdb=" O THR I3772 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU I3777 " --> pdb=" O ARG I3773 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET I3778 " --> pdb=" O GLY I3774 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU I3780 " --> pdb=" O ALA I3776 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN I3781 " --> pdb=" O GLU I3777 " (cutoff:3.500A) Processing helix chain 'I' and resid 3791 through 3805 removed outlier: 4.208A pdb=" N LYS I3799 " --> pdb=" O SER I3795 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU I3800 " --> pdb=" O SER I3796 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I3803 " --> pdb=" O LYS I3799 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU I3805 " --> pdb=" O GLY I3801 " (cutoff:3.500A) Processing helix chain 'I' and resid 3809 through 3824 removed outlier: 3.537A pdb=" N GLN I3814 " --> pdb=" O ALA I3810 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS I3815 " --> pdb=" O GLU I3811 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS I3824 " --> pdb=" O LEU I3820 " (cutoff:3.500A) Processing helix chain 'I' and resid 3827 through 3838 removed outlier: 3.619A pdb=" N ILE I3832 " --> pdb=" O PHE I3828 " (cutoff:3.500A) Processing helix chain 'I' and resid 3843 through 3854 Processing helix chain 'I' and resid 3880 through 3891 Processing helix chain 'I' and resid 3898 through 3905 Processing helix chain 'I' and resid 3914 through 3937 removed outlier: 3.803A pdb=" N CYS I3918 " --> pdb=" O ASN I3914 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I3920 " --> pdb=" O ILE I3916 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER I3929 " --> pdb=" O ARG I3925 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP I3935 " --> pdb=" O SER I3931 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR I3936 " --> pdb=" O ASP I3932 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR I3937 " --> pdb=" O PHE I3933 " (cutoff:3.500A) Processing helix chain 'I' and resid 3944 through 3967 removed outlier: 4.024A pdb=" N ALA I3954 " --> pdb=" O ASN I3950 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN I3960 " --> pdb=" O SER I3956 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU I3967 " --> pdb=" O ASN I3963 " (cutoff:3.500A) Processing helix chain 'I' and resid 3973 through 3983 removed outlier: 3.531A pdb=" N GLN I3977 " --> pdb=" O CYS I3973 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS I3982 " --> pdb=" O GLN I3978 " (cutoff:3.500A) Processing helix chain 'I' and resid 3984 through 4003 removed outlier: 3.739A pdb=" N VAL I3990 " --> pdb=" O TRP I3986 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY I3991 " --> pdb=" O ASP I3987 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE I3992 " --> pdb=" O ALA I3988 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS I3998 " --> pdb=" O HIS I3994 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET I4000 " --> pdb=" O PHE I3996 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET I4001 " --> pdb=" O ALA I3997 " (cutoff:3.500A) Processing helix chain 'I' and resid 4004 through 4006 No H-bonds generated for 'chain 'I' and resid 4004 through 4006' Processing helix chain 'I' and resid 4009 through 4030 Processing helix chain 'I' and resid 4039 through 4051 removed outlier: 3.609A pdb=" N VAL I4049 " --> pdb=" O VAL I4045 " (cutoff:3.500A) Processing helix chain 'I' and resid 4051 through 4065 removed outlier: 3.548A pdb=" N MET I4057 " --> pdb=" O SER I4053 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET I4064 " --> pdb=" O LYS I4060 " (cutoff:3.500A) Processing helix chain 'I' and resid 4066 through 4072 removed outlier: 3.911A pdb=" N ASP I4070 " --> pdb=" O LEU I4066 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL I4072 " --> pdb=" O LEU I4068 " (cutoff:3.500A) Processing helix chain 'I' and resid 4074 through 4079 removed outlier: 3.776A pdb=" N GLN I4078 " --> pdb=" O SER I4074 " (cutoff:3.500A) Processing helix chain 'I' and resid 4090 through 4100 removed outlier: 3.514A pdb=" N MET I4097 " --> pdb=" O PHE I4093 " (cutoff:3.500A) removed outlier: 3.917A 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 4132 removed outlier: 4.412A pdb=" N PHE I4132 " --> pdb=" O PHE I4128 " (cutoff:3.500A) Processing helix chain 'I' and resid 4132 through 4154 removed outlier: 3.594A pdb=" N ALA I4136 " --> pdb=" O PHE I4132 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP I4138 " --> pdb=" O GLU I4134 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE I4139 " --> pdb=" O PRO I4135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER I4151 " --> pdb=" O LEU I4147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU I4152 " --> pdb=" O THR I4148 " (cutoff:3.500A) removed outlier: 3.726A 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 4168 through 4175 removed outlier: 3.545A pdb=" N TYR I4173 " --> pdb=" O SER I4169 " (cutoff:3.500A) Processing helix chain 'I' and resid 4199 through 4206 removed outlier: 3.824A pdb=" N ALA I4203 " --> pdb=" O GLU I4199 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU I4206 " --> pdb=" O ARG I4202 " (cutoff:3.500A) Processing helix chain 'I' and resid 4207 through 4224 removed outlier: 4.106A pdb=" N SER I4213 " --> pdb=" O GLN I4209 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL I4222 " --> pdb=" O ILE I4218 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN I4223 " --> pdb=" O PHE I4219 " (cutoff:3.500A) Processing helix chain 'I' and resid 4228 through 4248 removed outlier: 4.024A pdb=" N PHE I4234 " --> pdb=" O LYS I4230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE I4242 " --> pdb=" O CYS I4238 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE I4243 " --> pdb=" O GLU I4239 " (cutoff:3.500A) Processing helix chain 'I' and resid 4321 through 4337 removed outlier: 3.537A pdb=" N UNK I4327 " --> pdb=" O UNK I4323 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK I4332 " --> pdb=" O UNK I4328 " (cutoff:3.500A) Processing helix chain 'I' and resid 4543 through 4556 removed outlier: 3.964A pdb=" N TYR I4554 " --> pdb=" O LYS I4550 " (cutoff:3.500A) Processing helix chain 'I' and resid 4558 through 4576 removed outlier: 3.535A pdb=" N ALA I4566 " --> pdb=" O LEU I4562 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE I4571 " --> pdb=" O LEU I4567 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA I4572 " --> pdb=" O PHE I4568 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE I4573 " --> pdb=" O LEU I4569 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN I4574 " --> pdb=" O ALA I4570 " (cutoff:3.500A) Processing helix chain 'I' and resid 4577 through 4580 removed outlier: 3.927A pdb=" N TYR I4580 " --> pdb=" O LEU I4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4577 through 4580' Processing helix chain 'I' and resid 4641 through 4665 removed outlier: 3.618A pdb=" N LEU I4648 " --> pdb=" O TRP I4644 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU I4649 " --> pdb=" O CYS I4645 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA I4654 " --> pdb=" O HIS I4650 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE I4658 " --> pdb=" O ALA I4654 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE I4659 " --> pdb=" O PHE I4655 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY I4660 " --> pdb=" O LEU I4656 " (cutoff:3.500A) Processing helix chain 'I' and resid 4665 through 4683 removed outlier: 3.539A pdb=" N LYS I4672 " --> pdb=" O LEU I4668 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I4677 " --> pdb=" O ARG I4673 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA I4678 " --> pdb=" O GLU I4674 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE I4683 " --> pdb=" O ARG I4679 " (cutoff:3.500A) Processing helix chain 'I' and resid 4697 through 4702 removed outlier: 3.578A pdb=" N ASP I4702 " --> pdb=" O LYS I4698 " (cutoff:3.500A) Processing helix chain 'I' and resid 4710 through 4714 removed outlier: 3.515A pdb=" N SER I4713 " --> pdb=" O SER I4710 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN I4714 " --> pdb=" O PHE I4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4710 through 4714' Processing helix chain 'I' and resid 4719 through 4728 removed outlier: 3.525A pdb=" N LEU I4725 " --> pdb=" O LYS I4721 " (cutoff:3.500A) Processing helix chain 'I' and resid 4733 through 4741 removed outlier: 3.552A pdb=" N LEU I4741 " --> pdb=" O ILE I4737 " (cutoff:3.500A) Processing helix chain 'I' and resid 4745 through 4750 Processing helix chain 'I' and resid 4751 through 4755 removed outlier: 4.040A pdb=" N GLU I4755 " --> pdb=" O ALA I4752 " (cutoff:3.500A) Processing helix chain 'I' and resid 4772 through 4786 removed outlier: 3.654A pdb=" N THR I4785 " --> pdb=" O GLY I4781 " (cutoff:3.500A) Processing helix chain 'I' and resid 4786 through 4802 removed outlier: 3.535A pdb=" N SER I4799 " --> pdb=" O TYR I4795 " (cutoff:3.500A) Processing helix chain 'I' and resid 4814 through 4820 removed outlier: 3.853A pdb=" N MET I4818 " --> pdb=" O LEU I4814 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL I4820 " --> pdb=" O ILE I4816 " (cutoff:3.500A) Processing helix chain 'I' and resid 4820 through 4833 removed outlier: 3.749A pdb=" N ILE I4826 " --> pdb=" O THR I4822 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I4830 " --> pdb=" O ILE I4826 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR I4831 " --> pdb=" O LEU I4827 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN I4833 " --> pdb=" O SER I4829 " (cutoff:3.500A) Processing helix chain 'I' and resid 4833 through 4858 removed outlier: 3.964A pdb=" N MET I4839 " --> pdb=" O LYS I4835 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY I4842 " --> pdb=" O VAL I4838 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU I4843 " --> pdb=" O MET I4839 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU I4844 " --> pdb=" O THR I4840 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL I4853 " --> pdb=" O TYR I4849 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL I4854 " --> pdb=" O LEU I4850 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA I4855 " --> pdb=" O TYR I4851 " (cutoff:3.500A) Processing helix chain 'I' and resid 4859 through 4863 removed outlier: 3.957A pdb=" N TYR I4863 " --> pdb=" O ARG I4860 " (cutoff:3.500A) Processing helix chain 'I' and resid 4878 through 4890 removed outlier: 3.654A pdb=" N MET I4887 " --> pdb=" O TYR I4883 " (cutoff:3.500A) Processing helix chain 'I' and resid 4909 through 4925 removed outlier: 3.681A pdb=" N ARG I4913 " --> pdb=" O TYR I4909 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL I4914 " --> pdb=" O GLU I4910 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I4915 " --> pdb=" O LEU I4911 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE I4918 " --> pdb=" O VAL I4914 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE I4923 " --> pdb=" O THR I4919 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE I4925 " --> pdb=" O PHE I4921 " (cutoff:3.500A) Processing helix chain 'I' and resid 4927 through 4957 removed outlier: 3.640A pdb=" N ILE I4932 " --> pdb=" O LEU I4928 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE I4936 " --> pdb=" O ILE I4932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU I4942 " --> pdb=" O ASP I4938 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU I4943 " --> pdb=" O ALA I4939 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN I4947 " --> pdb=" O LEU I4943 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS I4951 " --> pdb=" O GLN I4947 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS I4957 " --> pdb=" O ASP I4953 " (cutoff:3.500A) Processing helix chain 'I' and resid 4964 through 4971 removed outlier: 4.318A pdb=" N PHE I4968 " --> pdb=" O GLY I4964 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR I4971 " --> pdb=" O TYR I4967 " (cutoff:3.500A) Processing helix chain 'I' and resid 4973 through 4979 removed outlier: 3.761A pdb=" N THR I4977 " --> pdb=" O HIS I4973 " (cutoff:3.500A) Processing helix chain 'I' and resid 4986 through 4997 removed outlier: 4.008A pdb=" N PHE I4990 " --> pdb=" O ALA I4986 " (cutoff:3.500A) Processing helix chain 'I' and resid 5006 through 5017 removed outlier: 3.638A pdb=" N TRP I5011 " --> pdb=" O GLU I5007 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS I5012 " --> pdb=" O SER I5008 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET I5013 " --> pdb=" O TYR I5009 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.890A pdb=" N ILE E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 82 removed outlier: 3.748A pdb=" N GLN E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.965A pdb=" N THR E 254 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 Processing helix chain 'E' and resid 395 through 420 removed outlier: 4.051A pdb=" N GLN E 399 " --> pdb=" O GLN E 395 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 418 " --> pdb=" O PHE E 414 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 419 " --> pdb=" O ILE E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 452 removed outlier: 3.506A pdb=" N ASP E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 477 removed outlier: 3.913A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.583A pdb=" N CYS E 490 " --> pdb=" O LEU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 513 No H-bonds generated for 'chain 'E' and resid 511 through 513' Processing helix chain 'E' and resid 514 through 529 removed outlier: 3.503A pdb=" N ILE E 518 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 521 " --> pdb=" O GLU E 517 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 529 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 removed outlier: 3.513A pdb=" N ALA E 538 " --> pdb=" O ARG E 534 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 539 " --> pdb=" O ALA E 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 534 through 539' Processing helix chain 'E' and resid 543 through 551 removed outlier: 3.697A pdb=" N VAL E 548 " --> pdb=" O LEU E 544 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS E 550 " --> pdb=" O TRP E 546 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 551 " --> pdb=" O VAL E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 568 removed outlier: 3.521A pdb=" N LEU E 564 " --> pdb=" O ILE E 560 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 578 removed outlier: 3.516A pdb=" N ILE E 577 " --> pdb=" O VAL E 574 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 578 " --> pdb=" O LEU E 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 574 through 578' Processing helix chain 'E' and resid 581 through 593 Processing helix chain 'E' and resid 597 through 608 removed outlier: 3.753A pdb=" N LEU E 603 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 625 removed outlier: 4.130A pdb=" N GLN E 618 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR E 622 " --> pdb=" O GLN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 889 removed outlier: 3.581A pdb=" N ILE E 870 " --> pdb=" O HIS E 866 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 873 " --> pdb=" O ARG E 869 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 875 " --> pdb=" O ARG E 871 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN E 877 " --> pdb=" O LYS E 873 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG E 886 " --> pdb=" O TRP E 882 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 887 " --> pdb=" O ALA E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 932 removed outlier: 3.802A pdb=" N ASN E 919 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 920 " --> pdb=" O PRO E 916 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN E 921 " --> pdb=" O GLU E 917 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 927 " --> pdb=" O GLN E 923 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 928 " --> pdb=" O MET E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 980 through 1001 removed outlier: 4.097A pdb=" N LEU E 984 " --> pdb=" O ALA E 980 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP E 986 " --> pdb=" O THR E 982 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN E 991 " --> pdb=" O ARG E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1039 removed outlier: 3.509A pdb=" N LYS E1032 " --> pdb=" O ASP E1028 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E1039 " --> pdb=" O ASN E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1049 removed outlier: 3.892A pdb=" N LEU E1046 " --> pdb=" O ALA E1042 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU E1047 " --> pdb=" O VAL E1043 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY E1048 " --> pdb=" O ARG E1044 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E1049 " --> pdb=" O THR E1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1042 through 1049' Processing helix chain 'E' and resid 1078 through 1082 Processing helix chain 'E' and resid 1575 through 1580 removed outlier: 4.028A pdb=" N MET E1579 " --> pdb=" O LEU E1575 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E1580 " --> pdb=" O SER E1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1575 through 1580' Processing helix chain 'E' and resid 1623 through 1627 Processing helix chain 'E' and resid 1652 through 1657 removed outlier: 3.665A pdb=" N LEU E1657 " --> pdb=" O LEU E1653 " (cutoff:3.500A) Processing helix chain 'E' and resid 1658 through 1674 removed outlier: 3.758A pdb=" N HIS E1665 " --> pdb=" O ARG E1661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E1666 " --> pdb=" O PHE E1662 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR E1670 " --> pdb=" O THR E1666 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG E1671 " --> pdb=" O LEU E1667 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1686 removed outlier: 3.639A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS E1686 " --> pdb=" O ALA E1682 " (cutoff:3.500A) Processing helix chain 'E' and resid 1692 through 1697 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 1720 Processing helix chain 'E' and resid 1720 through 1730 removed outlier: 3.583A pdb=" N ARG E1725 " --> pdb=" O GLU E1721 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER E1726 " --> pdb=" O SER E1722 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1739 through 1744 Processing helix chain 'E' and resid 1803 through 1823 removed outlier: 3.612A pdb=" N MET E1814 " --> pdb=" O LYS E1810 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E1815 " --> pdb=" O ALA E1811 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E1817 " --> pdb=" O ARG E1813 " (cutoff:3.500A) Processing helix chain 'E' and resid 1833 through 1838 Processing helix chain 'E' and resid 1840 through 1851 removed outlier: 3.570A pdb=" N LEU E1848 " --> pdb=" O LEU E1844 " (cutoff:3.500A) removed outlier: 3.522A 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 1934 through 1977 removed outlier: 3.707A pdb=" N GLN E1938 " --> pdb=" O SER E1934 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E1945 " --> pdb=" O ASN E1941 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE E1946 " --> pdb=" O LEU E1942 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP E1948 " --> pdb=" O GLU E1944 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E1963 " --> pdb=" O ALA E1959 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL E1966 " --> pdb=" O ALA E1962 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS E1968 " --> pdb=" O ARG E1964 " (cutoff:3.500A) Processing helix chain 'E' and resid 1978 through 1980 No H-bonds generated for 'chain 'E' and resid 1978 through 1980' Processing helix chain 'E' and resid 1989 through 1994 removed outlier: 3.542A pdb=" N ARG E1994 " --> pdb=" O GLU E1990 " (cutoff:3.500A) Processing helix chain 'E' and resid 2001 through 2014 removed outlier: 3.681A pdb=" N ILE E2006 " --> pdb=" O PRO E2002 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS E2011 " --> pdb=" O ASN E2007 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE E2012 " --> pdb=" O MET E2008 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS E2013 " --> pdb=" O LEU E2009 " (cutoff:3.500A) Processing helix chain 'E' and resid 2028 through 2042 removed outlier: 3.896A pdb=" N LEU E2039 " --> pdb=" O HIS E2035 " (cutoff:3.500A) Processing helix chain 'E' and resid 2093 through 2107 removed outlier: 4.012A pdb=" N VAL E2103 " --> pdb=" O SER E2099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E2106 " --> pdb=" O VAL E2102 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2126 removed outlier: 3.744A pdb=" N VAL E2117 " --> pdb=" O SER E2113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG E2126 " --> pdb=" O SER E2122 " (cutoff:3.500A) Processing helix chain 'E' and resid 2129 through 2138 removed outlier: 3.798A pdb=" N ALA E2137 " --> pdb=" O GLU E2133 " (cutoff:3.500A) Processing helix chain 'E' and resid 2148 through 2166 removed outlier: 3.911A pdb=" N SER E2154 " --> pdb=" O GLU E2150 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS E2158 " --> pdb=" O SER E2154 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E2159 " --> pdb=" O LEU E2155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E2160 " --> pdb=" O LEU E2156 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN E2161 " --> pdb=" O GLU E2157 " (cutoff:3.500A) Processing helix chain 'E' and resid 2171 through 2187 removed outlier: 3.599A pdb=" N LEU E2177 " --> pdb=" O GLN E2173 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E2185 " --> pdb=" O SER E2181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN E2187 " --> pdb=" O GLY E2183 " (cutoff:3.500A) Processing helix chain 'E' and resid 2194 through 2201 removed outlier: 3.854A pdb=" N MET E2198 " --> pdb=" O HIS E2194 " (cutoff:3.500A) Processing helix chain 'E' and resid 2202 through 2216 removed outlier: 3.665A pdb=" N THR E2206 " --> pdb=" O GLY E2202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E2207 " --> pdb=" O MET E2203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN E2213 " --> pdb=" O GLU E2209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E2214 " --> pdb=" O VAL E2210 " (cutoff:3.500A) Processing helix chain 'E' and resid 2228 through 2242 removed outlier: 4.019A pdb=" N TYR E2238 " --> pdb=" O ARG E2234 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2252 removed outlier: 3.710A pdb=" N ASP E2252 " --> pdb=" O ARG E2248 " (cutoff:3.500A) Processing helix chain 'E' and resid 2253 through 2261 removed outlier: 3.704A pdb=" N ASN E2260 " --> pdb=" O TYR E2256 " (cutoff:3.500A) Processing helix chain 'E' and resid 2262 through 2264 No H-bonds generated for 'chain 'E' and resid 2262 through 2264' Processing helix chain 'E' and resid 2271 through 2279 Processing helix chain 'E' and resid 2294 through 2304 removed outlier: 3.703A pdb=" N VAL E2299 " --> pdb=" O LEU E2295 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER E2300 " --> pdb=" O GLU E2296 " (cutoff:3.500A) Processing helix chain 'E' and resid 2310 through 2315 removed outlier: 3.831A pdb=" N ALA E2315 " --> pdb=" O PRO E2311 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2331 Processing helix chain 'E' and resid 2335 through 2339 removed outlier: 3.550A pdb=" N ALA E2338 " --> pdb=" O LEU E2335 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2358 removed outlier: 3.618A pdb=" N ALA E2350 " --> pdb=" O VAL E2346 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL E2352 " --> pdb=" O GLU E2348 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL E2353 " --> pdb=" O ASN E2349 " (cutoff:3.500A) removed outlier: 3.561A 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 2389 removed outlier: 3.702A pdb=" N ILE E2380 " --> pdb=" O LEU E2376 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG E2385 " --> pdb=" O GLU E2381 " (cutoff:3.500A) Processing helix chain 'E' and resid 2390 through 2393 removed outlier: 3.552A pdb=" N ASP E2393 " --> pdb=" O PRO E2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2390 through 2393' Processing helix chain 'E' and resid 2419 through 2436 removed outlier: 3.616A pdb=" N MET E2423 " --> pdb=" O GLY E2419 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU E2433 " --> pdb=" O LEU E2429 " (cutoff:3.500A) Processing helix chain 'E' and resid 2440 through 2445 removed outlier: 4.071A pdb=" N ALA E2445 " --> pdb=" O HIS E2441 " (cutoff:3.500A) Processing helix chain 'E' and resid 2448 through 2461 removed outlier: 4.030A pdb=" N ILE E2453 " --> pdb=" O GLU E2449 " (cutoff:3.500A) Processing helix chain 'E' and resid 2464 through 2471 removed outlier: 3.606A pdb=" N ILE E2469 " --> pdb=" O ASP E2465 " (cutoff:3.500A) Processing helix chain 'E' and resid 2496 through 2500 Processing helix chain 'E' and resid 2502 through 2509 removed outlier: 3.770A pdb=" N UNK E2506 " --> pdb=" O UNK E2502 " (cutoff:3.500A) Processing helix chain 'E' and resid 2516 through 2530 removed outlier: 4.334A pdb=" N UNK E2523 " --> pdb=" O UNK E2519 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N UNK E2526 " --> pdb=" O UNK E2522 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N UNK E2527 " --> pdb=" O UNK E2523 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N UNK E2528 " --> pdb=" O UNK E2524 " (cutoff:3.500A) Processing helix chain 'E' and resid 2542 through 2548 removed outlier: 3.546A pdb=" N UNK E2546 " --> pdb=" O UNK E2542 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2557 removed outlier: 3.633A pdb=" N UNK E2555 " --> pdb=" O UNK E2551 " (cutoff:3.500A) Processing helix chain 'E' and resid 2566 through 2581 removed outlier: 4.125A pdb=" N UNK E2570 " --> pdb=" O UNK E2566 " (cutoff:3.500A) Processing helix chain 'E' and resid 2587 through 2601 removed outlier: 3.554A pdb=" N UNK E2597 " --> pdb=" O UNK E2593 " (cutoff:3.500A) Processing helix chain 'E' and resid 2602 through 2604 No H-bonds generated for 'chain 'E' and resid 2602 through 2604' Processing helix chain 'E' and resid 2610 through 2618 removed outlier: 3.763A pdb=" N UNK E2617 " --> pdb=" O UNK E2613 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK E2618 " --> pdb=" O UNK E2614 " (cutoff:3.500A) Processing helix chain 'E' and resid 2628 through 2640 removed outlier: 3.501A pdb=" N UNK E2632 " --> pdb=" O UNK E2628 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N UNK E2634 " --> pdb=" O UNK E2630 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK E2635 " --> pdb=" O UNK E2631 " (cutoff:3.500A) removed outlier: 3.585A 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 removed outlier: 3.555A pdb=" N UNK E2654 " --> pdb=" O UNK E2650 " (cutoff:3.500A) Processing helix chain 'E' and resid 2675 through 2680 removed outlier: 3.503A pdb=" N UNK E2680 " --> pdb=" O UNK E2676 " (cutoff:3.500A) Processing helix chain 'E' and resid 2683 through 2687 removed outlier: 3.888A pdb=" N UNK E2686 " --> pdb=" O UNK E2683 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK E2687 " --> pdb=" O UNK E2684 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2683 through 2687' Processing helix chain 'E' and resid 2741 through 2745 removed outlier: 3.948A pdb=" N ASN E2744 " --> pdb=" O GLU E2741 " (cutoff:3.500A) Processing helix chain 'E' and resid 2748 through 2773 removed outlier: 3.525A pdb=" N ASP E2752 " --> pdb=" O PRO E2748 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER E2753 " --> pdb=" O GLU E2749 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE E2754 " --> pdb=" O LYS E2750 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE E2768 " --> pdb=" O GLU E2764 " (cutoff:3.500A) Processing helix chain 'E' and resid 2793 through 2797 removed outlier: 3.909A pdb=" N THR E2796 " --> pdb=" O PRO E2793 " (cutoff:3.500A) Processing helix chain 'E' and resid 2800 through 2805 removed outlier: 3.957A pdb=" N ILE E2804 " --> pdb=" O LYS E2800 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR E2805 " --> pdb=" O ASP E2801 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2800 through 2805' Processing helix chain 'E' and resid 2809 through 2820 removed outlier: 3.905A pdb=" N ALA E2815 " --> pdb=" O GLU E2811 " (cutoff:3.500A) Processing helix chain 'E' and resid 2868 through 2895 removed outlier: 4.461A pdb=" N MET E2874 " --> pdb=" O GLU E2870 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E2875 " --> pdb=" O LEU E2871 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP E2886 " --> pdb=" O TYR E2882 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU E2895 " --> pdb=" O LYS E2891 " (cutoff:3.500A) Processing helix chain 'E' and resid 2907 through 2911 removed outlier: 3.587A pdb=" N THR E2910 " --> pdb=" O PRO E2907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E2911 " --> pdb=" O TYR E2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2907 through 2911' Processing helix chain 'E' and resid 2917 through 2932 removed outlier: 3.788A pdb=" N GLU E2921 " --> pdb=" O ALA E2917 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU E2926 " --> pdb=" O LYS E2922 " (cutoff:3.500A) Processing helix chain 'E' and resid 2950 through 2976 removed outlier: 3.958A pdb=" N UNK E2956 " --> pdb=" O UNK E2952 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK E2968 " --> pdb=" O UNK E2964 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N UNK E2969 " --> pdb=" O UNK E2965 " (cutoff:3.500A) Processing helix chain 'E' and resid 2997 through 3015 removed outlier: 3.745A pdb=" N UNK E3002 " --> pdb=" O UNK E2998 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK E3004 " --> pdb=" O UNK E3000 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N UNK E3006 " --> pdb=" O UNK E3002 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N UNK E3009 " --> pdb=" O UNK E3005 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK E3010 " --> pdb=" O UNK E3006 " (cutoff:3.500A) Processing helix chain 'E' and resid 3017 through 3022 Processing helix chain 'E' and resid 3024 through 3040 removed outlier: 4.187A pdb=" N UNK E3028 " --> pdb=" O UNK E3024 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNK E3032 " --> pdb=" O UNK E3028 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK E3040 " --> pdb=" O UNK E3036 " (cutoff:3.500A) Processing helix chain 'E' and resid 3050 through 3060 removed outlier: 4.090A pdb=" N UNK E3056 " --> pdb=" O UNK E3052 " (cutoff:3.500A) Processing helix chain 'E' and resid 3141 through 3146 Processing helix chain 'E' and resid 3146 through 3162 removed outlier: 3.923A pdb=" N UNK E3154 " --> pdb=" O UNK E3150 " (cutoff:3.500A) Processing helix chain 'E' and resid 3175 through 3187 Processing helix chain 'E' and resid 3188 through 3190 No H-bonds generated for 'chain 'E' and resid 3188 through 3190' Processing helix chain 'E' and resid 3198 through 3212 removed outlier: 3.723A pdb=" N UNK E3205 " --> pdb=" O UNK E3201 " (cutoff:3.500A) Processing helix chain 'E' and resid 3224 through 3230 removed outlier: 3.959A pdb=" N UNK E3228 " --> pdb=" O UNK E3224 " (cutoff:3.500A) Processing helix chain 'E' and resid 3248 through 3254 Processing helix chain 'E' and resid 3271 through 3285 removed outlier: 4.022A pdb=" N UNK E3282 " --> pdb=" O UNK E3278 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK E3284 " --> pdb=" O UNK E3280 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N UNK E3285 " --> pdb=" O UNK E3281 " (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 3315 through 3321 removed outlier: 3.873A pdb=" N UNK E3319 " --> pdb=" O UNK E3315 " (cutoff:3.500A) Processing helix chain 'E' and resid 3321 through 3331 removed outlier: 3.505A pdb=" N UNK E3330 " --> pdb=" O UNK E3326 " (cutoff:3.500A) Processing helix chain 'E' and resid 3344 through 3349 removed outlier: 3.619A pdb=" N UNK E3348 " --> pdb=" O UNK E3344 " (cutoff:3.500A) Processing helix chain 'E' and resid 3350 through 3354 Processing helix chain 'E' and resid 3361 through 3388 Processing helix chain 'E' and resid 3399 through 3407 removed outlier: 3.603A pdb=" N UNK E3403 " --> pdb=" O UNK E3399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK E3405 " --> pdb=" O UNK E3401 " (cutoff:3.500A) Processing helix chain 'E' and resid 3407 through 3425 removed outlier: 3.837A pdb=" N UNK E3413 " --> pdb=" O UNK E3409 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK E3416 " --> pdb=" O UNK E3412 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N UNK E3417 " --> pdb=" O UNK E3413 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N UNK E3420 " --> pdb=" O UNK E3416 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N UNK E3421 " --> pdb=" O UNK E3417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N UNK E3425 " --> pdb=" O UNK E3421 " (cutoff:3.500A) Processing helix chain 'E' and resid 3426 through 3431 Processing helix chain 'E' and resid 3437 through 3443 Processing helix chain 'E' and resid 3445 through 3450 Processing helix chain 'E' and resid 3457 through 3460 Processing helix chain 'E' and resid 3461 through 3468 Processing helix chain 'E' and resid 3522 through 3527 Processing helix chain 'E' and resid 3541 through 3547 removed outlier: 3.501A pdb=" N UNK E3545 " --> pdb=" O UNK E3541 " (cutoff:3.500A) Processing helix chain 'E' and resid 3551 through 3560 Processing helix chain 'E' and resid 3574 through 3583 removed outlier: 4.330A pdb=" N UNK E3580 " --> pdb=" O UNK E3576 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N UNK E3583 " --> pdb=" O UNK E3579 " (cutoff:3.500A) Processing helix chain 'E' and resid 3590 through 3608 removed outlier: 3.522A pdb=" N UNK E3595 " --> pdb=" O UNK E3591 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK E3596 " --> pdb=" O UNK E3592 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N UNK E3598 " --> pdb=" O UNK E3594 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N UNK E3600 " --> pdb=" O UNK E3596 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK E3601 " --> pdb=" O UNK E3597 " (cutoff:3.500A) Processing helix chain 'E' and resid 3645 through 3656 removed outlier: 3.726A pdb=" N GLU E3655 " --> pdb=" O ASN E3651 " (cutoff:3.500A) Processing helix chain 'E' and resid 3671 through 3680 removed outlier: 3.656A pdb=" N ASP E3676 " --> pdb=" O ARG E3672 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU E3677 " --> pdb=" O MET E3673 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E3678 " --> pdb=" O ILE E3674 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E3680 " --> pdb=" O ASP E3676 " (cutoff:3.500A) Processing helix chain 'E' and resid 3681 through 3687 removed outlier: 6.854A pdb=" N GLU E3684 " --> pdb=" O GLY E3681 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU E3685 " --> pdb=" O GLU E3682 " (cutoff:3.500A) Processing helix chain 'E' and resid 3696 through 3708 removed outlier: 3.601A pdb=" N LEU E3701 " --> pdb=" O PRO E3697 " (cutoff:3.500A) Processing helix chain 'E' and resid 3719 through 3738 removed outlier: 3.817A pdb=" N TYR E3725 " --> pdb=" O LEU E3721 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP E3727 " --> pdb=" O MET E3723 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS E3733 " --> pdb=" O MET E3729 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS E3734 " --> pdb=" O ALA E3730 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU E3736 " --> pdb=" O SER E3732 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E3737 " --> pdb=" O CYS E3733 " (cutoff:3.500A) Processing helix chain 'E' and resid 3752 through 3771 removed outlier: 3.723A pdb=" N GLU E3757 " --> pdb=" O PHE E3753 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E3758 " --> pdb=" O GLU E3754 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU E3759 " --> pdb=" O GLU E3755 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E3760 " --> pdb=" O LYS E3756 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E3765 " --> pdb=" O GLN E3761 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN E3766 " --> pdb=" O ARG E3762 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN E3767 " --> pdb=" O LEU E3763 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER E3768 " --> pdb=" O LEU E3764 " (cutoff:3.500A) Processing helix chain 'E' and resid 3771 through 3782 removed outlier: 3.696A pdb=" N ALA E3775 " --> pdb=" O HIS E3771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E3776 " --> pdb=" O THR E3772 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU E3777 " --> pdb=" O ARG E3773 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET E3778 " --> pdb=" O GLY E3774 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU E3780 " --> pdb=" O ALA E3776 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN E3781 " --> pdb=" O GLU E3777 " (cutoff:3.500A) Processing helix chain 'E' and resid 3791 through 3805 removed outlier: 4.207A pdb=" N LYS E3799 " --> pdb=" O SER E3795 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU E3800 " --> pdb=" O SER E3796 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E3803 " --> pdb=" O LYS E3799 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E3805 " --> pdb=" O GLY E3801 " (cutoff:3.500A) Processing helix chain 'E' and resid 3809 through 3824 removed outlier: 3.538A pdb=" N GLN E3814 " --> pdb=" O ALA E3810 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS E3815 " --> pdb=" O GLU E3811 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E3824 " --> pdb=" O LEU E3820 " (cutoff:3.500A) Processing helix chain 'E' and resid 3827 through 3838 removed outlier: 3.619A pdb=" N ILE E3832 " --> pdb=" O PHE E3828 " (cutoff:3.500A) Processing helix chain 'E' and resid 3843 through 3854 Processing helix chain 'E' and resid 3880 through 3891 Processing helix chain 'E' and resid 3898 through 3905 Processing helix chain 'E' and resid 3914 through 3937 removed outlier: 3.803A pdb=" N CYS E3918 " --> pdb=" O ASN E3914 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E3920 " --> pdb=" O ILE E3916 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E3929 " --> pdb=" O ARG E3925 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP E3935 " --> pdb=" O SER E3931 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E3936 " --> pdb=" O ASP E3932 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR E3937 " --> pdb=" O PHE E3933 " (cutoff:3.500A) Processing helix chain 'E' and resid 3944 through 3967 removed outlier: 4.025A pdb=" N ALA E3954 " --> pdb=" O ASN E3950 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E3960 " --> pdb=" O SER E3956 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E3967 " --> pdb=" O ASN E3963 " (cutoff:3.500A) Processing helix chain 'E' and resid 3973 through 3983 removed outlier: 3.530A pdb=" N GLN E3977 " --> pdb=" O CYS E3973 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS E3982 " --> pdb=" O GLN E3978 " (cutoff:3.500A) Processing helix chain 'E' and resid 3984 through 4003 removed outlier: 3.740A pdb=" N VAL E3990 " --> pdb=" O TRP E3986 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY E3991 " --> pdb=" O ASP E3987 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE E3992 " --> pdb=" O ALA E3988 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS E3998 " --> pdb=" O HIS E3994 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET E4000 " --> pdb=" O PHE E3996 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET E4001 " --> pdb=" O ALA E3997 " (cutoff:3.500A) Processing helix chain 'E' and resid 4004 through 4006 No H-bonds generated for 'chain 'E' and resid 4004 through 4006' Processing helix chain 'E' and resid 4009 through 4030 Processing helix chain 'E' and resid 4039 through 4051 removed outlier: 3.611A pdb=" N VAL E4049 " --> pdb=" O VAL E4045 " (cutoff:3.500A) Processing helix chain 'E' and resid 4051 through 4065 removed outlier: 3.548A pdb=" N MET E4057 " --> pdb=" O SER E4053 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET E4064 " --> pdb=" O LYS E4060 " (cutoff:3.500A) Processing helix chain 'E' and resid 4066 through 4072 removed outlier: 3.912A pdb=" N ASP E4070 " --> pdb=" O LEU E4066 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E4072 " --> pdb=" O LEU E4068 " (cutoff:3.500A) Processing helix chain 'E' and resid 4074 through 4079 removed outlier: 3.776A pdb=" N GLN E4078 " --> pdb=" O SER E4074 " (cutoff:3.500A) Processing helix chain 'E' and resid 4090 through 4100 removed outlier: 3.513A pdb=" N MET E4097 " --> pdb=" O PHE E4093 " (cutoff:3.500A) removed outlier: 3.917A 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 4132 removed outlier: 4.413A pdb=" N PHE E4132 " --> pdb=" O PHE E4128 " (cutoff:3.500A) Processing helix chain 'E' and resid 4132 through 4154 removed outlier: 3.593A pdb=" N ALA E4136 " --> pdb=" O PHE E4132 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP E4138 " --> pdb=" O GLU E4134 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE E4139 " --> pdb=" O PRO E4135 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E4151 " --> pdb=" O LEU E4147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E4152 " --> pdb=" O THR E4148 " (cutoff:3.500A) removed outlier: 3.726A 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 4168 through 4175 removed outlier: 3.546A pdb=" N TYR E4173 " --> pdb=" O SER E4169 " (cutoff:3.500A) Processing helix chain 'E' and resid 4199 through 4206 removed outlier: 3.824A pdb=" N ALA E4203 " --> pdb=" O GLU E4199 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU E4206 " --> pdb=" O ARG E4202 " (cutoff:3.500A) Processing helix chain 'E' and resid 4207 through 4224 removed outlier: 4.105A pdb=" N SER E4213 " --> pdb=" O GLN E4209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E4222 " --> pdb=" O ILE E4218 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E4223 " --> pdb=" O PHE E4219 " (cutoff:3.500A) Processing helix chain 'E' and resid 4228 through 4248 removed outlier: 4.024A pdb=" N PHE E4234 " --> pdb=" O LYS E4230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E4242 " --> pdb=" O CYS E4238 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE E4243 " --> pdb=" O GLU E4239 " (cutoff:3.500A) Processing helix chain 'E' and resid 4321 through 4337 removed outlier: 3.537A pdb=" N UNK E4327 " --> pdb=" O UNK E4323 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK E4332 " --> pdb=" O UNK E4328 " (cutoff:3.500A) Processing helix chain 'E' and resid 4543 through 4556 removed outlier: 3.965A pdb=" N TYR E4554 " --> pdb=" O LYS E4550 " (cutoff:3.500A) Processing helix chain 'E' and resid 4558 through 4576 removed outlier: 3.535A pdb=" N ALA E4566 " --> pdb=" O LEU E4562 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE E4571 " --> pdb=" O LEU E4567 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA E4572 " --> pdb=" O PHE E4568 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E4573 " --> pdb=" O LEU E4569 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E4574 " --> pdb=" O ALA E4570 " (cutoff:3.500A) Processing helix chain 'E' and resid 4577 through 4580 removed outlier: 3.927A pdb=" N TYR E4580 " --> pdb=" O LEU E4577 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4577 through 4580' Processing helix chain 'E' and resid 4641 through 4665 removed outlier: 3.618A pdb=" N LEU E4648 " --> pdb=" O TRP E4644 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E4649 " --> pdb=" O CYS E4645 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E4654 " --> pdb=" O HIS E4650 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E4658 " --> pdb=" O ALA E4654 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE E4659 " --> pdb=" O PHE E4655 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E4660 " --> pdb=" O LEU E4656 " (cutoff:3.500A) Processing helix chain 'E' and resid 4665 through 4683 removed outlier: 3.539A pdb=" N LYS E4672 " --> pdb=" O LEU E4668 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E4677 " --> pdb=" O ARG E4673 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA E4678 " --> pdb=" O GLU E4674 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E4683 " --> pdb=" O ARG E4679 " (cutoff:3.500A) Processing helix chain 'E' and resid 4697 through 4702 removed outlier: 3.577A pdb=" N ASP E4702 " --> pdb=" O LYS E4698 " (cutoff:3.500A) Processing helix chain 'E' and resid 4710 through 4714 removed outlier: 3.515A pdb=" N SER E4713 " --> pdb=" O SER E4710 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN E4714 " --> pdb=" O PHE E4711 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4710 through 4714' Processing helix chain 'E' and resid 4719 through 4728 removed outlier: 3.526A pdb=" N LEU E4725 " --> pdb=" O LYS E4721 " (cutoff:3.500A) Processing helix chain 'E' and resid 4733 through 4741 removed outlier: 3.553A pdb=" N LEU E4741 " --> pdb=" O ILE E4737 " (cutoff:3.500A) Processing helix chain 'E' and resid 4745 through 4750 Processing helix chain 'E' and resid 4751 through 4755 removed outlier: 4.040A pdb=" N GLU E4755 " --> pdb=" O ALA E4752 " (cutoff:3.500A) Processing helix chain 'E' and resid 4772 through 4786 removed outlier: 3.654A pdb=" N THR E4785 " --> pdb=" O GLY E4781 " (cutoff:3.500A) Processing helix chain 'E' and resid 4786 through 4802 removed outlier: 3.534A pdb=" N SER E4799 " --> pdb=" O TYR E4795 " (cutoff:3.500A) Processing helix chain 'E' and resid 4814 through 4820 removed outlier: 3.852A pdb=" N MET E4818 " --> pdb=" O LEU E4814 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL E4820 " --> pdb=" O ILE E4816 " (cutoff:3.500A) Processing helix chain 'E' and resid 4820 through 4833 removed outlier: 3.748A pdb=" N ILE E4826 " --> pdb=" O THR E4822 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E4830 " --> pdb=" O ILE E4826 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR E4831 " --> pdb=" O LEU E4827 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN E4833 " --> pdb=" O SER E4829 " (cutoff:3.500A) Processing helix chain 'E' and resid 4833 through 4858 removed outlier: 3.964A pdb=" N MET E4839 " --> pdb=" O LYS E4835 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY E4842 " --> pdb=" O VAL E4838 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E4843 " --> pdb=" O MET E4839 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E4844 " --> pdb=" O THR E4840 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL E4853 " --> pdb=" O TYR E4849 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E4854 " --> pdb=" O LEU E4850 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA E4855 " --> pdb=" O TYR E4851 " (cutoff:3.500A) Processing helix chain 'E' and resid 4859 through 4863 removed outlier: 3.957A pdb=" N TYR E4863 " --> pdb=" O ARG E4860 " (cutoff:3.500A) Processing helix chain 'E' and resid 4878 through 4890 removed outlier: 3.654A pdb=" N MET E4887 " --> pdb=" O TYR E4883 " (cutoff:3.500A) Processing helix chain 'E' and resid 4909 through 4925 removed outlier: 3.681A pdb=" N ARG E4913 " --> pdb=" O TYR E4909 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E4914 " --> pdb=" O GLU E4910 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E4915 " --> pdb=" O LEU E4911 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E4918 " --> pdb=" O VAL E4914 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E4923 " --> pdb=" O THR E4919 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E4925 " --> pdb=" O PHE E4921 " (cutoff:3.500A) Processing helix chain 'E' and resid 4927 through 4957 removed outlier: 3.640A pdb=" N ILE E4932 " --> pdb=" O LEU E4928 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE E4936 " --> pdb=" O ILE E4932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E4942 " --> pdb=" O ASP E4938 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E4943 " --> pdb=" O ALA E4939 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN E4947 " --> pdb=" O LEU E4943 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS E4951 " --> pdb=" O GLN E4947 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E4957 " --> pdb=" O ASP E4953 " (cutoff:3.500A) Processing helix chain 'E' and resid 4964 through 4971 removed outlier: 4.318A pdb=" N PHE E4968 " --> pdb=" O GLY E4964 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR E4971 " --> pdb=" O TYR E4967 " (cutoff:3.500A) Processing helix chain 'E' and resid 4973 through 4979 removed outlier: 3.762A pdb=" N THR E4977 " --> pdb=" O HIS E4973 " (cutoff:3.500A) Processing helix chain 'E' and resid 4986 through 4997 removed outlier: 4.009A pdb=" N PHE E4990 " --> pdb=" O ALA E4986 " (cutoff:3.500A) Processing helix chain 'E' and resid 5006 through 5017 removed outlier: 3.638A pdb=" N TRP E5011 " --> pdb=" O GLU E5007 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS E5012 " --> pdb=" O SER E5008 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET E5013 " --> pdb=" O TYR E5009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.716A pdb=" N PHE F 99 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 101 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.717A pdb=" N PHE A 99 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 101 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA6, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.717A pdb=" N PHE H 99 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL H 101 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'J' and resid 27 through 30 removed outlier: 3.717A pdb=" N PHE J 99 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 101 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 27 Processing sheet with id=AB2, first strand: chain 'B' and resid 106 through 107 removed outlier: 3.567A pdb=" N TRP B 148 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AB4, first strand: chain 'B' and resid 300 through 302 removed outlier: 3.674A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 289 " --> pdb=" O HIS B 284 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 291 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 391 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 389 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 230 through 233 removed outlier: 3.828A pdb=" N THR B 232 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AB7, first strand: chain 'B' and resid 358 through 359 Processing sheet with id=AB8, first strand: chain 'B' and resid 634 through 639 removed outlier: 4.131A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 636 " --> pdb=" O ALA B1638 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 713 through 716 removed outlier: 3.941A pdb=" N ALA B 687 " --> pdb=" O PHE B 778 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 781 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 644 " --> pdb=" O VAL B 781 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 783 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 642 " --> pdb=" O PHE B 783 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 763 through 768 removed outlier: 6.299A pdb=" N VAL B 764 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE B 759 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY B 766 " --> pdb=" O PHE B 757 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 757 " --> pdb=" O GLY B 766 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 744 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AC3, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AC4, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.568A pdb=" N THR B 892 " --> pdb=" O HIS B 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 939 through 941 Processing sheet with id=AC6, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.542A pdb=" N VAL B1102 " --> pdb=" O PHE B1124 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B1101 " --> pdb=" O SER B1193 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1256 through 1259 removed outlier: 3.662A pdb=" N UNK B1486 " --> pdb=" O UNK B1471 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1293 through 1294 removed outlier: 3.839A pdb=" N UNK B1459 " --> pdb=" O UNK B1495 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N UNK B1495 " --> pdb=" O UNK B1459 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1293 through 1294 removed outlier: 5.194A pdb=" N UNK B1458 " --> pdb=" O UNK B1289 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N UNK B1460 " --> pdb=" O UNK B1287 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK B1287 " --> pdb=" O UNK B1460 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK B1288 " --> pdb=" O GLN B1598 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1515 through 1516 Processing sheet with id=AD2, first strand: chain 'B' and resid 1734 through 1736 removed outlier: 6.484A pdb=" N TYR B1734 " --> pdb=" O TYR B2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 4178 through 4183 Processing sheet with id=AD4, first strand: chain 'G' and resid 67 through 68 Processing sheet with id=AD5, first strand: chain 'G' and resid 23 through 27 Processing sheet with id=AD6, first strand: chain 'G' and resid 106 through 107 removed outlier: 3.566A pdb=" N TRP G 148 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 181 through 184 Processing sheet with id=AD8, first strand: chain 'G' and resid 300 through 302 removed outlier: 3.674A pdb=" N VAL G 300 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 289 " --> pdb=" O HIS G 284 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 291 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE G 282 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 391 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE G 389 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 230 through 233 removed outlier: 3.828A pdb=" N THR G 232 " --> pdb=" O TYR G 246 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 314 through 317 Processing sheet with id=AE2, first strand: chain 'G' and resid 358 through 359 Processing sheet with id=AE3, first strand: chain 'G' and resid 634 through 639 removed outlier: 4.132A pdb=" N GLN G 634 " --> pdb=" O HIS G1640 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN G 636 " --> pdb=" O ALA G1638 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G1646 " --> pdb=" O ILE G1641 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 713 through 716 removed outlier: 3.941A pdb=" N ALA G 687 " --> pdb=" O PHE G 778 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G 781 " --> pdb=" O ILE G 644 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE G 644 " --> pdb=" O VAL G 781 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE G 783 " --> pdb=" O THR G 642 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR G 642 " --> pdb=" O PHE G 783 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 763 through 768 removed outlier: 6.299A pdb=" N VAL G 764 " --> pdb=" O ILE G 759 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE G 759 " --> pdb=" O VAL G 764 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY G 766 " --> pdb=" O PHE G 757 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE G 757 " --> pdb=" O GLY G 766 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL G 744 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL G 666 " --> pdb=" O VAL G 744 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AE7, first strand: chain 'G' and resid 839 through 840 Processing sheet with id=AE8, first strand: chain 'G' and resid 892 through 893 removed outlier: 6.568A pdb=" N THR G 892 " --> pdb=" O HIS G 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'G' and resid 939 through 941 Processing sheet with id=AF1, first strand: chain 'G' and resid 1136 through 1138 removed outlier: 3.542A pdb=" N VAL G1102 " --> pdb=" O PHE G1124 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG G1101 " --> pdb=" O SER G1193 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 1256 through 1259 removed outlier: 3.662A pdb=" N UNK G1486 " --> pdb=" O UNK G1471 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 1293 through 1294 removed outlier: 3.839A pdb=" N UNK G1459 " --> pdb=" O UNK G1495 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N UNK G1495 " --> pdb=" O UNK G1459 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 1293 through 1294 removed outlier: 5.194A pdb=" N UNK G1458 " --> pdb=" O UNK G1289 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK G1460 " --> pdb=" O UNK G1287 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK G1287 " --> pdb=" O UNK G1460 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N UNK G1288 " --> pdb=" O GLN G1598 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 1515 through 1516 Processing sheet with id=AF6, first strand: chain 'G' and resid 1734 through 1736 removed outlier: 6.484A pdb=" N TYR G1734 " --> pdb=" O TYR G2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'G' and resid 4178 through 4183 Processing sheet with id=AF8, first strand: chain 'I' and resid 67 through 68 Processing sheet with id=AF9, first strand: chain 'I' and resid 23 through 27 Processing sheet with id=AG1, first strand: chain 'I' and resid 106 through 107 removed outlier: 3.566A pdb=" N TRP I 148 " --> pdb=" O ILE I 107 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 181 through 184 Processing sheet with id=AG3, first strand: chain 'I' and resid 300 through 302 removed outlier: 3.675A pdb=" N VAL I 300 " --> pdb=" O ALA I 292 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG I 289 " --> pdb=" O HIS I 284 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 291 " --> pdb=" O ILE I 282 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE I 282 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR I 391 " --> pdb=" O ARG I 221 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE I 389 " --> pdb=" O PHE I 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 230 through 233 removed outlier: 3.829A pdb=" N THR I 232 " --> pdb=" O TYR I 246 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 314 through 317 Processing sheet with id=AG6, first strand: chain 'I' and resid 358 through 359 Processing sheet with id=AG7, first strand: chain 'I' and resid 634 through 639 removed outlier: 4.131A pdb=" N GLN I 634 " --> pdb=" O HIS I1640 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN I 636 " --> pdb=" O ALA I1638 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG I1646 " --> pdb=" O ILE I1641 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 713 through 716 removed outlier: 3.941A pdb=" N ALA I 687 " --> pdb=" O PHE I 778 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL I 781 " --> pdb=" O ILE I 644 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE I 644 " --> pdb=" O VAL I 781 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE I 783 " --> pdb=" O THR I 642 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR I 642 " --> pdb=" O PHE I 783 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 763 through 768 removed outlier: 6.298A pdb=" N VAL I 764 " --> pdb=" O ILE I 759 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE I 759 " --> pdb=" O VAL I 764 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY I 766 " --> pdb=" O PHE I 757 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE I 757 " --> pdb=" O GLY I 766 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP I 742 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL I 744 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 666 " --> pdb=" O VAL I 744 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AH2, first strand: chain 'I' and resid 839 through 840 Processing sheet with id=AH3, first strand: chain 'I' and resid 892 through 893 removed outlier: 6.568A pdb=" N THR I 892 " --> pdb=" O HIS I 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 939 through 941 Processing sheet with id=AH5, first strand: chain 'I' and resid 1136 through 1138 removed outlier: 3.541A pdb=" N VAL I1102 " --> pdb=" O PHE I1124 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG I1101 " --> pdb=" O SER I1193 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE I1074 " --> pdb=" O SER I1239 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 1256 through 1259 removed outlier: 3.661A pdb=" N UNK I1486 " --> pdb=" O UNK I1471 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 1293 through 1294 removed outlier: 3.839A pdb=" N UNK I1459 " --> pdb=" O UNK I1495 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N UNK I1495 " --> pdb=" O UNK I1459 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 1293 through 1294 removed outlier: 5.194A pdb=" N UNK I1458 " --> pdb=" O UNK I1289 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N UNK I1460 " --> pdb=" O UNK I1287 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK I1287 " --> pdb=" O UNK I1460 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK I1288 " --> pdb=" O GLN I1598 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 1515 through 1516 Processing sheet with id=AI1, first strand: chain 'I' and resid 1734 through 1736 removed outlier: 6.484A pdb=" N TYR I1734 " --> pdb=" O TYR I2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'I' and resid 4178 through 4183 Processing sheet with id=AI3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AI4, first strand: chain 'E' and resid 23 through 27 Processing sheet with id=AI5, first strand: chain 'E' and resid 106 through 107 removed outlier: 3.568A pdb=" N TRP E 148 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AI7, first strand: chain 'E' and resid 300 through 302 removed outlier: 3.675A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 289 " --> pdb=" O HIS E 284 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 291 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE E 282 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 391 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 389 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 230 through 233 removed outlier: 3.828A pdb=" N THR E 232 " --> pdb=" O TYR E 246 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AJ1, first strand: chain 'E' and resid 358 through 359 Processing sheet with id=AJ2, first strand: chain 'E' and resid 634 through 639 removed outlier: 4.132A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN E 636 " --> pdb=" O ALA E1638 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E1646 " --> pdb=" O ILE E1641 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 713 through 716 removed outlier: 3.941A pdb=" N ALA E 687 " --> pdb=" O PHE E 778 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL E 781 " --> pdb=" O ILE E 644 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE E 644 " --> pdb=" O VAL E 781 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 783 " --> pdb=" O THR E 642 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR E 642 " --> pdb=" O PHE E 783 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 763 through 768 removed outlier: 6.299A pdb=" N VAL E 764 " --> pdb=" O ILE E 759 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE E 759 " --> pdb=" O VAL E 764 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY E 766 " --> pdb=" O PHE E 757 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE E 757 " --> pdb=" O GLY E 766 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL E 744 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL E 666 " --> pdb=" O VAL E 744 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AJ6, first strand: chain 'E' and resid 839 through 840 Processing sheet with id=AJ7, first strand: chain 'E' and resid 892 through 893 removed outlier: 6.568A pdb=" N THR E 892 " --> pdb=" O HIS E 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'E' and resid 939 through 941 Processing sheet with id=AJ9, first strand: chain 'E' and resid 1136 through 1138 removed outlier: 3.543A pdb=" N VAL E1102 " --> pdb=" O PHE E1124 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG E1101 " --> pdb=" O SER E1193 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 1256 through 1259 removed outlier: 3.662A pdb=" N UNK E1486 " --> pdb=" O UNK E1471 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 1293 through 1294 removed outlier: 3.839A pdb=" N UNK E1459 " --> pdb=" O UNK E1495 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N UNK E1495 " --> pdb=" O UNK E1459 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1293 through 1294 removed outlier: 5.194A pdb=" N UNK E1458 " --> pdb=" O UNK E1289 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N UNK E1460 " --> pdb=" O UNK E1287 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK E1287 " --> pdb=" O UNK E1460 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N UNK E1288 " --> pdb=" O GLN E1598 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1515 through 1516 Processing sheet with id=AK5, first strand: chain 'E' and resid 1734 through 1736 removed outlier: 6.484A pdb=" N TYR E1734 " --> pdb=" O TYR E2142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'E' and resid 4178 through 4183 4841 hydrogen bonds defined for protein. 13983 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: 85.61 Time building geometry restraints manager: 35.37 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: 41065 1.34 - 1.46: 26087 1.46 - 1.58: 55356 1.58 - 1.70: 0 1.70 - 1.82: 1020 Bond restraints: 123528 Sorted by residual: bond pdb=" C LEU B1242 " pdb=" N PRO B1243 " ideal model delta sigma weight residual 1.334 1.264 0.070 2.34e-02 1.83e+03 8.98e+00 bond pdb=" C LEU I1242 " pdb=" N PRO I1243 " ideal model delta sigma weight residual 1.334 1.264 0.070 2.34e-02 1.83e+03 8.97e+00 bond pdb=" C LEU E1242 " pdb=" N PRO E1243 " ideal model delta sigma weight residual 1.334 1.264 0.070 2.34e-02 1.83e+03 8.97e+00 bond pdb=" C LEU G1242 " pdb=" N PRO G1243 " ideal model delta sigma weight residual 1.334 1.264 0.070 2.34e-02 1.83e+03 8.93e+00 bond pdb=" N PHE G4959 " pdb=" CA PHE G4959 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.28e-02 6.10e+03 8.28e+00 ... (remaining 123523 not shown) Histogram of bond angle deviations from ideal: 98.09 - 106.10: 2893 106.10 - 114.12: 71231 114.12 - 122.14: 69718 122.14 - 130.15: 23893 130.15 - 138.17: 701 Bond angle restraints: 168436 Sorted by residual: angle pdb=" CA LEU E 131 " pdb=" CB LEU E 131 " pdb=" CG LEU E 131 " ideal model delta sigma weight residual 116.30 133.56 -17.26 3.50e+00 8.16e-02 2.43e+01 angle pdb=" CA LEU I 131 " pdb=" CB LEU I 131 " pdb=" CG LEU I 131 " ideal model delta sigma weight residual 116.30 133.53 -17.23 3.50e+00 8.16e-02 2.42e+01 angle pdb=" CA LEU B 131 " pdb=" CB LEU B 131 " pdb=" CG LEU B 131 " ideal model delta sigma weight residual 116.30 133.53 -17.23 3.50e+00 8.16e-02 2.42e+01 angle pdb=" CA LEU G 131 " pdb=" CB LEU G 131 " pdb=" CG LEU G 131 " ideal model delta sigma weight residual 116.30 133.49 -17.19 3.50e+00 8.16e-02 2.41e+01 angle pdb=" C VAL E 752 " pdb=" N PRO E 753 " pdb=" CA PRO E 753 " ideal model delta sigma weight residual 127.00 138.17 -11.17 2.40e+00 1.74e-01 2.17e+01 ... (remaining 168431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 70629 15.45 - 30.90: 2243 30.90 - 46.36: 708 46.36 - 61.81: 56 61.81 - 77.26: 96 Dihedral angle restraints: 73732 sinusoidal: 23656 harmonic: 50076 Sorted by residual: dihedral pdb=" CA ASP E1828 " pdb=" C ASP E1828 " pdb=" N PRO E1829 " pdb=" CA PRO E1829 " ideal model delta harmonic sigma weight residual -180.00 -130.01 -49.99 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CA ASP G1828 " pdb=" C ASP G1828 " pdb=" N PRO G1829 " pdb=" CA PRO G1829 " ideal model delta harmonic sigma weight residual 180.00 -130.08 -49.92 0 5.00e+00 4.00e-02 9.97e+01 dihedral pdb=" CA ASP B1828 " pdb=" C ASP B1828 " pdb=" N PRO B1829 " pdb=" CA PRO B1829 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.97e+01 ... (remaining 73729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 17720 0.076 - 0.152: 1781 0.152 - 0.228: 155 0.228 - 0.304: 35 0.304 - 0.380: 13 Chirality restraints: 19704 Sorted by residual: chirality pdb=" CG LEU G 131 " pdb=" CB LEU G 131 " pdb=" CD1 LEU G 131 " pdb=" CD2 LEU G 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CG LEU B 131 " pdb=" CB LEU B 131 " pdb=" CD1 LEU B 131 " pdb=" CD2 LEU B 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CG LEU I 131 " pdb=" CB LEU I 131 " pdb=" CD1 LEU I 131 " pdb=" CD2 LEU I 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 19701 not shown) Planarity restraints: 22192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP G2807 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO G2808 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO G2808 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO G2808 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B2807 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B2808 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B2808 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B2808 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E2807 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO E2808 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO E2808 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E2808 " -0.055 5.00e-02 4.00e+02 ... (remaining 22189 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 12 2.08 - 2.78: 30705 2.78 - 3.49: 155991 3.49 - 4.19: 266473 4.19 - 4.90: 439993 Nonbonded interactions: 893174 Sorted by model distance: nonbonded pdb=" O UNK E1487 " pdb=" CB UNK E1551 " model vdw 1.374 3.440 nonbonded pdb=" O UNK I1487 " pdb=" CB UNK I1551 " model vdw 1.374 3.440 nonbonded pdb=" O UNK B3557 " pdb=" CB UNK B3561 " model vdw 1.374 3.440 nonbonded pdb=" O UNK G1487 " pdb=" CB UNK G1551 " model vdw 1.374 3.440 nonbonded pdb=" O UNK B1487 " pdb=" CB UNK B1551 " model vdw 1.374 3.440 ... (remaining 893169 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.530 Construct map_model_manager: 0.090 Extract box with map and model: 16.890 Check model and map are aligned: 1.300 Set scattering table: 0.810 Process input model: 284.250 Find NCS groups from input model: 6.150 Set up NCS constraints: 0.500 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 315.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 0.070 123528 Z= 0.259 Angle : 0.864 17.258 168436 Z= 0.449 Chirality : 0.048 0.380 19704 Planarity : 0.007 0.101 22192 Dihedral : 9.862 77.260 41164 Min Nonbonded Distance : 1.374 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.42 % Favored : 89.40 % Rotamer: Outliers : 0.46 % Allowed : 2.87 % Favored : 96.67 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.05), residues: 13356 helix: -3.76 (0.04), residues: 5336 sheet: -1.89 (0.16), residues: 928 loop : -3.06 (0.06), residues: 7092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I5019 HIS 0.011 0.002 HIS I5003 PHE 0.035 0.002 PHE I2012 TYR 0.031 0.002 TYR B1711 ARG 0.010 0.001 ARG B 392 *********************** 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 31 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8667 (mt-10) cc_final: 0.7554 (tm-30) REVERT: A 29 MET cc_start: 0.8198 (tpp) cc_final: 0.7992 (tpt) REVERT: A 30 LEU cc_start: 0.9375 (tp) cc_final: 0.9096 (tt) REVERT: A 47 LYS cc_start: 0.9496 (mttt) cc_final: 0.8954 (mmtm) REVERT: A 56 ILE cc_start: 0.8447 (pt) cc_final: 0.7941 (pt) REVERT: A 60 GLU cc_start: 0.9304 (tt0) cc_final: 0.9043 (pt0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1889 time to fit residues: 6.1484 Evaluate side-chains 14 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.075 Evaluate side-chains 652 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 640 time to evaluate : 2.136 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 70 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 76 ARG cc_start: 0.9306 (mmt180) cc_final: 0.8909 (ttt180) REVERT: B 121 LEU cc_start: 0.9268 (mt) cc_final: 0.8746 (mt) REVERT: B 334 MET cc_start: 0.7628 (mmm) cc_final: 0.7111 (mmt) REVERT: B 566 CYS cc_start: 0.8728 (m) cc_final: 0.6939 (m) REVERT: B 623 GLU cc_start: 0.9448 (tt0) cc_final: 0.9173 (tm-30) REVERT: B 899 ASP cc_start: 0.7157 (m-30) cc_final: 0.6809 (t70) REVERT: B 961 MET cc_start: 0.0113 (mmp) cc_final: -0.1989 (mmp) REVERT: B 1152 MET cc_start: 0.8446 (mtt) cc_final: 0.8000 (mtt) REVERT: B 1600 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.7803 (pt) REVERT: B 1652 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8496 (tp30) REVERT: B 1668 ARG cc_start: 0.8847 (ptm160) cc_final: 0.8502 (ttp80) REVERT: B 1713 ASP cc_start: 0.8341 (t70) cc_final: 0.7580 (t0) REVERT: B 1714 LEU cc_start: 0.9317 (tp) cc_final: 0.9117 (tp) REVERT: B 1771 LEU cc_start: 0.8899 (mm) cc_final: 0.8637 (mm) REVERT: B 1851 MET cc_start: 0.9156 (mtp) cc_final: 0.8708 (ttm) REVERT: B 2101 MET cc_start: 0.9112 (ttp) cc_final: 0.8874 (tmm) REVERT: B 2102 VAL cc_start: 0.9579 (t) cc_final: 0.8771 (p) REVERT: B 2134 LEU cc_start: 0.9399 (tp) cc_final: 0.9129 (pp) REVERT: B 2155 LEU cc_start: 0.9107 (mm) cc_final: 0.8893 (mt) REVERT: B 2165 LEU cc_start: 0.9535 (mp) cc_final: 0.9188 (tt) REVERT: B 2186 MET cc_start: 0.8472 (mmm) cc_final: 0.8209 (ppp) REVERT: B 2267 MET cc_start: 0.8269 (tpt) cc_final: 0.8037 (tpp) REVERT: B 2334 PHE cc_start: 0.8875 (t80) cc_final: 0.8489 (t80) REVERT: B 2349 ASN cc_start: 0.8437 (m-40) cc_final: 0.8170 (t0) REVERT: B 2441 HIS cc_start: 0.8787 (t70) cc_final: 0.8533 (t70) REVERT: B 2761 TYR cc_start: 0.7859 (t80) cc_final: 0.7265 (t80) REVERT: B 3669 PHE cc_start: 0.8694 (p90) cc_final: 0.8460 (p90) REVERT: B 3673 MET cc_start: 0.8853 (ttt) cc_final: 0.8467 (ttm) REVERT: B 3677 LEU cc_start: 0.9520 (mt) cc_final: 0.9108 (mm) REVERT: B 3698 LEU cc_start: 0.9479 (tp) cc_final: 0.8968 (tp) REVERT: B 3715 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8545 (ttpp) REVERT: B 3716 LEU cc_start: 0.9135 (tp) cc_final: 0.8523 (tt) REVERT: B 3723 MET cc_start: 0.9127 (mtt) cc_final: 0.8497 (mmm) REVERT: B 3754 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7794 (tp30) REVERT: B 3758 MET cc_start: 0.9170 (mmm) cc_final: 0.8947 (mmm) REVERT: B 3778 MET cc_start: 0.9322 (ppp) cc_final: 0.9053 (ppp) REVERT: B 3796 SER cc_start: 0.9039 (m) cc_final: 0.8526 (p) REVERT: B 3829 PHE cc_start: 0.9266 (m-80) cc_final: 0.8942 (m-10) REVERT: B 3836 MET cc_start: 0.9306 (ttm) cc_final: 0.8811 (ttp) REVERT: B 3921 ASP cc_start: 0.9409 (t70) cc_final: 0.9173 (t0) REVERT: B 3941 ASP cc_start: 0.8421 (p0) cc_final: 0.7835 (m-30) REVERT: B 3986 TRP cc_start: 0.7247 (m100) cc_final: 0.4845 (m100) REVERT: B 3989 VAL cc_start: 0.9295 (t) cc_final: 0.8977 (p) REVERT: B 4000 MET cc_start: 0.8885 (ttt) cc_final: 0.8580 (ttt) REVERT: B 4016 LEU cc_start: 0.9522 (tt) cc_final: 0.9269 (tt) REVERT: B 4017 LEU cc_start: 0.9633 (mt) cc_final: 0.9408 (mt) REVERT: B 4021 LYS cc_start: 0.9640 (ttpt) cc_final: 0.9255 (tptp) REVERT: B 4026 MET cc_start: 0.9487 (ttt) cc_final: 0.8887 (tpt) REVERT: B 4027 LEU cc_start: 0.9410 (mt) cc_final: 0.9172 (tp) REVERT: B 4029 SER cc_start: 0.9669 (m) cc_final: 0.9439 (t) REVERT: B 4062 PHE cc_start: 0.8643 (m-10) cc_final: 0.8143 (m-10) REVERT: B 4152 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8031 (tt0) REVERT: B 4164 LEU cc_start: 0.9243 (mt) cc_final: 0.8390 (mm) REVERT: B 4196 GLU cc_start: 0.8097 (tt0) cc_final: 0.7322 (tm-30) REVERT: B 4210 VAL cc_start: 0.9443 (t) cc_final: 0.9151 (p) REVERT: B 4573 ILE cc_start: 0.9719 (tt) cc_final: 0.9513 (tt) REVERT: B 4652 LEU cc_start: 0.9646 (tt) cc_final: 0.9307 (pp) REVERT: B 4676 GLU cc_start: 0.9237 (pt0) cc_final: 0.8994 (tm-30) REVERT: B 4680 LYS cc_start: 0.9427 (mttt) cc_final: 0.9104 (mmmt) REVERT: B 4686 LEU cc_start: 0.9316 (tp) cc_final: 0.9099 (mt) REVERT: B 4769 MET cc_start: 0.1761 (ptm) cc_final: 0.0294 (ttt) REVERT: B 4868 ASP cc_start: 0.8774 (t70) cc_final: 0.8514 (p0) REVERT: B 4874 MET cc_start: 0.8213 (mtp) cc_final: 0.7958 (mtp) REVERT: B 4938 ASP cc_start: 0.8769 (t70) cc_final: 0.8554 (p0) REVERT: B 4993 MET cc_start: 0.9066 (ttp) cc_final: 0.8464 (tmm) REVERT: B 5030 LYS cc_start: 0.9359 (tttm) cc_final: 0.9012 (tmtt) outliers start: 12 outliers final: 5 residues processed: 650 average time/residue: 0.3650 time to fit residues: 371.0101 Evaluate side-chains 342 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 336 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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: 8.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 HIS F 32 ASN F 43 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 71 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 379 HIS B 383 HIS B 395 GLN B 413 GLN B 520 ASN ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 HIS B 797 HIS B 921 ASN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1598 GLN B1688 HIS ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1775 HIS B1972 ASN B2007 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2260 ASN B2291 GLN B2349 ASN B2884 ASN B3700 GLN B3781 GLN ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3889 GLN B3960 GLN ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3998 HIS B4034 ASN B4054 ASN B4142 ASN B4209 GLN B4728 HIS B4803 HIS B4806 ASN B4833 ASN ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5015 GLN B5031 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 123528 Z= 0.260 Angle : 0.718 9.255 168436 Z= 0.369 Chirality : 0.040 0.229 19704 Planarity : 0.005 0.094 22192 Dihedral : 5.800 45.457 18156 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.30 % Favored : 89.61 % Rotamer: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.07), residues: 13356 helix: -1.48 (0.06), residues: 5800 sheet: -1.98 (0.14), residues: 1228 loop : -2.70 (0.07), residues: 6328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E5019 HIS 0.008 0.002 HIS B4983 PHE 0.022 0.002 PHE I1580 TYR 0.030 0.002 TYR G1712 ARG 0.014 0.001 ARG E4892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26708 Ramachandran restraints generated. 13354 Oldfield, 0 Emsley, 13354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26708 Ramachandran restraints generated. 13354 Oldfield, 0 Emsley, 13354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 3 GLU cc_start: 0.8829 (mt-10) cc_final: 0.7797 (tm-30) REVERT: F 30 LEU cc_start: 0.9360 (tp) cc_final: 0.9106 (tp) REVERT: F 47 LYS cc_start: 0.9448 (mttt) cc_final: 0.8965 (mmtm) REVERT: F 56 ILE cc_start: 0.8447 (pt) cc_final: 0.8068 (pt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1487 time to fit residues: 3.5126 Evaluate side-chains 15 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.079 Evaluate side-chains 423 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 421 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ARG cc_start: 0.9399 (mmt180) cc_final: 0.8929 (ttt180) REVERT: B 81 MET cc_start: 0.8923 (tmm) cc_final: 0.8584 (tmm) REVERT: B 116 MET cc_start: 0.8808 (mtm) cc_final: 0.8322 (mtp) REVERT: B 138 GLN cc_start: 0.6857 (mp10) cc_final: 0.6654 (mm110) REVERT: B 180 LEU cc_start: 0.9288 (tp) cc_final: 0.9064 (tp) REVERT: B 195 PHE cc_start: 0.4571 (m-80) cc_final: 0.4343 (m-10) REVERT: B 390 LEU cc_start: 0.8596 (mp) cc_final: 0.8240 (mp) REVERT: B 453 GLU cc_start: 0.9003 (tp30) cc_final: 0.8791 (tp30) REVERT: B 623 GLU cc_start: 0.9456 (tt0) cc_final: 0.9177 (tm-30) REVERT: B 961 MET cc_start: -0.1792 (mmp) cc_final: -0.2429 (mmp) REVERT: B 1152 MET cc_start: 0.8662 (mtt) cc_final: 0.7947 (mtt) REVERT: B 1180 ARG cc_start: 0.7669 (mpt180) cc_final: 0.7384 (mmt180) REVERT: B 1183 GLU cc_start: 0.8405 (pm20) cc_final: 0.8189 (pm20) REVERT: B 1648 MET cc_start: 0.9203 (ptp) cc_final: 0.8957 (ptp) REVERT: B 1771 LEU cc_start: 0.8881 (mm) cc_final: 0.8568 (mm) REVERT: B 1851 MET cc_start: 0.9304 (mtp) cc_final: 0.8706 (ttm) REVERT: B 2102 VAL cc_start: 0.9571 (t) cc_final: 0.9236 (p) REVERT: B 2165 LEU cc_start: 0.9525 (mp) cc_final: 0.9178 (tt) REVERT: B 2186 MET cc_start: 0.8771 (mmm) cc_final: 0.8196 (ppp) REVERT: B 2250 MET cc_start: 0.9416 (mmp) cc_final: 0.9091 (mmp) REVERT: B 2267 MET cc_start: 0.8311 (tpt) cc_final: 0.8106 (tpp) REVERT: B 2435 ARG cc_start: 0.8420 (mtt-85) cc_final: 0.8200 (tmt170) REVERT: B 2441 HIS cc_start: 0.8899 (t70) cc_final: 0.8657 (t70) REVERT: B 2932 MET cc_start: -0.0887 (mmm) cc_final: -0.1206 (mmm) REVERT: B 3673 MET cc_start: 0.8789 (ttt) cc_final: 0.8445 (ttm) REVERT: B 3715 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8567 (ttpp) REVERT: B 3716 LEU cc_start: 0.9183 (tp) cc_final: 0.8873 (tt) REVERT: B 3723 MET cc_start: 0.9042 (mtt) cc_final: 0.8784 (mmm) REVERT: B 3754 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7992 (tp30) REVERT: B 3829 PHE cc_start: 0.9282 (m-80) cc_final: 0.9033 (m-10) REVERT: B 3836 MET cc_start: 0.9172 (ttm) cc_final: 0.8682 (ttp) REVERT: B 3891 LEU cc_start: 0.9403 (mt) cc_final: 0.9195 (mt) REVERT: B 3941 ASP cc_start: 0.8519 (p0) cc_final: 0.7862 (m-30) REVERT: B 3986 TRP cc_start: 0.7341 (m100) cc_final: 0.6649 (m100) REVERT: B 3996 PHE cc_start: 0.8984 (m-10) cc_final: 0.8741 (m-10) REVERT: B 4000 MET cc_start: 0.9006 (ttt) cc_final: 0.8629 (ttt) REVERT: B 4021 LYS cc_start: 0.9700 (ttpt) cc_final: 0.9443 (ttpp) REVERT: B 4023 MET cc_start: 0.9043 (tmm) cc_final: 0.8659 (tmm) REVERT: B 4026 MET cc_start: 0.9395 (ttt) cc_final: 0.8983 (tpt) REVERT: B 4062 PHE cc_start: 0.8839 (m-10) cc_final: 0.8432 (m-10) REVERT: B 4097 MET cc_start: 0.6759 (tpt) cc_final: 0.6458 (tpp) REVERT: B 4149 ASN cc_start: 0.9151 (t0) cc_final: 0.8830 (t0) REVERT: B 4152 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7313 (tt0) REVERT: B 4172 GLU cc_start: 0.8837 (tp30) cc_final: 0.8508 (mm-30) REVERT: B 4184 MET cc_start: 0.7912 (tpt) cc_final: 0.7334 (tpt) REVERT: B 4196 GLU cc_start: 0.7923 (tt0) cc_final: 0.7562 (tm-30) REVERT: B 4239 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8557 (mt-10) REVERT: B 4691 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8464 (tp-100) REVERT: B 4769 MET cc_start: 0.1336 (ptm) cc_final: -0.0151 (ttt) REVERT: B 4868 ASP cc_start: 0.8730 (t70) cc_final: 0.8494 (p0) REVERT: B 4874 MET cc_start: 0.8302 (mtp) cc_final: 0.7959 (mtp) REVERT: B 4938 ASP cc_start: 0.8926 (t70) cc_final: 0.8610 (p0) REVERT: B 4963 ILE cc_start: 0.9005 (mt) cc_final: 0.8735 (mp) REVERT: B 4989 MET cc_start: 0.8048 (tmm) cc_final: 0.7688 (tmm) REVERT: B 4993 MET cc_start: 0.9205 (ttp) cc_final: 0.8789 (tmm) REVERT: B 5013 MET cc_start: 0.9053 (mtp) cc_final: 0.8654 (mmm) outliers start: 2 outliers final: 0 residues processed: 421 average time/residue: 0.3132 time to fit residues: 214.8163 Evaluate side-chains 278 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.443 ------------------------------------------------------------------------------- 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: 20.0000 chunk 24 optimal weight: 0.0770 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 0.0370 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 overall best weight: 0.2016 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN B 949 ASN B1041 GLN B1688 HIS B1719 HIS B1928 GLN B1972 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2931 GLN B3809 ASN B3833 GLN ** B3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3946 GLN B3950 ASN ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4714 ASN B4803 HIS ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 123528 Z= 0.241 Angle : 0.900 15.865 168436 Z= 0.441 Chirality : 0.048 0.486 19704 Planarity : 0.009 0.205 22192 Dihedral : 6.052 47.561 18156 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.81 % Favored : 89.07 % Rotamer: Outliers : 0.70 % Allowed : 3.60 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 1.83 % 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: -3.14 (0.07), residues: 13356 helix: -1.52 (0.06), residues: 5804 sheet: -1.73 (0.16), residues: 1016 loop : -2.69 (0.07), residues: 6536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP G2886 HIS 0.056 0.003 HIS E1688 PHE 0.048 0.003 PHE I1226 TYR 0.049 0.004 TYR G 920 ARG 0.096 0.002 ARG I 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26498 Ramachandran restraints generated. 13249 Oldfield, 0 Emsley, 13249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26498 Ramachandran restraints generated. 13249 Oldfield, 0 Emsley, 13249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7869 (tm-30) REVERT: H 47 LYS cc_start: 0.9440 (mttt) cc_final: 0.9018 (mmtm) REVERT: H 56 ILE cc_start: 0.8454 (pt) cc_final: 0.7986 (pt) outliers start: 4 outliers final: 0 residues processed: 22 average time/residue: 0.1899 time to fit residues: 4.4706 Evaluate side-chains 14 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.074 Evaluate side-chains 431 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 417 time to evaluate : 2.170 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: B 76 ARG cc_start: 0.9429 (mmt180) cc_final: 0.8940 (ttt180) REVERT: B 116 MET cc_start: 0.8756 (mtm) cc_final: 0.8356 (mtp) REVERT: B 180 LEU cc_start: 0.9295 (tp) cc_final: 0.9042 (tp) REVERT: B 390 LEU cc_start: 0.8551 (mp) cc_final: 0.8194 (mp) REVERT: B 453 GLU cc_start: 0.9010 (tp30) cc_final: 0.8771 (tp30) REVERT: B 622 THR cc_start: 0.9054 (m) cc_final: 0.8781 (p) REVERT: B 623 GLU cc_start: 0.9427 (tt0) cc_final: 0.9202 (tm-30) REVERT: B 667 MET cc_start: 0.9264 (tpt) cc_final: 0.8857 (tpp) REVERT: B 961 MET cc_start: -0.1831 (mmp) cc_final: -0.2616 (mmp) REVERT: B 1100 MET cc_start: 0.6551 (mtm) cc_final: 0.6147 (mtm) REVERT: B 1152 MET cc_start: 0.8824 (mtt) cc_final: 0.8046 (mtt) REVERT: B 1180 ARG cc_start: 0.7491 (mpt180) cc_final: 0.7226 (mmt180) REVERT: B 1608 MET cc_start: 0.8649 (mtt) cc_final: 0.8361 (mtt) REVERT: B 1695 LEU cc_start: 0.9298 (mp) cc_final: 0.8994 (mp) REVERT: B 1771 LEU cc_start: 0.8825 (mm) cc_final: 0.8567 (mm) REVERT: B 1786 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7717 (mp) REVERT: B 1935 VAL cc_start: 0.8157 (t) cc_final: 0.7901 (t) REVERT: B 2134 LEU cc_start: 0.9401 (tp) cc_final: 0.9199 (pp) REVERT: B 2155 LEU cc_start: 0.8795 (mt) cc_final: 0.8528 (mp) REVERT: B 2165 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9176 (tt) REVERT: B 2186 MET cc_start: 0.8782 (mmm) cc_final: 0.7822 (ppp) REVERT: B 2441 HIS cc_start: 0.8840 (t70) cc_final: 0.8592 (t70) REVERT: B 3673 MET cc_start: 0.8908 (ttt) cc_final: 0.8492 (ttm) REVERT: B 3715 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8547 (ttpp) REVERT: B 3716 LEU cc_start: 0.9285 (tp) cc_final: 0.8889 (tt) REVERT: B 3723 MET cc_start: 0.8872 (mtt) cc_final: 0.8632 (mmm) REVERT: B 3754 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7977 (tp30) REVERT: B 3758 MET cc_start: 0.9305 (mmp) cc_final: 0.8657 (mmm) REVERT: B 3836 MET cc_start: 0.9108 (ttm) cc_final: 0.8882 (ttp) REVERT: B 3883 ASP cc_start: 0.9559 (m-30) cc_final: 0.9277 (m-30) REVERT: B 3921 ASP cc_start: 0.9516 (t70) cc_final: 0.9251 (t0) REVERT: B 3932 ASP cc_start: 0.9421 (m-30) cc_final: 0.9070 (p0) REVERT: B 3941 ASP cc_start: 0.8508 (p0) cc_final: 0.7820 (m-30) REVERT: B 3996 PHE cc_start: 0.8897 (m-10) cc_final: 0.8240 (m-10) REVERT: B 4000 MET cc_start: 0.8716 (ttt) cc_final: 0.8392 (ttt) REVERT: B 4001 MET cc_start: 0.8565 (mmt) cc_final: 0.8323 (mmt) REVERT: B 4016 LEU cc_start: 0.8960 (tt) cc_final: 0.8479 (tt) REVERT: B 4021 LYS cc_start: 0.9658 (ttpt) cc_final: 0.9253 (tppt) REVERT: B 4026 MET cc_start: 0.9355 (ttt) cc_final: 0.8696 (tpt) REVERT: B 4028 LEU cc_start: 0.9416 (mt) cc_final: 0.9084 (mt) REVERT: B 4062 PHE cc_start: 0.8746 (m-10) cc_final: 0.8310 (m-10) REVERT: B 4097 MET cc_start: 0.6884 (tpt) cc_final: 0.6507 (tpp) REVERT: B 4168 GLU cc_start: 0.7773 (pm20) cc_final: 0.7425 (pm20) REVERT: B 4172 GLU cc_start: 0.8814 (tp30) cc_final: 0.8498 (mm-30) REVERT: B 4184 MET cc_start: 0.7787 (tpt) cc_final: 0.7362 (tpt) REVERT: B 4196 GLU cc_start: 0.7905 (tt0) cc_final: 0.7365 (tm-30) REVERT: B 4229 GLU cc_start: 0.9212 (mp0) cc_final: 0.9010 (mp0) REVERT: B 4239 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8270 (mt-10) REVERT: B 4240 ASP cc_start: 0.9021 (t70) cc_final: 0.8814 (p0) REVERT: B 4652 LEU cc_start: 0.9717 (tt) cc_final: 0.9392 (pp) REVERT: B 4769 MET cc_start: 0.1502 (ptm) cc_final: 0.0124 (ttt) REVERT: B 4874 MET cc_start: 0.8318 (mtp) cc_final: 0.7995 (mtp) REVERT: B 4963 ILE cc_start: 0.9061 (mt) cc_final: 0.8808 (mp) REVERT: B 4993 MET cc_start: 0.9131 (ttp) cc_final: 0.8915 (ttp) REVERT: B 5013 MET cc_start: 0.9007 (mtp) cc_final: 0.8625 (mmm) outliers start: 14 outliers final: 3 residues processed: 422 average time/residue: 0.2875 time to fit residues: 200.8846 Evaluate side-chains 296 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 291 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 0.0970 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN B2007 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN B4714 ASN ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 123528 Z= 0.234 Angle : 0.861 20.319 168436 Z= 0.426 Chirality : 0.046 0.600 19704 Planarity : 0.010 0.258 22192 Dihedral : 6.015 52.427 18156 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.87 % Favored : 88.98 % Rotamer: Outliers : 0.31 % Allowed : 3.10 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 1.83 % 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: -3.05 (0.07), residues: 13356 helix: -1.41 (0.06), residues: 5832 sheet: -1.68 (0.16), residues: 1012 loop : -2.69 (0.07), residues: 6512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP G 276 HIS 0.028 0.003 HIS B3982 PHE 0.075 0.004 PHE B2340 TYR 0.080 0.004 TYR B3720 ARG 0.045 0.002 ARG G4189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26292 Ramachandran restraints generated. 13146 Oldfield, 0 Emsley, 13146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26292 Ramachandran restraints generated. 13146 Oldfield, 0 Emsley, 13146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7816 (tm-30) REVERT: A 30 LEU cc_start: 0.9400 (tp) cc_final: 0.9141 (tt) REVERT: A 34 LYS cc_start: 0.4397 (mmtt) cc_final: 0.3948 (pttt) REVERT: A 47 LYS cc_start: 0.9502 (mttt) cc_final: 0.9063 (mmtm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1595 time to fit residues: 3.9535 Evaluate side-chains 16 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.106 Evaluate side-chains 391 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 383 time to evaluate : 2.174 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: B 76 ARG cc_start: 0.9389 (mmt180) cc_final: 0.9024 (ptm160) REVERT: B 81 MET cc_start: 0.9028 (tmm) cc_final: 0.8585 (tmm) REVERT: B 116 MET cc_start: 0.8803 (mtm) cc_final: 0.8425 (mtp) REVERT: B 180 LEU cc_start: 0.9282 (tp) cc_final: 0.9065 (tp) REVERT: B 390 LEU cc_start: 0.8557 (mp) cc_final: 0.8279 (mp) REVERT: B 453 GLU cc_start: 0.9025 (tp30) cc_final: 0.8797 (tp30) REVERT: B 622 THR cc_start: 0.9063 (m) cc_final: 0.8754 (p) REVERT: B 623 GLU cc_start: 0.9473 (tt0) cc_final: 0.9229 (tm-30) REVERT: B 667 MET cc_start: 0.9251 (tpt) cc_final: 0.8844 (tpp) REVERT: B 961 MET cc_start: -0.2175 (mmp) cc_final: -0.2606 (mmp) REVERT: B 1091 GLU cc_start: 0.7216 (tt0) cc_final: 0.6736 (pt0) REVERT: B 1152 MET cc_start: 0.8720 (mtt) cc_final: 0.8178 (mtt) REVERT: B 1608 MET cc_start: 0.8646 (mtt) cc_final: 0.8061 (mtt) REVERT: B 1713 ASP cc_start: 0.8601 (m-30) cc_final: 0.7785 (t0) REVERT: B 1771 LEU cc_start: 0.8831 (mm) cc_final: 0.8619 (mm) REVERT: B 1935 VAL cc_start: 0.8140 (t) cc_final: 0.7888 (t) REVERT: B 2134 LEU cc_start: 0.9429 (tp) cc_final: 0.9197 (pp) REVERT: B 2155 LEU cc_start: 0.8791 (mt) cc_final: 0.8495 (mt) REVERT: B 2165 LEU cc_start: 0.9487 (mp) cc_final: 0.9115 (tt) REVERT: B 2186 MET cc_start: 0.8843 (mmm) cc_final: 0.8199 (ppp) REVERT: B 2250 MET cc_start: 0.9164 (mmp) cc_final: 0.8671 (mmm) REVERT: B 2441 HIS cc_start: 0.8840 (t70) cc_final: 0.8589 (t70) REVERT: B 3673 MET cc_start: 0.8906 (ttt) cc_final: 0.8555 (ttm) REVERT: B 3715 LYS cc_start: 0.9162 (mtpt) cc_final: 0.8520 (ttpp) REVERT: B 3716 LEU cc_start: 0.9312 (tp) cc_final: 0.8903 (tt) REVERT: B 3754 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8052 (tp30) REVERT: B 3758 MET cc_start: 0.9306 (mmp) cc_final: 0.8824 (mmm) REVERT: B 3829 PHE cc_start: 0.9104 (m-80) cc_final: 0.8771 (m-10) REVERT: B 3836 MET cc_start: 0.9207 (ttm) cc_final: 0.8906 (ttp) REVERT: B 3883 ASP cc_start: 0.9595 (m-30) cc_final: 0.9287 (m-30) REVERT: B 3932 ASP cc_start: 0.9449 (m-30) cc_final: 0.9059 (p0) REVERT: B 3986 TRP cc_start: 0.7877 (m100) cc_final: 0.7603 (m100) REVERT: B 4000 MET cc_start: 0.8715 (ttt) cc_final: 0.8455 (ttt) REVERT: B 4001 MET cc_start: 0.8789 (mmt) cc_final: 0.8559 (mmt) REVERT: B 4021 LYS cc_start: 0.9594 (ttpt) cc_final: 0.9191 (tppt) REVERT: B 4026 MET cc_start: 0.9390 (ttt) cc_final: 0.8689 (tpt) REVERT: B 4028 LEU cc_start: 0.9286 (mt) cc_final: 0.9067 (mt) REVERT: B 4050 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8721 (mm-30) REVERT: B 4062 PHE cc_start: 0.8721 (m-10) cc_final: 0.8299 (m-10) REVERT: B 4097 MET cc_start: 0.6758 (tpt) cc_final: 0.6427 (tpp) REVERT: B 4196 GLU cc_start: 0.7768 (tt0) cc_final: 0.7183 (tm-30) REVERT: B 4652 LEU cc_start: 0.9715 (tt) cc_final: 0.9394 (pp) REVERT: B 4769 MET cc_start: 0.1329 (ptm) cc_final: -0.0098 (ttt) REVERT: B 4874 MET cc_start: 0.8350 (mtp) cc_final: 0.8010 (mtp) REVERT: B 4989 MET cc_start: 0.7998 (tmm) cc_final: 0.7657 (tmm) REVERT: B 5013 MET cc_start: 0.9029 (mtp) cc_final: 0.8633 (mmm) outliers start: 8 outliers final: 2 residues processed: 388 average time/residue: 0.3014 time to fit residues: 193.8468 Evaluate side-chains 281 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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: 50.0000 chunk 15 optimal weight: 40.0000 chunk 32 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.0670 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.8274 ------------------------------------------------------------------------------- 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 111 HIS ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN B4204 GLN ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4691 GLN B4714 ASN ** B4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 123528 Z= 0.239 Angle : 0.862 20.319 168436 Z= 0.426 Chirality : 0.046 0.600 19704 Planarity : 0.010 0.258 22192 Dihedral : 6.015 52.427 18156 Min Nonbonded Distance : 0.707 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.87 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 1.83 % 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: -3.05 (0.07), residues: 13356 helix: -1.41 (0.06), residues: 5832 sheet: -1.68 (0.16), residues: 1012 loop : -2.69 (0.07), residues: 6512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP B 276 HIS 0.028 0.003 HIS B3982 PHE 0.075 0.004 PHE B2340 TYR 0.080 0.004 TYR B3720 ARG 0.045 0.002 ARG G4189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26292 Ramachandran restraints generated. 13146 Oldfield, 0 Emsley, 13146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26292 Ramachandran restraints generated. 13146 Oldfield, 0 Emsley, 13146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 3 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7873 (tm-30) REVERT: F 30 LEU cc_start: 0.9391 (tp) cc_final: 0.9165 (tt) REVERT: F 34 LYS cc_start: 0.4365 (mmtt) cc_final: 0.3935 (pttt) REVERT: F 47 LYS cc_start: 0.9487 (mttt) cc_final: 0.9067 (mmtm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1279 time to fit residues: 2.9601 Evaluate side-chains 16 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.089 Evaluate side-chains 363 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.177 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 76 ARG cc_start: 0.9384 (mmt180) cc_final: 0.9018 (ptm160) REVERT: B 81 MET cc_start: 0.9029 (tmm) cc_final: 0.8584 (tmm) REVERT: B 116 MET cc_start: 0.8796 (mtm) cc_final: 0.8439 (mtp) REVERT: B 180 LEU cc_start: 0.9292 (tp) cc_final: 0.9068 (tp) REVERT: B 390 LEU cc_start: 0.8543 (mp) cc_final: 0.8261 (mp) REVERT: B 453 GLU cc_start: 0.9022 (tp30) cc_final: 0.8793 (tp30) REVERT: B 622 THR cc_start: 0.9055 (m) cc_final: 0.8748 (p) REVERT: B 623 GLU cc_start: 0.9473 (tt0) cc_final: 0.9229 (tm-30) REVERT: B 667 MET cc_start: 0.9248 (tpt) cc_final: 0.8855 (tpp) REVERT: B 1091 GLU cc_start: 0.7209 (tt0) cc_final: 0.6737 (pt0) REVERT: B 1152 MET cc_start: 0.8724 (mtt) cc_final: 0.8176 (mtt) REVERT: B 1601 MET cc_start: 0.8476 (mpp) cc_final: 0.8260 (mmt) REVERT: B 1608 MET cc_start: 0.8645 (mtt) cc_final: 0.8062 (mtt) REVERT: B 1713 ASP cc_start: 0.8576 (m-30) cc_final: 0.7777 (t0) REVERT: B 1771 LEU cc_start: 0.8839 (mm) cc_final: 0.8622 (mm) REVERT: B 1935 VAL cc_start: 0.8182 (t) cc_final: 0.7887 (t) REVERT: B 2134 LEU cc_start: 0.9425 (tp) cc_final: 0.9198 (pp) REVERT: B 2155 LEU cc_start: 0.8799 (mt) cc_final: 0.8493 (mt) REVERT: B 2165 LEU cc_start: 0.9474 (mp) cc_final: 0.9111 (tt) REVERT: B 2186 MET cc_start: 0.8855 (mmm) cc_final: 0.8200 (ppp) REVERT: B 2250 MET cc_start: 0.9173 (mmp) cc_final: 0.8671 (mmm) REVERT: B 2441 HIS cc_start: 0.8838 (t70) cc_final: 0.8590 (t70) REVERT: B 3673 MET cc_start: 0.8925 (ttt) cc_final: 0.8562 (ttm) REVERT: B 3715 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8513 (ttpp) REVERT: B 3754 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8060 (tp30) REVERT: B 3758 MET cc_start: 0.9270 (mmp) cc_final: 0.8847 (mmm) REVERT: B 3829 PHE cc_start: 0.9164 (m-80) cc_final: 0.8785 (m-10) REVERT: B 3836 MET cc_start: 0.9182 (ttm) cc_final: 0.8918 (ttp) REVERT: B 3883 ASP cc_start: 0.9602 (m-30) cc_final: 0.9287 (m-30) REVERT: B 3921 ASP cc_start: 0.9537 (t70) cc_final: 0.9333 (t0) REVERT: B 3932 ASP cc_start: 0.9448 (m-30) cc_final: 0.9064 (p0) REVERT: B 3941 ASP cc_start: 0.8395 (p0) cc_final: 0.7762 (m-30) REVERT: B 3986 TRP cc_start: 0.7860 (m100) cc_final: 0.7597 (m100) REVERT: B 4000 MET cc_start: 0.8756 (ttt) cc_final: 0.8448 (ttt) REVERT: B 4001 MET cc_start: 0.8802 (mmt) cc_final: 0.8574 (mmt) REVERT: B 4021 LYS cc_start: 0.9579 (ttpt) cc_final: 0.9185 (tppt) REVERT: B 4026 MET cc_start: 0.9392 (ttt) cc_final: 0.8693 (tpt) REVERT: B 4028 LEU cc_start: 0.9285 (mt) cc_final: 0.9072 (mt) REVERT: B 4044 MET cc_start: 0.8883 (mmp) cc_final: 0.8333 (mmm) REVERT: B 4050 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 4062 PHE cc_start: 0.8732 (m-10) cc_final: 0.8297 (m-10) REVERT: B 4097 MET cc_start: 0.6745 (tpt) cc_final: 0.6409 (tpp) REVERT: B 4196 GLU cc_start: 0.7751 (tt0) cc_final: 0.7173 (tm-30) REVERT: B 4229 GLU cc_start: 0.9132 (mp0) cc_final: 0.8924 (mp0) REVERT: B 4652 LEU cc_start: 0.9712 (tt) cc_final: 0.9376 (pp) REVERT: B 4769 MET cc_start: 0.1273 (ptm) cc_final: -0.0136 (ttt) REVERT: B 4796 MET cc_start: 0.9019 (tpp) cc_final: 0.8467 (tpt) REVERT: B 4874 MET cc_start: 0.8345 (mtp) cc_final: 0.8009 (mtp) REVERT: B 4989 MET cc_start: 0.7944 (tmm) cc_final: 0.7657 (tmm) REVERT: B 5013 MET cc_start: 0.9027 (mtp) cc_final: 0.8636 (mmm) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3085 time to fit residues: 186.9049 Evaluate side-chains 275 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.212 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.0020 chunk 22 optimal weight: 40.0000 chunk 28 optimal weight: 4.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN B1972 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN B4204 GLN B4691 GLN B4714 ASN ** B4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 123528 Z= 0.237 Angle : 0.840 18.463 168436 Z= 0.413 Chirality : 0.048 0.492 19704 Planarity : 0.008 0.222 22192 Dihedral : 5.949 51.026 18156 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.08 % Favored : 88.77 % Rotamer: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 1.83 % 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: -3.01 (0.07), residues: 13356 helix: -1.34 (0.06), residues: 5796 sheet: -1.73 (0.16), residues: 972 loop : -2.69 (0.07), residues: 6588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP E 276 HIS 0.028 0.002 HIS B3982 PHE 0.051 0.003 PHE E2340 TYR 0.069 0.004 TYR B1670 ARG 0.044 0.002 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26292 Ramachandran restraints generated. 13146 Oldfield, 0 Emsley, 13146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26292 Ramachandran restraints generated. 13146 Oldfield, 0 Emsley, 13146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 3 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8070 (tm-30) REVERT: F 30 LEU cc_start: 0.9331 (tp) cc_final: 0.9047 (tt) REVERT: F 34 LYS cc_start: 0.4572 (mmtt) cc_final: 0.3639 (pttt) REVERT: F 47 LYS cc_start: 0.9454 (mttt) cc_final: 0.8996 (mmtm) REVERT: F 66 MET cc_start: 0.8801 (tpp) cc_final: 0.8447 (tpp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1324 time to fit residues: 2.9333 Evaluate side-chains 16 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.078 Evaluate side-chains 371 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 370 time to evaluate : 2.202 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: B 76 ARG cc_start: 0.9410 (mmt180) cc_final: 0.9086 (ttt180) REVERT: B 81 MET cc_start: 0.9048 (tmm) cc_final: 0.8615 (tmm) REVERT: B 116 MET cc_start: 0.8871 (mtm) cc_final: 0.8511 (mtp) REVERT: B 180 LEU cc_start: 0.9297 (tp) cc_final: 0.9070 (tp) REVERT: B 453 GLU cc_start: 0.9021 (tp30) cc_final: 0.8807 (tp30) REVERT: B 623 GLU cc_start: 0.9469 (tt0) cc_final: 0.9208 (tm-30) REVERT: B 667 MET cc_start: 0.9261 (tpt) cc_final: 0.8857 (tpp) REVERT: B 1091 GLU cc_start: 0.7146 (tt0) cc_final: 0.6613 (pt0) REVERT: B 1152 MET cc_start: 0.8748 (mtt) cc_final: 0.8188 (mtt) REVERT: B 1608 MET cc_start: 0.8631 (mtt) cc_final: 0.8067 (mtt) REVERT: B 1771 LEU cc_start: 0.8852 (mm) cc_final: 0.8632 (mm) REVERT: B 1935 VAL cc_start: 0.8166 (t) cc_final: 0.7651 (t) REVERT: B 1939 MET cc_start: 0.9170 (mtp) cc_final: 0.8921 (mtp) REVERT: B 2120 MET cc_start: 0.9182 (ttt) cc_final: 0.8619 (tpp) REVERT: B 2134 LEU cc_start: 0.9421 (tp) cc_final: 0.9203 (pp) REVERT: B 2155 LEU cc_start: 0.8807 (mt) cc_final: 0.8480 (mt) REVERT: B 2165 LEU cc_start: 0.9522 (mp) cc_final: 0.9211 (tt) REVERT: B 2186 MET cc_start: 0.8851 (mmm) cc_final: 0.8176 (ppp) REVERT: B 2250 MET cc_start: 0.9159 (mmp) cc_final: 0.8645 (mmm) REVERT: B 2441 HIS cc_start: 0.8845 (t70) cc_final: 0.8588 (t70) REVERT: B 3715 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8528 (ttpp) REVERT: B 3716 LEU cc_start: 0.9242 (tp) cc_final: 0.8943 (tt) REVERT: B 3723 MET cc_start: 0.8773 (mmm) cc_final: 0.8454 (mmm) REVERT: B 3754 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7881 (tp30) REVERT: B 3758 MET cc_start: 0.9171 (mmp) cc_final: 0.8807 (mmm) REVERT: B 3804 ILE cc_start: 0.9459 (mm) cc_final: 0.9224 (mm) REVERT: B 3829 PHE cc_start: 0.9131 (m-80) cc_final: 0.8809 (m-10) REVERT: B 3836 MET cc_start: 0.9184 (ttm) cc_final: 0.8659 (ttp) REVERT: B 3883 ASP cc_start: 0.9599 (m-30) cc_final: 0.9287 (m-30) REVERT: B 3891 LEU cc_start: 0.9504 (mt) cc_final: 0.9275 (mt) REVERT: B 3932 ASP cc_start: 0.9459 (m-30) cc_final: 0.9085 (p0) REVERT: B 3941 ASP cc_start: 0.8546 (p0) cc_final: 0.7917 (m-30) REVERT: B 3986 TRP cc_start: 0.7845 (m100) cc_final: 0.7609 (m100) REVERT: B 3995 VAL cc_start: 0.9103 (t) cc_final: 0.8771 (t) REVERT: B 3996 PHE cc_start: 0.8959 (m-80) cc_final: 0.8712 (m-10) REVERT: B 4000 MET cc_start: 0.8842 (ttt) cc_final: 0.8544 (ttt) REVERT: B 4020 GLN cc_start: 0.8967 (mp10) cc_final: 0.8624 (mp10) REVERT: B 4021 LYS cc_start: 0.9625 (ttpt) cc_final: 0.9223 (tppt) REVERT: B 4026 MET cc_start: 0.9381 (ttt) cc_final: 0.8667 (tpt) REVERT: B 4028 LEU cc_start: 0.9293 (mt) cc_final: 0.9044 (mt) REVERT: B 4044 MET cc_start: 0.8903 (mmp) cc_final: 0.8624 (mmm) REVERT: B 4062 PHE cc_start: 0.8700 (m-10) cc_final: 0.8231 (m-10) REVERT: B 4097 MET cc_start: 0.6910 (tpt) cc_final: 0.6607 (tpp) REVERT: B 4196 GLU cc_start: 0.7673 (tt0) cc_final: 0.7141 (tm-30) REVERT: B 4229 GLU cc_start: 0.9131 (mp0) cc_final: 0.8923 (mp0) REVERT: B 4652 LEU cc_start: 0.9715 (tt) cc_final: 0.9390 (pp) REVERT: B 4769 MET cc_start: 0.1278 (ptm) cc_final: -0.0106 (ttt) REVERT: B 4796 MET cc_start: 0.8958 (tpp) cc_final: 0.8370 (tpt) REVERT: B 4874 MET cc_start: 0.8075 (mtp) cc_final: 0.7733 (mtp) REVERT: B 4989 MET cc_start: 0.7988 (tmm) cc_final: 0.7654 (tmm) REVERT: B 5013 MET cc_start: 0.9005 (mtp) cc_final: 0.8622 (mmm) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.2896 time to fit residues: 180.3048 Evaluate side-chains 274 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.509 > 50: distance: 0 - 1: 18.906 distance: 1 - 2: 26.844 distance: 1 - 4: 16.766 distance: 2 - 3: 39.022 distance: 2 - 7: 15.386 distance: 4 - 5: 30.541 distance: 4 - 6: 41.411 distance: 7 - 8: 8.459 distance: 8 - 9: 20.298 distance: 8 - 11: 8.554 distance: 9 - 10: 28.487 distance: 9 - 12: 17.883 distance: 12 - 13: 37.365 distance: 13 - 14: 16.884 distance: 13 - 16: 20.072 distance: 14 - 15: 49.777 distance: 14 - 24: 15.182 distance: 16 - 17: 14.577 distance: 17 - 18: 8.498 distance: 17 - 19: 10.380 distance: 18 - 20: 28.482 distance: 19 - 21: 19.312 distance: 20 - 22: 9.282 distance: 21 - 22: 10.171 distance: 22 - 23: 16.109 distance: 24 - 25: 24.230 distance: 25 - 26: 29.697 distance: 26 - 27: 20.591 distance: 26 - 28: 15.436 distance: 28 - 29: 26.807 distance: 29 - 30: 12.020 distance: 29 - 32: 16.259 distance: 30 - 31: 27.639 distance: 30 - 33: 38.946 distance: 33 - 34: 17.152 distance: 34 - 35: 19.586 distance: 34 - 37: 26.545 distance: 35 - 36: 30.914 distance: 35 - 40: 32.644 distance: 37 - 38: 34.136 distance: 37 - 39: 30.403 distance: 40 - 41: 26.226 distance: 41 - 42: 24.944 distance: 42 - 43: 28.732 distance: 42 - 44: 43.607 distance: 44 - 45: 11.783 distance: 45 - 46: 22.189 distance: 45 - 48: 47.181 distance: 46 - 47: 38.889 distance: 46 - 54: 7.602 distance: 48 - 49: 16.454 distance: 49 - 50: 33.349 distance: 49 - 51: 32.630 distance: 50 - 52: 27.334 distance: 51 - 53: 62.722 distance: 52 - 53: 52.407 distance: 54 - 55: 40.045 distance: 54 - 60: 40.005 distance: 55 - 56: 25.673 distance: 55 - 58: 44.029 distance: 56 - 57: 20.672 distance: 56 - 61: 32.368 distance: 58 - 59: 24.513 distance: 59 - 60: 39.605 distance: 62 - 63: 25.581 distance: 63 - 64: 17.426