Starting phenix.real_space_refine on Wed Mar 20 11:01:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x34_22017/03_2024/6x34_22017_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x34_22017/03_2024/6x34_22017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x34_22017/03_2024/6x34_22017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x34_22017/03_2024/6x34_22017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x34_22017/03_2024/6x34_22017_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x34_22017/03_2024/6x34_22017_neut.pdb" } resolution = 4.7 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= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 368 5.16 5 C 62484 2.51 5 N 17484 2.21 5 O 17548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 1110": "NH1" <-> "NH2" Residue "B ARG 1259": "NH1" <-> "NH2" Residue "B ARG 1271": "NH1" <-> "NH2" Residue "B ARG 1290": "NH1" <-> "NH2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B GLU 1644": "OE1" <-> "OE2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1798": "NH1" <-> "NH2" Residue "B GLU 2349": "OE1" <-> "OE2" Residue "B ARG 2453": "NH1" <-> "NH2" Residue "B ARG 2455": "NH1" <-> "NH2" Residue "B GLU 3661": "OE1" <-> "OE2" Residue "B GLU 3714": "OE1" <-> "OE2" Residue "B ARG 3881": "NH1" <-> "NH2" Residue "B ARG 3944": "NH1" <-> "NH2" Residue "B ARG 4037": "NH1" <-> "NH2" Residue "B ARG 4187": "NH1" <-> "NH2" Residue "B ARG 4671": "NH1" <-> "NH2" Residue "B ARG 4734": "NH1" <-> "NH2" Residue "B PHE 4805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4858": "NH1" <-> "NH2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "D ARG 683": "NH1" <-> "NH2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ARG 1110": "NH1" <-> "NH2" Residue "D ARG 1259": "NH1" <-> "NH2" Residue "D ARG 1271": "NH1" <-> "NH2" Residue "D ARG 1290": "NH1" <-> "NH2" Residue "D ARG 1594": "NH1" <-> "NH2" Residue "D GLU 1644": "OE1" <-> "OE2" Residue "D ARG 1656": "NH1" <-> "NH2" Residue "D ARG 1725": "NH1" <-> "NH2" Residue "D ARG 1798": "NH1" <-> "NH2" Residue "D GLU 2349": "OE1" <-> "OE2" Residue "D ARG 2453": "NH1" <-> "NH2" Residue "D ARG 2455": "NH1" <-> "NH2" Residue "D GLU 3661": "OE1" <-> "OE2" Residue "D GLU 3714": "OE1" <-> "OE2" Residue "D ARG 3881": "NH1" <-> "NH2" Residue "D ARG 3944": "NH1" <-> "NH2" Residue "D ARG 4037": "NH1" <-> "NH2" Residue "D ARG 4187": "NH1" <-> "NH2" Residue "D ARG 4671": "NH1" <-> "NH2" Residue "D ARG 4734": "NH1" <-> "NH2" Residue "D PHE 4805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4858": "NH1" <-> "NH2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F GLU 462": "OE1" <-> "OE2" Residue "F ARG 474": "NH1" <-> "NH2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "F ARG 683": "NH1" <-> "NH2" Residue "F ARG 835": "NH1" <-> "NH2" Residue "F ARG 1110": "NH1" <-> "NH2" Residue "F ARG 1259": "NH1" <-> "NH2" Residue "F ARG 1271": "NH1" <-> "NH2" Residue "F ARG 1290": "NH1" <-> "NH2" Residue "F ARG 1594": "NH1" <-> "NH2" Residue "F GLU 1644": "OE1" <-> "OE2" Residue "F ARG 1656": "NH1" <-> "NH2" Residue "F ARG 1725": "NH1" <-> "NH2" Residue "F ARG 1798": "NH1" <-> "NH2" Residue "F GLU 2349": "OE1" <-> "OE2" Residue "F ARG 2453": "NH1" <-> "NH2" Residue "F ARG 2455": "NH1" <-> "NH2" Residue "F GLU 3661": "OE1" <-> "OE2" Residue "F GLU 3714": "OE1" <-> "OE2" Residue "F ARG 3881": "NH1" <-> "NH2" Residue "F ARG 3944": "NH1" <-> "NH2" Residue "F ARG 4037": "NH1" <-> "NH2" Residue "F ARG 4187": "NH1" <-> "NH2" Residue "F ARG 4671": "NH1" <-> "NH2" Residue "F ARG 4734": "NH1" <-> "NH2" Residue "F PHE 4805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4858": "NH1" <-> "NH2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H GLU 462": "OE1" <-> "OE2" Residue "H ARG 474": "NH1" <-> "NH2" Residue "H ARG 553": "NH1" <-> "NH2" Residue "H ARG 683": "NH1" <-> "NH2" Residue "H ARG 835": "NH1" <-> "NH2" Residue "H ARG 1110": "NH1" <-> "NH2" Residue "H ARG 1259": "NH1" <-> "NH2" Residue "H ARG 1271": "NH1" <-> "NH2" Residue "H ARG 1290": "NH1" <-> "NH2" Residue "H ARG 1594": "NH1" <-> "NH2" Residue "H GLU 1644": "OE1" <-> "OE2" Residue "H ARG 1656": "NH1" <-> "NH2" Residue "H ARG 1725": "NH1" <-> "NH2" Residue "H ARG 1798": "NH1" <-> "NH2" Residue "H GLU 2349": "OE1" <-> "OE2" Residue "H ARG 2453": "NH1" <-> "NH2" Residue "H ARG 2455": "NH1" <-> "NH2" Residue "H GLU 3661": "OE1" <-> "OE2" Residue "H GLU 3714": "OE1" <-> "OE2" Residue "H ARG 3881": "NH1" <-> "NH2" Residue "H ARG 3944": "NH1" <-> "NH2" Residue "H ARG 4037": "NH1" <-> "NH2" Residue "H ARG 4187": "NH1" <-> "NH2" Residue "H ARG 4671": "NH1" <-> "NH2" Residue "H ARG 4734": "NH1" <-> "NH2" Residue "H PHE 4805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4858": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 97888 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 659 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 23812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5792 Unresolved non-hydrogen angles: 7380 Unresolved non-hydrogen dihedrals: 4543 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 Conformer: "B" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5792 Unresolved non-hydrogen angles: 7380 Unresolved non-hydrogen dihedrals: 4543 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 bond proxies already assigned to first conformer: 24205 Chain: "C" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 659 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 23812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5792 Unresolved non-hydrogen angles: 7380 Unresolved non-hydrogen dihedrals: 4543 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 Conformer: "B" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5792 Unresolved non-hydrogen angles: 7380 Unresolved non-hydrogen dihedrals: 4543 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 bond proxies already assigned to first conformer: 24205 Chain: "E" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 659 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "F" Number of atoms: 23812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5795 Unresolved non-hydrogen angles: 7383 Unresolved non-hydrogen dihedrals: 4546 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 Conformer: "B" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5795 Unresolved non-hydrogen angles: 7383 Unresolved non-hydrogen dihedrals: 4546 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 bond proxies already assigned to first conformer: 24205 Chain: "G" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 659 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 23812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5792 Unresolved non-hydrogen angles: 7380 Unresolved non-hydrogen dihedrals: 4543 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 Conformer: "B" Number of residues, atoms: 3715, 23797 Classifications: {'peptide': 3715} Incomplete info: {'truncation_to_alanine': 1696} Link IDs: {'PTRANS': 154, 'TRANS': 3560} Chain breaks: 58 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5792 Unresolved non-hydrogen angles: 7380 Unresolved non-hydrogen dihedrals: 4543 Unresolved non-hydrogen chiralities: 305 Planarities with less than four sites: {'GLN:plan1': 78, 'UNK:plan-1': 329, 'ASP:plan': 139, 'TYR:plan': 31, 'ASN:plan1': 57, 'TRP:plan': 12, 'HIS:plan': 33, 'PHE:plan': 33, 'GLU:plan': 230, 'ARG:plan': 135} Unresolved non-hydrogen planarities: 3512 bond proxies already assigned to first conformer: 24205 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23998 SG CYS B4959 206.836 179.289 84.554 1.00137.67 S ATOM 48469 SG CYS D4959 179.315 176.765 84.555 1.00137.67 S ATOM 72940 SG CYS F4959 176.791 204.287 84.557 1.00137.67 S ATOM 97411 SG CYS H4959 204.311 206.811 84.556 1.00137.67 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALYS B2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS B2750 " occ=0.50 residue: pdb=" N ALYS D2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS D2750 " occ=0.50 residue: pdb=" N ALYS F2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS F2750 " occ=0.50 residue: pdb=" N ALYS H2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS H2750 " occ=0.50 Time building chain proxies: 72.32, per 1000 atoms: 0.74 Number of scatterers: 97888 At special positions: 0 Unit cell: (385, 385, 205.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 368 16.00 O 17548 8.00 N 17484 7.00 C 62484 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: 27.34 Conformation dependent library (CDL) restraints added in 26.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4959 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4981 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4976 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4959 " pdb="ZN ZN D5101 " - pdb=" ND1 HIS D4981 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4976 " pdb=" ZN F5101 " pdb="ZN ZN F5101 " - pdb=" SG CYS F4959 " pdb="ZN ZN F5101 " - pdb=" ND1 HIS F4981 " pdb="ZN ZN F5101 " - pdb=" NE2 HIS F4976 " pdb=" ZN H5101 " pdb="ZN ZN H5101 " - pdb=" SG CYS H4959 " pdb="ZN ZN H5101 " - pdb=" ND1 HIS H4981 " pdb="ZN ZN H5101 " - pdb=" NE2 HIS H4976 " 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28848 Finding SS restraints... Secondary structure from input PDB file: 604 helices and 108 sheets defined 59.2% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.56 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.693A pdb=" N GLN A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 394 through 424 removed outlier: 3.701A pdb=" N SER B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 removed outlier: 3.795A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 451 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 480 Processing helix chain 'B' and resid 482 through 496 removed outlier: 3.914A pdb=" N LEU B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.517A pdb=" N PHE B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 Processing helix chain 'B' and resid 533 through 540 removed outlier: 4.136A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 571 removed outlier: 4.077A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.163A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 578' Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.731A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 608 removed outlier: 4.166A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 601 " --> pdb=" O HIS B 597 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 626 removed outlier: 3.648A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 889 removed outlier: 3.653A pdb=" N GLU B 868 " --> pdb=" O PRO B 864 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 934 Processing helix chain 'B' and resid 981 through 1003 Processing helix chain 'B' and resid 1028 through 1050 removed outlier: 3.850A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS B1040 " --> pdb=" O ARG B1036 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1216 removed outlier: 3.671A pdb=" N ILE B1216 " --> pdb=" O PHE B1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1213 through 1216' Processing helix chain 'B' and resid 1217 through 1222 Processing helix chain 'B' and resid 1575 through 1580 removed outlier: 3.561A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) Processing helix chain 'B' and resid 1656 through 1674 removed outlier: 3.562A pdb=" N GLN B1660 " --> pdb=" O ARG B1656 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B1661 " --> pdb=" O LEU B1657 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS B1674 " --> pdb=" O TYR B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1679 through 1689 removed outlier: 3.668A pdb=" N HIS B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 removed outlier: 3.586A pdb=" N LEU B1694 " --> pdb=" O ASP B1690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B1695 " --> pdb=" O GLN B1691 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1720 Processing helix chain 'B' and resid 1721 through 1729 removed outlier: 3.752A pdb=" N ARG B1725 " --> pdb=" O GLU B1721 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.507A pdb=" N ALA B1744 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1826 Processing helix chain 'B' and resid 1830 through 1833 Processing helix chain 'B' and resid 1834 through 1852 removed outlier: 3.593A pdb=" N GLN B1838 " --> pdb=" O SER B1834 " (cutoff:3.500A) Proline residue: B1841 - end of helix removed outlier: 3.705A pdb=" N MET B1852 " --> pdb=" O THR B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1856 through 1868 Processing helix chain 'B' and resid 1933 through 1984 removed outlier: 4.125A pdb=" N LYS B1983 " --> pdb=" O GLY B1979 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B1984 " --> pdb=" O ILE B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 2000 Processing helix chain 'B' and resid 2002 through 2011 Processing helix chain 'B' and resid 2025 through 2044 removed outlier: 3.952A pdb=" N ARG B2029 " --> pdb=" O PRO B2025 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B2031 " --> pdb=" O GLU B2027 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2110 removed outlier: 4.204A pdb=" N ASP B2110 " --> pdb=" O TRP B2106 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2130 Processing helix chain 'B' and resid 2131 through 2138 Processing helix chain 'B' and resid 2149 through 2169 Processing helix chain 'B' and resid 2172 through 2188 removed outlier: 3.555A pdb=" N MET B2187 " --> pdb=" O ILE B2183 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN B2188 " --> pdb=" O GLY B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 removed outlier: 3.861A pdb=" N PHE B2192 " --> pdb=" O ASN B2189 " (cutoff:3.500A) Processing helix chain 'B' and resid 2195 through 2203 Processing helix chain 'B' and resid 2203 through 2216 Processing helix chain 'B' and resid 2226 through 2242 removed outlier: 3.638A pdb=" N ARG B2242 " --> pdb=" O CYS B2238 " (cutoff:3.500A) Processing helix chain 'B' and resid 2244 through 2252 Processing helix chain 'B' and resid 2254 through 2263 removed outlier: 3.653A pdb=" N GLY B2263 " --> pdb=" O LEU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2282 removed outlier: 3.575A pdb=" N VAL B2276 " --> pdb=" O THR B2272 " (cutoff:3.500A) Processing helix chain 'B' and resid 2285 through 2290 Processing helix chain 'B' and resid 2292 through 2307 removed outlier: 4.189A pdb=" N LEU B2296 " --> pdb=" O GLN B2292 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B2307 " --> pdb=" O LEU B2303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2317 removed outlier: 3.531A pdb=" N ALA B2316 " --> pdb=" O PRO B2312 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B2317 " --> pdb=" O MET B2313 " (cutoff:3.500A) Processing helix chain 'B' and resid 2325 through 2341 removed outlier: 4.134A pdb=" N PHE B2335 " --> pdb=" O ARG B2331 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B2336 " --> pdb=" O TYR B2332 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B2341 " --> pdb=" O ARG B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2360 Processing helix chain 'B' and resid 2361 through 2365 removed outlier: 3.543A pdb=" N CYS B2364 " --> pdb=" O LYS B2361 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B2365 " --> pdb=" O PRO B2362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2361 through 2365' Processing helix chain 'B' and resid 2378 through 2385 Processing helix chain 'B' and resid 2423 through 2437 Processing helix chain 'B' and resid 2441 through 2446 Processing helix chain 'B' and resid 2449 through 2462 removed outlier: 4.304A pdb=" N ARG B2453 " --> pdb=" O GLY B2449 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE B2454 " --> pdb=" O GLU B2450 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B2461 " --> pdb=" O ILE B2457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B2462 " --> pdb=" O LEU B2458 " (cutoff:3.500A) Processing helix chain 'B' and resid 2463 through 2472 removed outlier: 3.610A pdb=" N LEU B2467 " --> pdb=" O PRO B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2496 through 2511 removed outlier: 4.356A pdb=" N LYS B2500 " --> pdb=" O VAL B2496 " (cutoff:3.500A) Processing helix chain 'B' and resid 2519 through 2527 Processing helix chain 'B' and resid 2549 through 2558 removed outlier: 3.656A pdb=" N LEU B2555 " --> pdb=" O LEU B2551 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS B2556 " --> pdb=" O ASN B2552 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B2558 " --> pdb=" O TYR B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2558 through 2566 Processing helix chain 'B' and resid 2580 through 2593 removed outlier: 3.704A pdb=" N LEU B2584 " --> pdb=" O VAL B2580 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B2585 " --> pdb=" O ASP B2581 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B2586 " --> pdb=" O SER B2582 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B2587 " --> pdb=" O MET B2583 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B2588 " --> pdb=" O LEU B2584 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B2593 " --> pdb=" O ARG B2589 " (cutoff:3.500A) Processing helix chain 'B' and resid 2597 through 2611 removed outlier: 3.840A pdb=" N ASP B2602 " --> pdb=" O LYS B2598 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B2603 " --> pdb=" O ALA B2599 " (cutoff:3.500A) Processing helix chain 'B' and resid 2618 through 2629 removed outlier: 3.633A pdb=" N LEU B2627 " --> pdb=" O LEU B2623 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B2628 " --> pdb=" O LEU B2624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2644 through 2653 removed outlier: 3.572A pdb=" N UNK B2650 " --> pdb=" O UNK B2646 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N UNK B2652 " --> pdb=" O UNK B2648 " (cutoff:3.500A) Processing helix chain 'B' and resid 2665 through 2683 removed outlier: 3.836A pdb=" N UNK B2677 " --> pdb=" O UNK B2673 " (cutoff:3.500A) Processing helix chain 'B' and resid 2689 through 2697 Processing helix chain 'B' and resid 2698 through 2700 No H-bonds generated for 'chain 'B' and resid 2698 through 2700' Processing helix chain 'B' and resid 2748 through 2750 No H-bonds generated for 'chain 'B' and resid 2748 through 2750' Processing helix chain 'B' and resid 2751 through 2772 Processing helix chain 'B' and resid 2793 through 2797 Processing helix chain 'B' and resid 2798 through 2819 removed outlier: 3.758A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) Proline residue: B2808 - end of helix removed outlier: 3.542A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2897 removed outlier: 3.533A pdb=" N GLU B2876 " --> pdb=" O GLN B2872 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B2877 " --> pdb=" O ALA B2873 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2933 removed outlier: 4.422A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B2922 " --> pdb=" O ARG B2918 " (cutoff:3.500A) Processing helix chain 'B' and resid 2957 through 2978 removed outlier: 3.565A pdb=" N UNK B2975 " --> pdb=" O UNK B2971 " (cutoff:3.500A) Processing helix chain 'B' and resid 3000 through 3018 removed outlier: 3.590A pdb=" N UNK B3009 " --> pdb=" O UNK B3005 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N UNK B3010 " --> pdb=" O UNK B3006 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK B3015 " --> pdb=" O UNK B3011 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N UNK B3016 " --> pdb=" O UNK B3012 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK B3017 " --> pdb=" O UNK B3013 " (cutoff:3.500A) Processing helix chain 'B' and resid 3033 through 3045 removed outlier: 3.552A pdb=" N UNK B3039 " --> pdb=" O UNK B3035 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N UNK B3043 " --> pdb=" O UNK B3039 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N UNK B3044 " --> pdb=" O UNK B3040 " (cutoff:3.500A) Processing helix chain 'B' and resid 3052 through 3059 removed outlier: 3.572A pdb=" N UNK B3056 " --> pdb=" O UNK B3052 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N UNK B3059 " --> pdb=" O UNK B3055 " (cutoff:3.500A) Processing helix chain 'B' and resid 3147 through 3166 removed outlier: 3.722A pdb=" N UNK B3156 " --> pdb=" O UNK B3152 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK B3163 " --> pdb=" O UNK B3159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK B3166 " --> pdb=" O UNK B3162 " (cutoff:3.500A) Processing helix chain 'B' and resid 3174 through 3187 removed outlier: 3.624A pdb=" N UNK B3179 " --> pdb=" O UNK B3175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK B3182 " --> pdb=" O UNK B3178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK B3185 " --> pdb=" O UNK B3181 " (cutoff:3.500A) Processing helix chain 'B' and resid 3203 through 3217 removed outlier: 3.655A pdb=" N UNK B3212 " --> pdb=" O UNK B3208 " (cutoff:3.500A) Processing helix chain 'B' and resid 3226 through 3237 removed outlier: 3.721A pdb=" N UNK B3230 " --> pdb=" O UNK B3226 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N UNK B3237 " --> pdb=" O UNK B3233 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3308 removed outlier: 3.524A pdb=" N UNK B3301 " --> pdb=" O UNK B3297 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3334 removed outlier: 3.770A pdb=" N UNK B3325 " --> pdb=" O UNK B3321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK B3328 " --> pdb=" O UNK B3324 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK B3331 " --> pdb=" O UNK B3327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3347 through 3358 removed outlier: 3.500A pdb=" N UNK B3354 " --> pdb=" O UNK B3350 " (cutoff:3.500A) Processing helix chain 'B' and resid 3367 through 3385 Processing helix chain 'B' and resid 3399 through 3427 removed outlier: 3.520A pdb=" N ALA B3408 " --> pdb=" O ARG B3404 " (cutoff:3.500A) Proline residue: B3411 - end of helix removed outlier: 3.864A pdb=" N ASP B3418 " --> pdb=" O ILE B3414 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN B3419 " --> pdb=" O ARG B3415 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG B3421 " --> pdb=" O VAL B3417 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA B3422 " --> pdb=" O ASP B3418 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B3426 " --> pdb=" O ALA B3422 " (cutoff:3.500A) Processing helix chain 'B' and resid 3429 through 3449 removed outlier: 3.676A pdb=" N ILE B3442 " --> pdb=" O MET B3438 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B3445 " --> pdb=" O GLU B3441 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B3447 " --> pdb=" O PHE B3443 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B3448 " --> pdb=" O ILE B3444 " (cutoff:3.500A) Processing helix chain 'B' and resid 3449 through 3459 removed outlier: 3.576A pdb=" N GLN B3457 " --> pdb=" O LYS B3453 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B3459 " --> pdb=" O GLU B3455 " (cutoff:3.500A) Processing helix chain 'B' and resid 3510 through 3526 Processing helix chain 'B' and resid 3535 through 3544 removed outlier: 3.528A pdb=" N UNK B3539 " --> pdb=" O UNK B3535 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK B3540 " --> pdb=" O UNK B3536 " (cutoff:3.500A) Processing helix chain 'B' and resid 3549 through 3555 Processing helix chain 'B' and resid 3567 through 3574 Processing helix chain 'B' and resid 3587 through 3606 Processing helix chain 'B' and resid 3641 through 3658 removed outlier: 3.809A pdb=" N ASN B3647 " --> pdb=" O HIS B3643 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B3649 " --> pdb=" O ALA B3645 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU B3650 " --> pdb=" O CYS B3646 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B3651 " --> pdb=" O ASN B3647 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B3652 " --> pdb=" O MET B3648 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B3654 " --> pdb=" O LEU B3650 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B3655 " --> pdb=" O GLU B3651 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B3657 " --> pdb=" O TYR B3653 " (cutoff:3.500A) Processing helix chain 'B' and resid 3665 through 3674 removed outlier: 3.992A pdb=" N ILE B3670 " --> pdb=" O GLU B3666 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B3671 " --> pdb=" O ASP B3667 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B3672 " --> pdb=" O ARG B3668 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B3673 " --> pdb=" O MET B3669 " (cutoff:3.500A) Processing helix chain 'B' and resid 3694 through 3706 removed outlier: 4.198A pdb=" N VAL B3698 " --> pdb=" O LEU B3694 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B3701 " --> pdb=" O LEU B3697 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B3702 " --> pdb=" O VAL B3698 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B3703 " --> pdb=" O LEU B3699 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B3704 " --> pdb=" O HIS B3700 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3731 removed outlier: 3.558A pdb=" N MET B3719 " --> pdb=" O ASP B3715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B3723 " --> pdb=" O MET B3719 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B3724 " --> pdb=" O ALA B3720 " (cutoff:3.500A) Processing helix chain 'B' and resid 3748 through 3767 removed outlier: 3.993A pdb=" N LEU B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3781 removed outlier: 3.628A pdb=" N MET B3773 " --> pdb=" O GLY B3769 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B3774 " --> pdb=" O ALA B3770 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B3775 " --> pdb=" O ALA B3771 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B3778 " --> pdb=" O VAL B3774 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B3779 " --> pdb=" O LEU B3775 " (cutoff:3.500A) Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 3.698A pdb=" N SER B3798 " --> pdb=" O LYS B3794 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B3799 " --> pdb=" O LEU B3795 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B3800 " --> pdb=" O GLY B3796 " (cutoff:3.500A) Processing helix chain 'B' and resid 3808 through 3813 removed outlier: 3.655A pdb=" N ASP B3813 " --> pdb=" O GLN B3809 " (cutoff:3.500A) Processing helix chain 'B' and resid 3813 through 3818 Processing helix chain 'B' and resid 3822 through 3833 removed outlier: 3.683A pdb=" N ILE B3827 " --> pdb=" O PHE B3823 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN B3828 " --> pdb=" O PHE B3824 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B3829 " --> pdb=" O GLN B3825 " (cutoff:3.500A) Processing helix chain 'B' and resid 3838 through 3850 removed outlier: 3.716A pdb=" N ARG B3844 " --> pdb=" O ASN B3840 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B3846 " --> pdb=" O PHE B3842 " (cutoff:3.500A) Processing helix chain 'B' and resid 3875 through 3885 removed outlier: 3.668A pdb=" N PHE B3880 " --> pdb=" O THR B3876 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B3881 " --> pdb=" O GLN B3877 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B3883 " --> pdb=" O LEU B3879 " (cutoff:3.500A) Processing helix chain 'B' and resid 3886 through 3888 No H-bonds generated for 'chain 'B' and resid 3886 through 3888' Processing helix chain 'B' and resid 3891 through 3900 removed outlier: 3.614A pdb=" N GLN B3895 " --> pdb=" O ASN B3891 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR B3897 " --> pdb=" O ASP B3893 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B3898 " --> pdb=" O PHE B3894 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B3899 " --> pdb=" O GLN B3895 " (cutoff:3.500A) Processing helix chain 'B' and resid 3909 through 3933 removed outlier: 3.961A pdb=" N CYS B3913 " --> pdb=" O ASN B3909 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR B3917 " --> pdb=" O CYS B3913 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B3918 " --> pdb=" O THR B3914 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B3923 " --> pdb=" O LEU B3919 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B3928 " --> pdb=" O SER B3924 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B3932 " --> pdb=" O PHE B3928 " (cutoff:3.500A) Processing helix chain 'B' and resid 3939 through 3964 removed outlier: 3.917A pdb=" N PHE B3957 " --> pdb=" O ALA B3953 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B3962 " --> pdb=" O ASN B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3969 through 3978 removed outlier: 3.622A pdb=" N GLN B3973 " --> pdb=" O THR B3969 " (cutoff:3.500A) Processing helix chain 'B' and resid 3979 through 4001 removed outlier: 3.564A pdb=" N VAL B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B3985 " --> pdb=" O TRP B3981 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B3986 " --> pdb=" O ASP B3982 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B3990 " --> pdb=" O GLY B3986 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS B3993 " --> pdb=" O HIS B3989 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET B3996 " --> pdb=" O ALA B3992 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B4000 " --> pdb=" O MET B3996 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B4001 " --> pdb=" O LYS B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4004 through 4026 removed outlier: 3.676A pdb=" N LEU B4008 " --> pdb=" O GLN B4004 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B4014 " --> pdb=" O GLU B4010 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B4015 " --> pdb=" O LEU B4011 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B4017 " --> pdb=" O ASP B4013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B4020 " --> pdb=" O LYS B4016 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET B4021 " --> pdb=" O ASP B4017 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B4022 " --> pdb=" O MET B4018 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B4023 " --> pdb=" O VAL B4019 " (cutoff:3.500A) Processing helix chain 'B' and resid 4035 through 4037 No H-bonds generated for 'chain 'B' and resid 4035 through 4037' Processing helix chain 'B' and resid 4038 through 4046 removed outlier: 3.513A pdb=" N LEU B4043 " --> pdb=" O MET B4039 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B4044 " --> pdb=" O VAL B4040 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B4045 " --> pdb=" O ASP B4041 " (cutoff:3.500A) Processing helix chain 'B' and resid 4046 through 4067 removed outlier: 4.084A pdb=" N MET B4052 " --> pdb=" O SER B4048 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B4053 " --> pdb=" O ASN B4049 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B4060 " --> pdb=" O PHE B4056 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B4064 " --> pdb=" O PHE B4060 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP B4065 " --> pdb=" O LEU B4061 " (cutoff:3.500A) Processing helix chain 'B' and resid 4069 through 4076 removed outlier: 3.632A pdb=" N GLN B4073 " --> pdb=" O SER B4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 4127 through 4149 removed outlier: 3.668A pdb=" N ALA B4131 " --> pdb=" O PHE B4127 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B4133 " --> pdb=" O GLU B4129 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B4134 " --> pdb=" O PRO B4130 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B4139 " --> pdb=" O GLY B4135 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B4146 " --> pdb=" O LEU B4142 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B4147 " --> pdb=" O THR B4143 " (cutoff:3.500A) Processing helix chain 'B' and resid 4152 through 4162 Processing helix chain 'B' and resid 4162 through 4169 removed outlier: 3.507A pdb=" N TYR B4168 " --> pdb=" O SER B4164 " (cutoff:3.500A) Processing helix chain 'B' and resid 4193 through 4201 removed outlier: 3.693A pdb=" N GLU B4201 " --> pdb=" O ARG B4197 " (cutoff:3.500A) Processing helix chain 'B' and resid 4202 through 4216 removed outlier: 3.618A pdb=" N PHE B4214 " --> pdb=" O ARG B4210 " (cutoff:3.500A) Processing helix chain 'B' and resid 4221 through 4239 removed outlier: 3.603A pdb=" N MET B4226 " --> pdb=" O GLU B4222 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU B4227 " --> pdb=" O SER B4223 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B4228 " --> pdb=" O GLU B4224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B4229 " --> pdb=" O LYS B4225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B4230 " --> pdb=" O MET B4226 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B4238 " --> pdb=" O GLU B4234 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B4239 " --> pdb=" O ASP B4235 " (cutoff:3.500A) Processing helix chain 'B' and resid 4544 through 4556 removed outlier: 3.501A pdb=" N LEU B4550 " --> pdb=" O ARG B4546 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B4551 " --> pdb=" O VAL B4547 " (cutoff:3.500A) Processing helix chain 'B' and resid 4556 through 4576 removed outlier: 3.530A pdb=" N ARG B4561 " --> pdb=" O PHE B4557 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B4562 " --> pdb=" O TYR B4558 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B4563 " --> pdb=" O THR B4559 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B4564 " --> pdb=" O LEU B4560 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B4565 " --> pdb=" O ARG B4561 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B4568 " --> pdb=" O ALA B4564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B4569 " --> pdb=" O LEU B4565 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B4573 " --> pdb=" O PHE B4569 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE B4574 " --> pdb=" O ALA B4570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B4575 " --> pdb=" O ILE B4571 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B4576 " --> pdb=" O ASN B4572 " (cutoff:3.500A) Processing helix chain 'B' and resid 4639 through 4661 removed outlier: 3.645A pdb=" N SER B4645 " --> pdb=" O LEU B4641 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B4646 " --> pdb=" O ARG B4642 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B4647 " --> pdb=" O CYS B4643 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B4649 " --> pdb=" O SER B4645 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B4652 " --> pdb=" O HIS B4648 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B4656 " --> pdb=" O ALA B4652 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B4657 " --> pdb=" O PHE B4653 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B4661 " --> pdb=" O ILE B4657 " (cutoff:3.500A) Processing helix chain 'B' and resid 4663 through 4681 removed outlier: 3.794A pdb=" N GLU B4674 " --> pdb=" O LYS B4670 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B4680 " --> pdb=" O ALA B4676 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4700 Processing helix chain 'B' and resid 4721 through 4726 removed outlier: 3.797A pdb=" N LYS B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4726 through 4735 removed outlier: 4.481A pdb=" N TYR B4730 " --> pdb=" O HIS B4726 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B4732 " --> pdb=" O ASP B4728 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLU B4733 " --> pdb=" O ILE B4729 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B4734 " --> pdb=" O TYR B4730 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B4735 " --> pdb=" O GLY B4731 " (cutoff:3.500A) Processing helix chain 'B' and resid 4762 through 4767 Processing helix chain 'B' and resid 4770 through 4784 removed outlier: 3.656A pdb=" N TRP B4776 " --> pdb=" O LYS B4772 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B4780 " --> pdb=" O TRP B4776 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B4781 " --> pdb=" O LYS B4777 " (cutoff:3.500A) Processing helix chain 'B' and resid 4784 through 4799 removed outlier: 3.609A pdb=" N TYR B4793 " --> pdb=" O TYR B4789 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B4794 " --> pdb=" O LEU B4790 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B4796 " --> pdb=" O TRP B4792 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B4797 " --> pdb=" O TYR B4793 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B4798 " --> pdb=" O MET B4794 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B4799 " --> pdb=" O VAL B4795 " (cutoff:3.500A) Processing helix chain 'B' and resid 4800 through 4802 No H-bonds generated for 'chain 'B' and resid 4800 through 4802' Processing helix chain 'B' and resid 4806 through 4815 removed outlier: 3.974A pdb=" N HIS B4810 " --> pdb=" O PHE B4806 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B4812 " --> pdb=" O ALA B4808 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B4813 " --> pdb=" O ALA B4809 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B4815 " --> pdb=" O LEU B4811 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4830 removed outlier: 4.083A pdb=" N LEU B4825 " --> pdb=" O LEU B4821 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B4829 " --> pdb=" O LEU B4825 " (cutoff:3.500A) Processing helix chain 'B' and resid 4831 through 4856 removed outlier: 3.933A pdb=" N LEU B4835 " --> pdb=" O ASN B4831 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET B4837 " --> pdb=" O LYS B4833 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B4846 " --> pdb=" O LEU B4842 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B4852 " --> pdb=" O LEU B4848 " (cutoff:3.500A) Processing helix chain 'B' and resid 4872 through 4875 removed outlier: 3.741A pdb=" N ASP B4875 " --> pdb=" O MET B4872 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4872 through 4875' Processing helix chain 'B' and resid 4876 through 4892 removed outlier: 3.775A pdb=" N TYR B4881 " --> pdb=" O MET B4877 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B4889 " --> pdb=" O MET B4885 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B4890 " --> pdb=" O TYR B4886 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B4892 " --> pdb=" O GLY B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4898 removed outlier: 3.944A pdb=" N ASP B4897 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4907 through 4922 removed outlier: 3.562A pdb=" N VAL B4922 " --> pdb=" O PHE B4918 " (cutoff:3.500A) Processing helix chain 'B' and resid 4924 through 4955 removed outlier: 3.530A pdb=" N ALA B4928 " --> pdb=" O VAL B4924 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B4934 " --> pdb=" O ILE B4930 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B4953 " --> pdb=" O ARG B4949 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4968 removed outlier: 4.034A pdb=" N ASP B4967 " --> pdb=" O ASP B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4972 through 4977 removed outlier: 4.287A pdb=" N THR B4977 " --> pdb=" O PHE B4973 " (cutoff:3.500A) Processing helix chain 'B' and resid 4986 through 4996 Processing helix chain 'B' and resid 4997 through 5001 removed outlier: 3.548A pdb=" N HIS B5001 " --> pdb=" O GLU B4998 " (cutoff:3.500A) Processing helix chain 'B' and resid 5002 through 5014 removed outlier: 3.610A pdb=" N TYR B5007 " --> pdb=" O GLY B5003 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B5014 " --> pdb=" O LYS B5010 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 56 through 65 removed outlier: 3.693A pdb=" N GLN C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 394 through 424 removed outlier: 3.701A pdb=" N SER D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 452 removed outlier: 3.795A pdb=" N GLY D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 480 Processing helix chain 'D' and resid 482 through 496 removed outlier: 3.914A pdb=" N LEU D 486 " --> pdb=" O GLY D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.517A pdb=" N PHE D 503 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 531 Processing helix chain 'D' and resid 533 through 540 removed outlier: 4.136A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 571 removed outlier: 4.077A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 4.164A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 573 through 578' Processing helix chain 'D' and resid 579 through 593 removed outlier: 3.731A pdb=" N ILE D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 608 removed outlier: 4.166A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP D 601 " --> pdb=" O HIS D 597 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 626 removed outlier: 3.648A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 864 through 889 removed outlier: 3.654A pdb=" N GLU D 868 " --> pdb=" O PRO D 864 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 934 Processing helix chain 'D' and resid 981 through 1003 Processing helix chain 'D' and resid 1028 through 1050 removed outlier: 3.850A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS D1040 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D1050 " --> pdb=" O LEU D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1213 through 1216 removed outlier: 3.671A pdb=" N ILE D1216 " --> pdb=" O PHE D1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1213 through 1216' Processing helix chain 'D' and resid 1217 through 1222 Processing helix chain 'D' and resid 1575 through 1580 removed outlier: 3.562A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1674 removed outlier: 3.562A pdb=" N GLN D1660 " --> pdb=" O ARG D1656 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D1661 " --> pdb=" O LEU D1657 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS D1674 " --> pdb=" O TYR D1670 " (cutoff:3.500A) Processing helix chain 'D' and resid 1679 through 1689 removed outlier: 3.667A pdb=" N HIS D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1700 removed outlier: 3.585A pdb=" N LEU D1694 " --> pdb=" O ASP D1690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D1695 " --> pdb=" O GLN D1691 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1720 Processing helix chain 'D' and resid 1721 through 1729 removed outlier: 3.752A pdb=" N ARG D1725 " --> pdb=" O GLU D1721 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.507A pdb=" N ALA D1744 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1804 through 1826 Processing helix chain 'D' and resid 1830 through 1833 Processing helix chain 'D' and resid 1834 through 1852 removed outlier: 3.593A pdb=" N GLN D1838 " --> pdb=" O SER D1834 " (cutoff:3.500A) Proline residue: D1841 - end of helix removed outlier: 3.704A pdb=" N MET D1852 " --> pdb=" O THR D1848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1856 through 1868 Processing helix chain 'D' and resid 1933 through 1984 removed outlier: 4.126A pdb=" N LYS D1983 " --> pdb=" O GLY D1979 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA D1984 " --> pdb=" O ILE D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1988 through 2000 Processing helix chain 'D' and resid 2002 through 2011 Processing helix chain 'D' and resid 2025 through 2044 removed outlier: 3.951A pdb=" N ARG D2029 " --> pdb=" O PRO D2025 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP D2031 " --> pdb=" O GLU D2027 " (cutoff:3.500A) Processing helix chain 'D' and resid 2094 through 2110 removed outlier: 4.204A pdb=" N ASP D2110 " --> pdb=" O TRP D2106 " (cutoff:3.500A) Processing helix chain 'D' and resid 2114 through 2130 Processing helix chain 'D' and resid 2131 through 2138 Processing helix chain 'D' and resid 2149 through 2169 Processing helix chain 'D' and resid 2172 through 2188 removed outlier: 3.555A pdb=" N MET D2187 " --> pdb=" O ILE D2183 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN D2188 " --> pdb=" O GLY D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2194 removed outlier: 3.860A pdb=" N PHE D2192 " --> pdb=" O ASN D2189 " (cutoff:3.500A) Processing helix chain 'D' and resid 2195 through 2203 Processing helix chain 'D' and resid 2203 through 2216 Processing helix chain 'D' and resid 2226 through 2242 removed outlier: 3.638A pdb=" N ARG D2242 " --> pdb=" O CYS D2238 " (cutoff:3.500A) Processing helix chain 'D' and resid 2244 through 2252 Processing helix chain 'D' and resid 2254 through 2263 removed outlier: 3.653A pdb=" N GLY D2263 " --> pdb=" O LEU D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2272 through 2282 removed outlier: 3.575A pdb=" N VAL D2276 " --> pdb=" O THR D2272 " (cutoff:3.500A) Processing helix chain 'D' and resid 2285 through 2290 Processing helix chain 'D' and resid 2292 through 2307 removed outlier: 4.189A pdb=" N LEU D2296 " --> pdb=" O GLN D2292 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D2307 " --> pdb=" O LEU D2303 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2317 removed outlier: 3.531A pdb=" N ALA D2316 " --> pdb=" O PRO D2312 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D2317 " --> pdb=" O MET D2313 " (cutoff:3.500A) Processing helix chain 'D' and resid 2325 through 2341 removed outlier: 4.134A pdb=" N PHE D2335 " --> pdb=" O ARG D2331 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D2336 " --> pdb=" O TYR D2332 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D2341 " --> pdb=" O ARG D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2347 through 2360 Processing helix chain 'D' and resid 2361 through 2365 removed outlier: 3.544A pdb=" N CYS D2364 " --> pdb=" O LYS D2361 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D2365 " --> pdb=" O PRO D2362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2361 through 2365' Processing helix chain 'D' and resid 2378 through 2385 Processing helix chain 'D' and resid 2423 through 2437 Processing helix chain 'D' and resid 2441 through 2446 Processing helix chain 'D' and resid 2449 through 2462 removed outlier: 4.304A pdb=" N ARG D2453 " --> pdb=" O GLY D2449 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE D2454 " --> pdb=" O GLU D2450 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D2461 " --> pdb=" O ILE D2457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D2462 " --> pdb=" O LEU D2458 " (cutoff:3.500A) Processing helix chain 'D' and resid 2463 through 2472 removed outlier: 3.610A pdb=" N LEU D2467 " --> pdb=" O PRO D2463 " (cutoff:3.500A) Processing helix chain 'D' and resid 2496 through 2511 removed outlier: 4.355A pdb=" N LYS D2500 " --> pdb=" O VAL D2496 " (cutoff:3.500A) Processing helix chain 'D' and resid 2519 through 2527 Processing helix chain 'D' and resid 2549 through 2558 removed outlier: 3.656A pdb=" N LEU D2555 " --> pdb=" O LEU D2551 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS D2556 " --> pdb=" O ASN D2552 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D2558 " --> pdb=" O TYR D2554 " (cutoff:3.500A) Processing helix chain 'D' and resid 2558 through 2566 Processing helix chain 'D' and resid 2580 through 2593 removed outlier: 3.704A pdb=" N LEU D2584 " --> pdb=" O VAL D2580 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS D2585 " --> pdb=" O ASP D2581 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D2586 " --> pdb=" O SER D2582 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D2587 " --> pdb=" O MET D2583 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR D2588 " --> pdb=" O LEU D2584 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D2593 " --> pdb=" O ARG D2589 " (cutoff:3.500A) Processing helix chain 'D' and resid 2597 through 2611 removed outlier: 3.839A pdb=" N ASP D2602 " --> pdb=" O LYS D2598 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL D2603 " --> pdb=" O ALA D2599 " (cutoff:3.500A) Processing helix chain 'D' and resid 2618 through 2629 removed outlier: 3.501A pdb=" N HIS D2622 " --> pdb=" O SER D2618 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D2627 " --> pdb=" O LEU D2623 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D2628 " --> pdb=" O LEU D2624 " (cutoff:3.500A) Processing helix chain 'D' and resid 2643 through 2653 removed outlier: 3.572A pdb=" N UNK D2650 " --> pdb=" O UNK D2646 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK D2652 " --> pdb=" O UNK D2648 " (cutoff:3.500A) Processing helix chain 'D' and resid 2665 through 2683 removed outlier: 3.836A pdb=" N UNK D2677 " --> pdb=" O UNK D2673 " (cutoff:3.500A) Processing helix chain 'D' and resid 2689 through 2697 Processing helix chain 'D' and resid 2698 through 2700 No H-bonds generated for 'chain 'D' and resid 2698 through 2700' Processing helix chain 'D' and resid 2748 through 2750 No H-bonds generated for 'chain 'D' and resid 2748 through 2750' Processing helix chain 'D' and resid 2751 through 2772 Processing helix chain 'D' and resid 2793 through 2797 Processing helix chain 'D' and resid 2798 through 2819 removed outlier: 3.758A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR D2805 " --> pdb=" O ASP D2801 " (cutoff:3.500A) Proline residue: D2808 - end of helix removed outlier: 3.541A pdb=" N TRP D2819 " --> pdb=" O ALA D2815 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2897 removed outlier: 3.533A pdb=" N GLU D2876 " --> pdb=" O GLN D2872 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN D2877 " --> pdb=" O ALA D2873 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2933 removed outlier: 4.422A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D2922 " --> pdb=" O ARG D2918 " (cutoff:3.500A) Processing helix chain 'D' and resid 2957 through 2978 removed outlier: 3.565A pdb=" N UNK D2975 " --> pdb=" O UNK D2971 " (cutoff:3.500A) Processing helix chain 'D' and resid 3000 through 3018 removed outlier: 3.590A pdb=" N UNK D3009 " --> pdb=" O UNK D3005 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N UNK D3010 " --> pdb=" O UNK D3006 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK D3015 " --> pdb=" O UNK D3011 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N UNK D3016 " --> pdb=" O UNK D3012 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK D3017 " --> pdb=" O UNK D3013 " (cutoff:3.500A) Processing helix chain 'D' and resid 3033 through 3045 removed outlier: 3.552A pdb=" N UNK D3039 " --> pdb=" O UNK D3035 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK D3043 " --> pdb=" O UNK D3039 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N UNK D3044 " --> pdb=" O UNK D3040 " (cutoff:3.500A) Processing helix chain 'D' and resid 3052 through 3059 removed outlier: 3.572A pdb=" N UNK D3056 " --> pdb=" O UNK D3052 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N UNK D3059 " --> pdb=" O UNK D3055 " (cutoff:3.500A) Processing helix chain 'D' and resid 3147 through 3166 removed outlier: 3.722A pdb=" N UNK D3156 " --> pdb=" O UNK D3152 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK D3163 " --> pdb=" O UNK D3159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK D3166 " --> pdb=" O UNK D3162 " (cutoff:3.500A) Processing helix chain 'D' and resid 3174 through 3187 removed outlier: 3.624A pdb=" N UNK D3179 " --> pdb=" O UNK D3175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK D3182 " --> pdb=" O UNK D3178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK D3185 " --> pdb=" O UNK D3181 " (cutoff:3.500A) Processing helix chain 'D' and resid 3203 through 3217 removed outlier: 3.654A pdb=" N UNK D3212 " --> pdb=" O UNK D3208 " (cutoff:3.500A) Processing helix chain 'D' and resid 3226 through 3237 removed outlier: 3.721A pdb=" N UNK D3230 " --> pdb=" O UNK D3226 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N UNK D3237 " --> pdb=" O UNK D3233 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3308 removed outlier: 3.524A pdb=" N UNK D3301 " --> pdb=" O UNK D3297 " (cutoff:3.500A) Processing helix chain 'D' and resid 3321 through 3334 removed outlier: 3.770A pdb=" N UNK D3325 " --> pdb=" O UNK D3321 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK D3328 " --> pdb=" O UNK D3324 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK D3331 " --> pdb=" O UNK D3327 " (cutoff:3.500A) Processing helix chain 'D' and resid 3347 through 3358 removed outlier: 3.501A pdb=" N UNK D3354 " --> pdb=" O UNK D3350 " (cutoff:3.500A) Processing helix chain 'D' and resid 3367 through 3385 Processing helix chain 'D' and resid 3399 through 3427 removed outlier: 3.519A pdb=" N ALA D3408 " --> pdb=" O ARG D3404 " (cutoff:3.500A) Proline residue: D3411 - end of helix removed outlier: 3.864A pdb=" N ASP D3418 " --> pdb=" O ILE D3414 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN D3419 " --> pdb=" O ARG D3415 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG D3421 " --> pdb=" O VAL D3417 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA D3422 " --> pdb=" O ASP D3418 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR D3426 " --> pdb=" O ALA D3422 " (cutoff:3.500A) Processing helix chain 'D' and resid 3429 through 3449 removed outlier: 3.676A pdb=" N ILE D3442 " --> pdb=" O MET D3438 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR D3445 " --> pdb=" O GLU D3441 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D3447 " --> pdb=" O PHE D3443 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D3448 " --> pdb=" O ILE D3444 " (cutoff:3.500A) Processing helix chain 'D' and resid 3449 through 3459 removed outlier: 3.576A pdb=" N GLN D3457 " --> pdb=" O LYS D3453 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D3459 " --> pdb=" O GLU D3455 " (cutoff:3.500A) Processing helix chain 'D' and resid 3510 through 3526 Processing helix chain 'D' and resid 3535 through 3544 removed outlier: 3.527A pdb=" N UNK D3539 " --> pdb=" O UNK D3535 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK D3540 " --> pdb=" O UNK D3536 " (cutoff:3.500A) Processing helix chain 'D' and resid 3549 through 3555 Processing helix chain 'D' and resid 3567 through 3574 Processing helix chain 'D' and resid 3587 through 3606 Processing helix chain 'D' and resid 3641 through 3658 removed outlier: 3.809A pdb=" N ASN D3647 " --> pdb=" O HIS D3643 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D3649 " --> pdb=" O ALA D3645 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D3650 " --> pdb=" O CYS D3646 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU D3651 " --> pdb=" O ASN D3647 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D3652 " --> pdb=" O MET D3648 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D3654 " --> pdb=" O LEU D3650 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D3655 " --> pdb=" O GLU D3651 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP D3657 " --> pdb=" O TYR D3653 " (cutoff:3.500A) Processing helix chain 'D' and resid 3665 through 3674 removed outlier: 3.992A pdb=" N ILE D3670 " --> pdb=" O GLU D3666 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP D3671 " --> pdb=" O ASP D3667 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D3672 " --> pdb=" O ARG D3668 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D3673 " --> pdb=" O MET D3669 " (cutoff:3.500A) Processing helix chain 'D' and resid 3694 through 3706 removed outlier: 4.198A pdb=" N VAL D3698 " --> pdb=" O LEU D3694 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D3701 " --> pdb=" O LEU D3697 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER D3702 " --> pdb=" O VAL D3698 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D3703 " --> pdb=" O LEU D3699 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR D3704 " --> pdb=" O HIS D3700 " (cutoff:3.500A) Processing helix chain 'D' and resid 3715 through 3731 removed outlier: 3.557A pdb=" N MET D3719 " --> pdb=" O ASP D3715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP D3723 " --> pdb=" O MET D3719 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D3724 " --> pdb=" O ALA D3720 " (cutoff:3.500A) Processing helix chain 'D' and resid 3748 through 3767 removed outlier: 3.994A pdb=" N LEU D3765 " --> pdb=" O GLN D3761 " (cutoff:3.500A) Processing helix chain 'D' and resid 3769 through 3781 removed outlier: 3.627A pdb=" N MET D3773 " --> pdb=" O GLY D3769 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D3774 " --> pdb=" O ALA D3770 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D3775 " --> pdb=" O ALA D3771 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE D3778 " --> pdb=" O VAL D3774 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D3779 " --> pdb=" O LEU D3775 " (cutoff:3.500A) Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 3.698A pdb=" N SER D3798 " --> pdb=" O LYS D3794 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D3799 " --> pdb=" O LEU D3795 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D3800 " --> pdb=" O GLY D3796 " (cutoff:3.500A) Processing helix chain 'D' and resid 3808 through 3813 removed outlier: 3.655A pdb=" N ASP D3813 " --> pdb=" O GLN D3809 " (cutoff:3.500A) Processing helix chain 'D' and resid 3813 through 3818 Processing helix chain 'D' and resid 3822 through 3833 removed outlier: 3.683A pdb=" N ILE D3827 " --> pdb=" O PHE D3823 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN D3828 " --> pdb=" O PHE D3824 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D3829 " --> pdb=" O GLN D3825 " (cutoff:3.500A) Processing helix chain 'D' and resid 3838 through 3850 removed outlier: 3.716A pdb=" N ARG D3844 " --> pdb=" O ASN D3840 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D3846 " --> pdb=" O PHE D3842 " (cutoff:3.500A) Processing helix chain 'D' and resid 3875 through 3885 removed outlier: 3.668A pdb=" N PHE D3880 " --> pdb=" O THR D3876 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D3881 " --> pdb=" O GLN D3877 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D3883 " --> pdb=" O LEU D3879 " (cutoff:3.500A) Processing helix chain 'D' and resid 3886 through 3888 No H-bonds generated for 'chain 'D' and resid 3886 through 3888' Processing helix chain 'D' and resid 3891 through 3900 removed outlier: 3.615A pdb=" N GLN D3895 " --> pdb=" O ASN D3891 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR D3897 " --> pdb=" O ASP D3893 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D3898 " --> pdb=" O PHE D3894 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D3899 " --> pdb=" O GLN D3895 " (cutoff:3.500A) Processing helix chain 'D' and resid 3909 through 3933 removed outlier: 3.961A pdb=" N CYS D3913 " --> pdb=" O ASN D3909 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR D3917 " --> pdb=" O CYS D3913 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU D3918 " --> pdb=" O THR D3914 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D3923 " --> pdb=" O LEU D3919 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D3928 " --> pdb=" O SER D3924 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR D3932 " --> pdb=" O PHE D3928 " (cutoff:3.500A) Processing helix chain 'D' and resid 3939 through 3964 removed outlier: 3.916A pdb=" N PHE D3957 " --> pdb=" O ALA D3953 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D3962 " --> pdb=" O ASN D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3969 through 3978 removed outlier: 3.622A pdb=" N GLN D3973 " --> pdb=" O THR D3969 " (cutoff:3.500A) Processing helix chain 'D' and resid 3979 through 4001 removed outlier: 3.564A pdb=" N VAL D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D3985 " --> pdb=" O TRP D3981 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D3986 " --> pdb=" O ASP D3982 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D3990 " --> pdb=" O GLY D3986 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS D3993 " --> pdb=" O HIS D3989 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N MET D3996 " --> pdb=" O ALA D3992 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D4000 " --> pdb=" O MET D3996 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP D4001 " --> pdb=" O LYS D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4004 through 4026 removed outlier: 3.676A pdb=" N LEU D4008 " --> pdb=" O GLN D4004 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D4014 " --> pdb=" O GLU D4010 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN D4015 " --> pdb=" O LEU D4011 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D4017 " --> pdb=" O ASP D4013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D4020 " --> pdb=" O LYS D4016 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET D4021 " --> pdb=" O ASP D4017 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU D4022 " --> pdb=" O MET D4018 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D4023 " --> pdb=" O VAL D4019 " (cutoff:3.500A) Processing helix chain 'D' and resid 4035 through 4037 No H-bonds generated for 'chain 'D' and resid 4035 through 4037' Processing helix chain 'D' and resid 4038 through 4046 removed outlier: 3.513A pdb=" N LEU D4043 " --> pdb=" O MET D4039 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D4044 " --> pdb=" O VAL D4040 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU D4045 " --> pdb=" O ASP D4041 " (cutoff:3.500A) Processing helix chain 'D' and resid 4046 through 4067 removed outlier: 4.083A pdb=" N MET D4052 " --> pdb=" O SER D4048 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D4053 " --> pdb=" O ASN D4049 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D4060 " --> pdb=" O PHE D4056 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D4064 " --> pdb=" O PHE D4060 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP D4065 " --> pdb=" O LEU D4061 " (cutoff:3.500A) Processing helix chain 'D' and resid 4069 through 4076 removed outlier: 3.632A pdb=" N GLN D4073 " --> pdb=" O SER D4069 " (cutoff:3.500A) Processing helix chain 'D' and resid 4127 through 4149 removed outlier: 3.669A pdb=" N ALA D4131 " --> pdb=" O PHE D4127 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP D4133 " --> pdb=" O GLU D4129 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D4134 " --> pdb=" O PRO D4130 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D4139 " --> pdb=" O GLY D4135 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D4146 " --> pdb=" O LEU D4142 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D4147 " --> pdb=" O THR D4143 " (cutoff:3.500A) Processing helix chain 'D' and resid 4152 through 4162 Processing helix chain 'D' and resid 4162 through 4169 removed outlier: 3.506A pdb=" N TYR D4168 " --> pdb=" O SER D4164 " (cutoff:3.500A) Processing helix chain 'D' and resid 4193 through 4201 removed outlier: 3.694A pdb=" N GLU D4201 " --> pdb=" O ARG D4197 " (cutoff:3.500A) Processing helix chain 'D' and resid 4202 through 4216 removed outlier: 3.618A pdb=" N PHE D4214 " --> pdb=" O ARG D4210 " (cutoff:3.500A) Processing helix chain 'D' and resid 4221 through 4239 removed outlier: 3.602A pdb=" N MET D4226 " --> pdb=" O GLU D4222 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU D4227 " --> pdb=" O SER D4223 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D4228 " --> pdb=" O GLU D4224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D4229 " --> pdb=" O LYS D4225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL D4230 " --> pdb=" O MET D4226 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D4238 " --> pdb=" O GLU D4234 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D4239 " --> pdb=" O ASP D4235 " (cutoff:3.500A) Processing helix chain 'D' and resid 4544 through 4556 removed outlier: 3.500A pdb=" N LEU D4550 " --> pdb=" O ARG D4546 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN D4551 " --> pdb=" O VAL D4547 " (cutoff:3.500A) Processing helix chain 'D' and resid 4556 through 4576 removed outlier: 3.530A pdb=" N ARG D4561 " --> pdb=" O PHE D4557 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE D4562 " --> pdb=" O TYR D4558 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D4563 " --> pdb=" O THR D4559 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D4564 " --> pdb=" O LEU D4560 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D4565 " --> pdb=" O ARG D4561 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA D4568 " --> pdb=" O ALA D4564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D4569 " --> pdb=" O LEU D4565 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE D4573 " --> pdb=" O PHE D4569 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE D4574 " --> pdb=" O ALA D4570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D4575 " --> pdb=" O ILE D4571 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D4576 " --> pdb=" O ASN D4572 " (cutoff:3.500A) Processing helix chain 'D' and resid 4639 through 4661 removed outlier: 3.645A pdb=" N SER D4645 " --> pdb=" O LEU D4641 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D4646 " --> pdb=" O ARG D4642 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D4647 " --> pdb=" O CYS D4643 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D4649 " --> pdb=" O SER D4645 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D4652 " --> pdb=" O HIS D4648 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D4656 " --> pdb=" O ALA D4652 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D4657 " --> pdb=" O PHE D4653 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS D4661 " --> pdb=" O ILE D4657 " (cutoff:3.500A) Processing helix chain 'D' and resid 4663 through 4681 removed outlier: 3.794A pdb=" N GLU D4674 " --> pdb=" O LYS D4670 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D4680 " --> pdb=" O ALA D4676 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4700 Processing helix chain 'D' and resid 4721 through 4726 removed outlier: 3.797A pdb=" N LYS D4725 " --> pdb=" O LYS D4721 " (cutoff:3.500A) Processing helix chain 'D' and resid 4726 through 4735 removed outlier: 4.479A pdb=" N TYR D4730 " --> pdb=" O HIS D4726 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG D4732 " --> pdb=" O ASP D4728 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLU D4733 " --> pdb=" O ILE D4729 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG D4734 " --> pdb=" O TYR D4730 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D4735 " --> pdb=" O GLY D4731 " (cutoff:3.500A) Processing helix chain 'D' and resid 4762 through 4767 Processing helix chain 'D' and resid 4770 through 4784 removed outlier: 3.656A pdb=" N TRP D4776 " --> pdb=" O LYS D4772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D4780 " --> pdb=" O TRP D4776 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D4781 " --> pdb=" O LYS D4777 " (cutoff:3.500A) Processing helix chain 'D' and resid 4784 through 4799 removed outlier: 3.610A pdb=" N TYR D4793 " --> pdb=" O TYR D4789 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D4794 " --> pdb=" O LEU D4790 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET D4796 " --> pdb=" O TRP D4792 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D4797 " --> pdb=" O TYR D4793 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D4798 " --> pdb=" O MET D4794 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D4799 " --> pdb=" O VAL D4795 " (cutoff:3.500A) Processing helix chain 'D' and resid 4800 through 4802 No H-bonds generated for 'chain 'D' and resid 4800 through 4802' Processing helix chain 'D' and resid 4806 through 4815 removed outlier: 3.974A pdb=" N HIS D4810 " --> pdb=" O PHE D4806 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D4812 " --> pdb=" O ALA D4808 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP D4813 " --> pdb=" O ALA D4809 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D4815 " --> pdb=" O LEU D4811 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4830 removed outlier: 4.083A pdb=" N LEU D4825 " --> pdb=" O LEU D4821 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR D4829 " --> pdb=" O LEU D4825 " (cutoff:3.500A) Processing helix chain 'D' and resid 4831 through 4856 removed outlier: 3.933A pdb=" N LEU D4835 " --> pdb=" O ASN D4831 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET D4837 " --> pdb=" O LYS D4833 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D4846 " --> pdb=" O LEU D4842 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D4852 " --> pdb=" O LEU D4848 " (cutoff:3.500A) Processing helix chain 'D' and resid 4872 through 4875 removed outlier: 3.741A pdb=" N ASP D4875 " --> pdb=" O MET D4872 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4872 through 4875' Processing helix chain 'D' and resid 4876 through 4892 removed outlier: 3.775A pdb=" N TYR D4881 " --> pdb=" O MET D4877 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D4889 " --> pdb=" O MET D4885 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D4890 " --> pdb=" O TYR D4886 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D4892 " --> pdb=" O GLY D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4898 removed outlier: 3.945A pdb=" N ASP D4897 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4907 through 4922 removed outlier: 3.563A pdb=" N VAL D4922 " --> pdb=" O PHE D4918 " (cutoff:3.500A) Processing helix chain 'D' and resid 4924 through 4955 removed outlier: 3.531A pdb=" N ALA D4928 " --> pdb=" O VAL D4924 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D4934 " --> pdb=" O ILE D4930 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU D4953 " --> pdb=" O ARG D4949 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4968 removed outlier: 4.034A pdb=" N ASP D4967 " --> pdb=" O ASP D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4972 through 4977 removed outlier: 4.288A pdb=" N THR D4977 " --> pdb=" O PHE D4973 " (cutoff:3.500A) Processing helix chain 'D' and resid 4986 through 4996 Processing helix chain 'D' and resid 4997 through 5001 removed outlier: 3.548A pdb=" N HIS D5001 " --> pdb=" O GLU D4998 " (cutoff:3.500A) Processing helix chain 'D' and resid 5002 through 5014 removed outlier: 3.610A pdb=" N TYR D5007 " --> pdb=" O GLY D5003 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D5014 " --> pdb=" O LYS D5010 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 56 through 65 removed outlier: 3.693A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 84 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 394 through 424 removed outlier: 3.701A pdb=" N SER F 398 " --> pdb=" O GLN F 394 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 452 removed outlier: 3.795A pdb=" N GLY F 450 " --> pdb=" O GLN F 446 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 480 Processing helix chain 'F' and resid 482 through 496 removed outlier: 3.914A pdb=" N LEU F 486 " --> pdb=" O GLY F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.516A pdb=" N PHE F 503 " --> pdb=" O THR F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 531 Processing helix chain 'F' and resid 533 through 540 removed outlier: 4.136A pdb=" N CYS F 537 " --> pdb=" O ASN F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 571 removed outlier: 4.077A pdb=" N ILE F 560 " --> pdb=" O ALA F 556 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE F 569 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU F 570 " --> pdb=" O CYS F 566 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER F 571 " --> pdb=" O VAL F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 578 removed outlier: 4.164A pdb=" N ILE F 577 " --> pdb=" O GLU F 573 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 578 " --> pdb=" O VAL F 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 573 through 578' Processing helix chain 'F' and resid 579 through 593 removed outlier: 3.731A pdb=" N ILE F 583 " --> pdb=" O GLN F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 608 removed outlier: 4.166A pdb=" N LEU F 600 " --> pdb=" O ASN F 596 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP F 601 " --> pdb=" O HIS F 597 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 608 " --> pdb=" O CYS F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 626 removed outlier: 3.648A pdb=" N LEU F 626 " --> pdb=" O THR F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 889 removed outlier: 3.654A pdb=" N GLU F 868 " --> pdb=" O PRO F 864 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS F 873 " --> pdb=" O ARG F 869 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 934 Processing helix chain 'F' and resid 981 through 1003 Processing helix chain 'F' and resid 1028 through 1050 removed outlier: 3.850A pdb=" N LEU F1039 " --> pdb=" O ASN F1035 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS F1040 " --> pdb=" O ARG F1036 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F1050 " --> pdb=" O LEU F1046 " (cutoff:3.500A) Processing helix chain 'F' and resid 1213 through 1216 removed outlier: 3.670A pdb=" N ILE F1216 " --> pdb=" O PHE F1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1213 through 1216' Processing helix chain 'F' and resid 1217 through 1222 Processing helix chain 'F' and resid 1575 through 1580 removed outlier: 3.561A pdb=" N PHE F1580 " --> pdb=" O SER F1576 " (cutoff:3.500A) Processing helix chain 'F' and resid 1656 through 1674 removed outlier: 3.562A pdb=" N GLN F1660 " --> pdb=" O ARG F1656 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN F1661 " --> pdb=" O LEU F1657 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE F1662 " --> pdb=" O ASP F1658 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS F1674 " --> pdb=" O TYR F1670 " (cutoff:3.500A) Processing helix chain 'F' and resid 1679 through 1689 removed outlier: 3.667A pdb=" N HIS F1683 " --> pdb=" O ASN F1679 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA F1684 " --> pdb=" O ARG F1680 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS F1688 " --> pdb=" O ALA F1684 " (cutoff:3.500A) Processing helix chain 'F' and resid 1690 through 1700 removed outlier: 3.586A pdb=" N LEU F1694 " --> pdb=" O ASP F1690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F1695 " --> pdb=" O GLN F1691 " (cutoff:3.500A) Processing helix chain 'F' and resid 1704 through 1720 Processing helix chain 'F' and resid 1721 through 1729 removed outlier: 3.752A pdb=" N ARG F1725 " --> pdb=" O GLU F1721 " (cutoff:3.500A) Processing helix chain 'F' and resid 1739 through 1745 removed outlier: 3.506A pdb=" N ALA F1744 " --> pdb=" O GLU F1741 " (cutoff:3.500A) Processing helix chain 'F' and resid 1804 through 1826 Processing helix chain 'F' and resid 1830 through 1833 Processing helix chain 'F' and resid 1834 through 1852 removed outlier: 3.594A pdb=" N GLN F1838 " --> pdb=" O SER F1834 " (cutoff:3.500A) Proline residue: F1841 - end of helix removed outlier: 3.705A pdb=" N MET F1852 " --> pdb=" O THR F1848 " (cutoff:3.500A) Processing helix chain 'F' and resid 1856 through 1868 Processing helix chain 'F' and resid 1933 through 1984 removed outlier: 4.126A pdb=" N LYS F1983 " --> pdb=" O GLY F1979 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA F1984 " --> pdb=" O ILE F1980 " (cutoff:3.500A) Processing helix chain 'F' and resid 1988 through 2000 Processing helix chain 'F' and resid 2002 through 2011 Processing helix chain 'F' and resid 2025 through 2044 removed outlier: 3.952A pdb=" N ARG F2029 " --> pdb=" O PRO F2025 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP F2031 " --> pdb=" O GLU F2027 " (cutoff:3.500A) Processing helix chain 'F' and resid 2094 through 2110 removed outlier: 4.204A pdb=" N ASP F2110 " --> pdb=" O TRP F2106 " (cutoff:3.500A) Processing helix chain 'F' and resid 2114 through 2130 Processing helix chain 'F' and resid 2131 through 2138 Processing helix chain 'F' and resid 2149 through 2169 Processing helix chain 'F' and resid 2172 through 2188 removed outlier: 3.555A pdb=" N MET F2187 " --> pdb=" O ILE F2183 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN F2188 " --> pdb=" O GLY F2184 " (cutoff:3.500A) Processing helix chain 'F' and resid 2189 through 2194 removed outlier: 3.861A pdb=" N PHE F2192 " --> pdb=" O ASN F2189 " (cutoff:3.500A) Processing helix chain 'F' and resid 2195 through 2203 Processing helix chain 'F' and resid 2203 through 2216 Processing helix chain 'F' and resid 2226 through 2242 removed outlier: 3.638A pdb=" N ARG F2242 " --> pdb=" O CYS F2238 " (cutoff:3.500A) Processing helix chain 'F' and resid 2244 through 2252 Processing helix chain 'F' and resid 2254 through 2263 removed outlier: 3.653A pdb=" N GLY F2263 " --> pdb=" O LEU F2259 " (cutoff:3.500A) Processing helix chain 'F' and resid 2272 through 2282 removed outlier: 3.575A pdb=" N VAL F2276 " --> pdb=" O THR F2272 " (cutoff:3.500A) Processing helix chain 'F' and resid 2285 through 2290 Processing helix chain 'F' and resid 2292 through 2307 removed outlier: 4.189A pdb=" N LEU F2296 " --> pdb=" O GLN F2292 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY F2307 " --> pdb=" O LEU F2303 " (cutoff:3.500A) Processing helix chain 'F' and resid 2311 through 2317 removed outlier: 3.531A pdb=" N ALA F2316 " --> pdb=" O PRO F2312 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F2317 " --> pdb=" O MET F2313 " (cutoff:3.500A) Processing helix chain 'F' and resid 2325 through 2341 removed outlier: 4.135A pdb=" N PHE F2335 " --> pdb=" O ARG F2331 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU F2336 " --> pdb=" O TYR F2332 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F2341 " --> pdb=" O ARG F2337 " (cutoff:3.500A) Processing helix chain 'F' and resid 2347 through 2360 Processing helix chain 'F' and resid 2361 through 2365 removed outlier: 3.544A pdb=" N CYS F2364 " --> pdb=" O LYS F2361 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE F2365 " --> pdb=" O PRO F2362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2361 through 2365' Processing helix chain 'F' and resid 2378 through 2385 Processing helix chain 'F' and resid 2423 through 2437 Processing helix chain 'F' and resid 2441 through 2446 Processing helix chain 'F' and resid 2449 through 2462 removed outlier: 4.304A pdb=" N ARG F2453 " --> pdb=" O GLY F2449 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE F2454 " --> pdb=" O GLU F2450 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F2461 " --> pdb=" O ILE F2457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL F2462 " --> pdb=" O LEU F2458 " (cutoff:3.500A) Processing helix chain 'F' and resid 2463 through 2472 removed outlier: 3.610A pdb=" N LEU F2467 " --> pdb=" O PRO F2463 " (cutoff:3.500A) Processing helix chain 'F' and resid 2496 through 2511 removed outlier: 4.355A pdb=" N LYS F2500 " --> pdb=" O VAL F2496 " (cutoff:3.500A) Processing helix chain 'F' and resid 2519 through 2527 Processing helix chain 'F' and resid 2549 through 2558 removed outlier: 3.657A pdb=" N LEU F2555 " --> pdb=" O LEU F2551 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS F2556 " --> pdb=" O ASN F2552 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA F2558 " --> pdb=" O TYR F2554 " (cutoff:3.500A) Processing helix chain 'F' and resid 2558 through 2566 Processing helix chain 'F' and resid 2580 through 2593 removed outlier: 3.705A pdb=" N LEU F2584 " --> pdb=" O VAL F2580 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS F2585 " --> pdb=" O ASP F2581 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR F2586 " --> pdb=" O SER F2582 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F2587 " --> pdb=" O MET F2583 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR F2588 " --> pdb=" O LEU F2584 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY F2593 " --> pdb=" O ARG F2589 " (cutoff:3.500A) Processing helix chain 'F' and resid 2597 through 2611 removed outlier: 3.839A pdb=" N ASP F2602 " --> pdb=" O LYS F2598 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL F2603 " --> pdb=" O ALA F2599 " (cutoff:3.500A) Processing helix chain 'F' and resid 2618 through 2629 removed outlier: 3.501A pdb=" N HIS F2622 " --> pdb=" O SER F2618 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU F2627 " --> pdb=" O LEU F2623 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL F2628 " --> pdb=" O LEU F2624 " (cutoff:3.500A) Processing helix chain 'F' and resid 2644 through 2653 removed outlier: 3.572A pdb=" N UNK F2650 " --> pdb=" O UNK F2646 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK F2652 " --> pdb=" O UNK F2648 " (cutoff:3.500A) Processing helix chain 'F' and resid 2665 through 2683 removed outlier: 3.836A pdb=" N UNK F2677 " --> pdb=" O UNK F2673 " (cutoff:3.500A) Processing helix chain 'F' and resid 2689 through 2697 Processing helix chain 'F' and resid 2698 through 2700 No H-bonds generated for 'chain 'F' and resid 2698 through 2700' Processing helix chain 'F' and resid 2748 through 2750 No H-bonds generated for 'chain 'F' and resid 2748 through 2750' Processing helix chain 'F' and resid 2751 through 2772 Processing helix chain 'F' and resid 2793 through 2797 Processing helix chain 'F' and resid 2798 through 2819 removed outlier: 3.758A pdb=" N ILE F2804 " --> pdb=" O LYS F2800 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR F2805 " --> pdb=" O ASP F2801 " (cutoff:3.500A) Proline residue: F2808 - end of helix removed outlier: 3.542A pdb=" N TRP F2819 " --> pdb=" O ALA F2815 " (cutoff:3.500A) Processing helix chain 'F' and resid 2868 through 2897 removed outlier: 3.533A pdb=" N GLU F2876 " --> pdb=" O GLN F2872 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN F2877 " --> pdb=" O ALA F2873 " (cutoff:3.500A) Processing helix chain 'F' and resid 2912 through 2933 removed outlier: 4.422A pdb=" N ARG F2918 " --> pdb=" O LYS F2914 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP F2919 " --> pdb=" O GLU F2915 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F2922 " --> pdb=" O ARG F2918 " (cutoff:3.500A) Processing helix chain 'F' and resid 2957 through 2978 removed outlier: 3.566A pdb=" N UNK F2975 " --> pdb=" O UNK F2971 " (cutoff:3.500A) Processing helix chain 'F' and resid 3000 through 3018 removed outlier: 3.589A pdb=" N UNK F3009 " --> pdb=" O UNK F3005 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N UNK F3010 " --> pdb=" O UNK F3006 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK F3015 " --> pdb=" O UNK F3011 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N UNK F3016 " --> pdb=" O UNK F3012 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK F3017 " --> pdb=" O UNK F3013 " (cutoff:3.500A) Processing helix chain 'F' and resid 3033 through 3045 removed outlier: 3.551A pdb=" N UNK F3039 " --> pdb=" O UNK F3035 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N UNK F3043 " --> pdb=" O UNK F3039 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N UNK F3044 " --> pdb=" O UNK F3040 " (cutoff:3.500A) Processing helix chain 'F' and resid 3052 through 3059 removed outlier: 3.573A pdb=" N UNK F3056 " --> pdb=" O UNK F3052 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N UNK F3059 " --> pdb=" O UNK F3055 " (cutoff:3.500A) Processing helix chain 'F' and resid 3147 through 3166 removed outlier: 3.722A pdb=" N UNK F3156 " --> pdb=" O UNK F3152 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK F3163 " --> pdb=" O UNK F3159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK F3166 " --> pdb=" O UNK F3162 " (cutoff:3.500A) Processing helix chain 'F' and resid 3174 through 3187 removed outlier: 3.624A pdb=" N UNK F3179 " --> pdb=" O UNK F3175 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK F3182 " --> pdb=" O UNK F3178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N UNK F3185 " --> pdb=" O UNK F3181 " (cutoff:3.500A) Processing helix chain 'F' and resid 3203 through 3217 removed outlier: 3.656A pdb=" N UNK F3212 " --> pdb=" O UNK F3208 " (cutoff:3.500A) Processing helix chain 'F' and resid 3226 through 3237 removed outlier: 3.721A pdb=" N UNK F3230 " --> pdb=" O UNK F3226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK F3237 " --> pdb=" O UNK F3233 " (cutoff:3.500A) Processing helix chain 'F' and resid 3293 through 3308 removed outlier: 3.524A pdb=" N UNK F3301 " --> pdb=" O UNK F3297 " (cutoff:3.500A) Processing helix chain 'F' and resid 3321 through 3334 removed outlier: 3.769A pdb=" N UNK F3325 " --> pdb=" O UNK F3321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK F3328 " --> pdb=" O UNK F3324 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK F3331 " --> pdb=" O UNK F3327 " (cutoff:3.500A) Processing helix chain 'F' and resid 3347 through 3358 removed outlier: 3.502A pdb=" N UNK F3354 " --> pdb=" O UNK F3350 " (cutoff:3.500A) Processing helix chain 'F' and resid 3367 through 3385 Processing helix chain 'F' and resid 3399 through 3427 removed outlier: 3.520A pdb=" N ALA F3408 " --> pdb=" O ARG F3404 " (cutoff:3.500A) Proline residue: F3411 - end of helix removed outlier: 3.864A pdb=" N ASP F3418 " --> pdb=" O ILE F3414 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN F3419 " --> pdb=" O ARG F3415 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F3421 " --> pdb=" O VAL F3417 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA F3422 " --> pdb=" O ASP F3418 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR F3426 " --> pdb=" O ALA F3422 " (cutoff:3.500A) Processing helix chain 'F' and resid 3429 through 3449 removed outlier: 3.676A pdb=" N ILE F3442 " --> pdb=" O MET F3438 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR F3445 " --> pdb=" O GLU F3441 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER F3447 " --> pdb=" O PHE F3443 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS F3448 " --> pdb=" O ILE F3444 " (cutoff:3.500A) Processing helix chain 'F' and resid 3449 through 3459 removed outlier: 3.576A pdb=" N GLN F3457 " --> pdb=" O LYS F3453 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F3459 " --> pdb=" O GLU F3455 " (cutoff:3.500A) Processing helix chain 'F' and resid 3510 through 3526 Processing helix chain 'F' and resid 3535 through 3544 removed outlier: 3.528A pdb=" N UNK F3539 " --> pdb=" O UNK F3535 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK F3540 " --> pdb=" O UNK F3536 " (cutoff:3.500A) Processing helix chain 'F' and resid 3549 through 3555 Processing helix chain 'F' and resid 3567 through 3574 Processing helix chain 'F' and resid 3587 through 3606 Processing helix chain 'F' and resid 3641 through 3658 removed outlier: 3.809A pdb=" N ASN F3647 " --> pdb=" O HIS F3643 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE F3649 " --> pdb=" O ALA F3645 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU F3650 " --> pdb=" O CYS F3646 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU F3651 " --> pdb=" O ASN F3647 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER F3652 " --> pdb=" O MET F3648 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F3654 " --> pdb=" O LEU F3650 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA F3655 " --> pdb=" O GLU F3651 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP F3657 " --> pdb=" O TYR F3653 " (cutoff:3.500A) Processing helix chain 'F' and resid 3665 through 3674 removed outlier: 3.992A pdb=" N ILE F3670 " --> pdb=" O GLU F3666 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F3671 " --> pdb=" O ASP F3667 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP F3672 " --> pdb=" O ARG F3668 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU F3673 " --> pdb=" O MET F3669 " (cutoff:3.500A) Processing helix chain 'F' and resid 3694 through 3706 removed outlier: 4.198A pdb=" N VAL F3698 " --> pdb=" O LEU F3694 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F3701 " --> pdb=" O LEU F3697 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER F3702 " --> pdb=" O VAL F3698 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG F3703 " --> pdb=" O LEU F3699 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR F3704 " --> pdb=" O HIS F3700 " (cutoff:3.500A) Processing helix chain 'F' and resid 3715 through 3731 removed outlier: 3.557A pdb=" N MET F3719 " --> pdb=" O ASP F3715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP F3723 " --> pdb=" O MET F3719 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F3724 " --> pdb=" O ALA F3720 " (cutoff:3.500A) Processing helix chain 'F' and resid 3748 through 3767 removed outlier: 3.993A pdb=" N LEU F3765 " --> pdb=" O GLN F3761 " (cutoff:3.500A) Processing helix chain 'F' and resid 3769 through 3781 removed outlier: 3.629A pdb=" N MET F3773 " --> pdb=" O GLY F3769 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL F3774 " --> pdb=" O ALA F3770 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F3775 " --> pdb=" O ALA F3771 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE F3778 " --> pdb=" O VAL F3774 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F3779 " --> pdb=" O LEU F3775 " (cutoff:3.500A) Processing helix chain 'F' and resid 3786 through 3800 removed outlier: 3.698A pdb=" N SER F3798 " --> pdb=" O LYS F3794 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F3799 " --> pdb=" O LEU F3795 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU F3800 " --> pdb=" O GLY F3796 " (cutoff:3.500A) Processing helix chain 'F' and resid 3808 through 3813 removed outlier: 3.655A pdb=" N ASP F3813 " --> pdb=" O GLN F3809 " (cutoff:3.500A) Processing helix chain 'F' and resid 3813 through 3818 Processing helix chain 'F' and resid 3822 through 3833 removed outlier: 3.683A pdb=" N ILE F3827 " --> pdb=" O PHE F3823 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN F3828 " --> pdb=" O PHE F3824 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA F3829 " --> pdb=" O GLN F3825 " (cutoff:3.500A) Processing helix chain 'F' and resid 3838 through 3850 removed outlier: 3.716A pdb=" N ARG F3844 " --> pdb=" O ASN F3840 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN F3846 " --> pdb=" O PHE F3842 " (cutoff:3.500A) Processing helix chain 'F' and resid 3875 through 3885 removed outlier: 3.668A pdb=" N PHE F3880 " --> pdb=" O THR F3876 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG F3881 " --> pdb=" O GLN F3877 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F3883 " --> pdb=" O LEU F3879 " (cutoff:3.500A) Processing helix chain 'F' and resid 3886 through 3888 No H-bonds generated for 'chain 'F' and resid 3886 through 3888' Processing helix chain 'F' and resid 3891 through 3900 removed outlier: 3.614A pdb=" N GLN F3895 " --> pdb=" O ASN F3891 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR F3897 " --> pdb=" O ASP F3893 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F3898 " --> pdb=" O PHE F3894 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F3899 " --> pdb=" O GLN F3895 " (cutoff:3.500A) Processing helix chain 'F' and resid 3909 through 3933 removed outlier: 3.961A pdb=" N CYS F3913 " --> pdb=" O ASN F3909 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR F3917 " --> pdb=" O CYS F3913 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU F3918 " --> pdb=" O THR F3914 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F3923 " --> pdb=" O LEU F3919 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE F3928 " --> pdb=" O SER F3924 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR F3932 " --> pdb=" O PHE F3928 " (cutoff:3.500A) Processing helix chain 'F' and resid 3939 through 3964 removed outlier: 3.917A pdb=" N PHE F3957 " --> pdb=" O ALA F3953 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU F3962 " --> pdb=" O ASN F3958 " (cutoff:3.500A) Processing helix chain 'F' and resid 3969 through 3978 removed outlier: 3.621A pdb=" N GLN F3973 " --> pdb=" O THR F3969 " (cutoff:3.500A) Processing helix chain 'F' and resid 3979 through 4001 removed outlier: 3.564A pdb=" N VAL F3984 " --> pdb=" O LEU F3980 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL F3985 " --> pdb=" O TRP F3981 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY F3986 " --> pdb=" O ASP F3982 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F3990 " --> pdb=" O GLY F3986 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS F3993 " --> pdb=" O HIS F3989 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET F3996 " --> pdb=" O ALA F3992 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN F4000 " --> pdb=" O MET F3996 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP F4001 " --> pdb=" O LYS F3997 " (cutoff:3.500A) Processing helix chain 'F' and resid 4004 through 4026 removed outlier: 3.675A pdb=" N LEU F4008 " --> pdb=" O GLN F4004 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F4014 " --> pdb=" O GLU F4010 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F4015 " --> pdb=" O LEU F4011 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP F4017 " --> pdb=" O ASP F4013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F4020 " --> pdb=" O LYS F4016 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET F4021 " --> pdb=" O ASP F4017 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU F4022 " --> pdb=" O MET F4018 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU F4023 " --> pdb=" O VAL F4019 " (cutoff:3.500A) Processing helix chain 'F' and resid 4035 through 4037 No H-bonds generated for 'chain 'F' and resid 4035 through 4037' Processing helix chain 'F' and resid 4038 through 4046 removed outlier: 3.514A pdb=" N LEU F4043 " --> pdb=" O MET F4039 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL F4044 " --> pdb=" O VAL F4040 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU F4045 " --> pdb=" O ASP F4041 " (cutoff:3.500A) Processing helix chain 'F' and resid 4046 through 4067 removed outlier: 4.083A pdb=" N MET F4052 " --> pdb=" O SER F4048 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE F4053 " --> pdb=" O ASN F4049 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE F4056 " --> pdb=" O MET F4052 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE F4060 " --> pdb=" O PHE F4056 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS F4064 " --> pdb=" O PHE F4060 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP F4065 " --> pdb=" O LEU F4061 " (cutoff:3.500A) Processing helix chain 'F' and resid 4069 through 4076 removed outlier: 3.632A pdb=" N GLN F4073 " --> pdb=" O SER F4069 " (cutoff:3.500A) Processing helix chain 'F' and resid 4127 through 4149 removed outlier: 3.669A pdb=" N ALA F4131 " --> pdb=" O PHE F4127 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP F4133 " --> pdb=" O GLU F4129 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE F4134 " --> pdb=" O PRO F4130 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F4139 " --> pdb=" O GLY F4135 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER F4146 " --> pdb=" O LEU F4142 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU F4147 " --> pdb=" O THR F4143 " (cutoff:3.500A) Processing helix chain 'F' and resid 4152 through 4162 Processing helix chain 'F' and resid 4162 through 4169 removed outlier: 3.507A pdb=" N TYR F4168 " --> pdb=" O SER F4164 " (cutoff:3.500A) Processing helix chain 'F' and resid 4193 through 4201 removed outlier: 3.693A pdb=" N GLU F4201 " --> pdb=" O ARG F4197 " (cutoff:3.500A) Processing helix chain 'F' and resid 4202 through 4216 removed outlier: 3.618A pdb=" N PHE F4214 " --> pdb=" O ARG F4210 " (cutoff:3.500A) Processing helix chain 'F' and resid 4221 through 4239 removed outlier: 3.602A pdb=" N MET F4226 " --> pdb=" O GLU F4222 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU F4227 " --> pdb=" O SER F4223 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F4228 " --> pdb=" O GLU F4224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F4229 " --> pdb=" O LYS F4225 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL F4230 " --> pdb=" O MET F4226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER F4231 " --> pdb=" O GLU F4227 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F4238 " --> pdb=" O GLU F4234 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU F4239 " --> pdb=" O ASP F4235 " (cutoff:3.500A) Processing helix chain 'F' and resid 4544 through 4556 removed outlier: 3.501A pdb=" N LEU F4550 " --> pdb=" O ARG F4546 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN F4551 " --> pdb=" O VAL F4547 " (cutoff:3.500A) Processing helix chain 'F' and resid 4556 through 4576 removed outlier: 3.529A pdb=" N ARG F4561 " --> pdb=" O PHE F4557 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE F4562 " --> pdb=" O TYR F4558 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU F4563 " --> pdb=" O THR F4559 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F4564 " --> pdb=" O LEU F4560 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F4565 " --> pdb=" O ARG F4561 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA F4568 " --> pdb=" O ALA F4564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F4569 " --> pdb=" O LEU F4565 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE F4573 " --> pdb=" O PHE F4569 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE F4574 " --> pdb=" O ALA F4570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F4575 " --> pdb=" O ILE F4571 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU F4576 " --> pdb=" O ASN F4572 " (cutoff:3.500A) Processing helix chain 'F' and resid 4639 through 4661 removed outlier: 3.645A pdb=" N SER F4645 " --> pdb=" O LEU F4641 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU F4646 " --> pdb=" O ARG F4642 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F4647 " --> pdb=" O CYS F4643 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR F4649 " --> pdb=" O SER F4645 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F4652 " --> pdb=" O HIS F4648 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F4656 " --> pdb=" O ALA F4652 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE F4657 " --> pdb=" O PHE F4653 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS F4661 " --> pdb=" O ILE F4657 " (cutoff:3.500A) Processing helix chain 'F' and resid 4663 through 4681 removed outlier: 3.794A pdb=" N GLU F4674 " --> pdb=" O LYS F4670 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F4680 " --> pdb=" O ALA F4676 " (cutoff:3.500A) Processing helix chain 'F' and resid 4696 through 4700 Processing helix chain 'F' and resid 4721 through 4726 removed outlier: 3.797A pdb=" N LYS F4725 " --> pdb=" O LYS F4721 " (cutoff:3.500A) Processing helix chain 'F' and resid 4726 through 4735 removed outlier: 4.481A pdb=" N TYR F4730 " --> pdb=" O HIS F4726 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG F4732 " --> pdb=" O ASP F4728 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLU F4733 " --> pdb=" O ILE F4729 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG F4734 " --> pdb=" O TYR F4730 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F4735 " --> pdb=" O GLY F4731 " (cutoff:3.500A) Processing helix chain 'F' and resid 4762 through 4767 Processing helix chain 'F' and resid 4770 through 4784 removed outlier: 3.656A pdb=" N TRP F4776 " --> pdb=" O LYS F4772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F4780 " --> pdb=" O TRP F4776 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F4781 " --> pdb=" O LYS F4777 " (cutoff:3.500A) Processing helix chain 'F' and resid 4784 through 4799 removed outlier: 3.609A pdb=" N TYR F4793 " --> pdb=" O TYR F4789 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET F4794 " --> pdb=" O LEU F4790 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET F4796 " --> pdb=" O TRP F4792 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F4797 " --> pdb=" O TYR F4793 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F4798 " --> pdb=" O MET F4794 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU F4799 " --> pdb=" O VAL F4795 " (cutoff:3.500A) Processing helix chain 'F' and resid 4800 through 4802 No H-bonds generated for 'chain 'F' and resid 4800 through 4802' Processing helix chain 'F' and resid 4806 through 4815 removed outlier: 3.974A pdb=" N HIS F4810 " --> pdb=" O PHE F4806 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F4812 " --> pdb=" O ALA F4808 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP F4813 " --> pdb=" O ALA F4809 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA F4815 " --> pdb=" O LEU F4811 " (cutoff:3.500A) Processing helix chain 'F' and resid 4821 through 4830 removed outlier: 4.083A pdb=" N LEU F4825 " --> pdb=" O LEU F4821 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR F4829 " --> pdb=" O LEU F4825 " (cutoff:3.500A) Processing helix chain 'F' and resid 4831 through 4856 removed outlier: 3.933A pdb=" N LEU F4835 " --> pdb=" O ASN F4831 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET F4837 " --> pdb=" O LYS F4833 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F4846 " --> pdb=" O LEU F4842 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F4852 " --> pdb=" O LEU F4848 " (cutoff:3.500A) Processing helix chain 'F' and resid 4872 through 4875 removed outlier: 3.741A pdb=" N ASP F4875 " --> pdb=" O MET F4872 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 4872 through 4875' Processing helix chain 'F' and resid 4876 through 4892 removed outlier: 3.775A pdb=" N TYR F4881 " --> pdb=" O MET F4877 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F4889 " --> pdb=" O MET F4885 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG F4890 " --> pdb=" O TYR F4886 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY F4892 " --> pdb=" O GLY F4888 " (cutoff:3.500A) Processing helix chain 'F' and resid 4894 through 4898 removed outlier: 3.944A pdb=" N ASP F4897 " --> pdb=" O GLY F4894 " (cutoff:3.500A) Processing helix chain 'F' and resid 4907 through 4922 removed outlier: 3.563A pdb=" N VAL F4922 " --> pdb=" O PHE F4918 " (cutoff:3.500A) Processing helix chain 'F' and resid 4924 through 4955 removed outlier: 3.531A pdb=" N ALA F4928 " --> pdb=" O VAL F4924 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F4934 " --> pdb=" O ILE F4930 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU F4953 " --> pdb=" O ARG F4949 " (cutoff:3.500A) Processing helix chain 'F' and resid 4964 through 4968 removed outlier: 4.035A pdb=" N ASP F4967 " --> pdb=" O ASP F4964 " (cutoff:3.500A) Processing helix chain 'F' and resid 4972 through 4977 removed outlier: 4.287A pdb=" N THR F4977 " --> pdb=" O PHE F4973 " (cutoff:3.500A) Processing helix chain 'F' and resid 4986 through 4996 Processing helix chain 'F' and resid 4997 through 5001 removed outlier: 3.548A pdb=" N HIS F5001 " --> pdb=" O GLU F4998 " (cutoff:3.500A) Processing helix chain 'F' and resid 5002 through 5014 removed outlier: 3.610A pdb=" N TYR F5007 " --> pdb=" O GLY F5003 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU F5014 " --> pdb=" O LYS F5010 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 43 Processing helix chain 'G' and resid 56 through 65 removed outlier: 3.693A pdb=" N GLN G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 84 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'H' and resid 394 through 424 removed outlier: 3.701A pdb=" N SER H 398 " --> pdb=" O GLN H 394 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS H 424 " --> pdb=" O SER H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 452 removed outlier: 3.795A pdb=" N GLY H 450 " --> pdb=" O GLN H 446 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR H 451 " --> pdb=" O ASP H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 480 Processing helix chain 'H' and resid 482 through 496 removed outlier: 3.914A pdb=" N LEU H 486 " --> pdb=" O GLY H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 507 removed outlier: 3.517A pdb=" N PHE H 503 " --> pdb=" O THR H 499 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 531 Processing helix chain 'H' and resid 533 through 540 removed outlier: 4.136A pdb=" N CYS H 537 " --> pdb=" O ASN H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 552 Processing helix chain 'H' and resid 556 through 571 removed outlier: 4.077A pdb=" N ILE H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 569 " --> pdb=" O TYR H 565 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU H 570 " --> pdb=" O CYS H 566 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER H 571 " --> pdb=" O VAL H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 578 removed outlier: 4.163A pdb=" N ILE H 577 " --> pdb=" O GLU H 573 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE H 578 " --> pdb=" O VAL H 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 573 through 578' Processing helix chain 'H' and resid 579 through 593 removed outlier: 3.731A pdb=" N ILE H 583 " --> pdb=" O GLN H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 608 removed outlier: 4.166A pdb=" N LEU H 600 " --> pdb=" O ASN H 596 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP H 601 " --> pdb=" O HIS H 597 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 608 " --> pdb=" O CYS H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 615 through 626 removed outlier: 3.648A pdb=" N LEU H 626 " --> pdb=" O THR H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 864 through 889 removed outlier: 3.654A pdb=" N GLU H 868 " --> pdb=" O PRO H 864 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS H 873 " --> pdb=" O ARG H 869 " (cutoff:3.500A) Processing helix chain 'H' and resid 914 through 934 Processing helix chain 'H' and resid 981 through 1003 Processing helix chain 'H' and resid 1028 through 1050 removed outlier: 3.850A pdb=" N LEU H1039 " --> pdb=" O ASN H1035 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS H1040 " --> pdb=" O ARG H1036 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY H1050 " --> pdb=" O LEU H1046 " (cutoff:3.500A) Processing helix chain 'H' and resid 1213 through 1216 removed outlier: 3.671A pdb=" N ILE H1216 " --> pdb=" O PHE H1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1213 through 1216' Processing helix chain 'H' and resid 1217 through 1222 Processing helix chain 'H' and resid 1575 through 1580 removed outlier: 3.561A pdb=" N PHE H1580 " --> pdb=" O SER H1576 " (cutoff:3.500A) Processing helix chain 'H' and resid 1656 through 1674 removed outlier: 3.562A pdb=" N GLN H1660 " --> pdb=" O ARG H1656 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN H1661 " --> pdb=" O LEU H1657 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE H1662 " --> pdb=" O ASP H1658 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS H1674 " --> pdb=" O TYR H1670 " (cutoff:3.500A) Processing helix chain 'H' and resid 1679 through 1689 removed outlier: 3.669A pdb=" N HIS H1683 " --> pdb=" O ASN H1679 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA H1684 " --> pdb=" O ARG H1680 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS H1688 " --> pdb=" O ALA H1684 " (cutoff:3.500A) Processing helix chain 'H' and resid 1690 through 1700 removed outlier: 3.585A pdb=" N LEU H1694 " --> pdb=" O ASP H1690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H1695 " --> pdb=" O GLN H1691 " (cutoff:3.500A) Processing helix chain 'H' and resid 1704 through 1720 Processing helix chain 'H' and resid 1721 through 1729 removed outlier: 3.753A pdb=" N ARG H1725 " --> pdb=" O GLU H1721 " (cutoff:3.500A) Processing helix chain 'H' and resid 1739 through 1745 removed outlier: 3.507A pdb=" N ALA H1744 " --> pdb=" O GLU H1741 " (cutoff:3.500A) Processing helix chain 'H' and resid 1804 through 1826 Processing helix chain 'H' and resid 1830 through 1833 Processing helix chain 'H' and resid 1834 through 1852 removed outlier: 3.593A pdb=" N GLN H1838 " --> pdb=" O SER H1834 " (cutoff:3.500A) Proline residue: H1841 - end of helix removed outlier: 3.705A pdb=" N MET H1852 " --> pdb=" O THR H1848 " (cutoff:3.500A) Processing helix chain 'H' and resid 1856 through 1868 Processing helix chain 'H' and resid 1933 through 1984 removed outlier: 4.126A pdb=" N LYS H1983 " --> pdb=" O GLY H1979 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA H1984 " --> pdb=" O ILE H1980 " (cutoff:3.500A) Processing helix chain 'H' and resid 1988 through 2000 Processing helix chain 'H' and resid 2002 through 2011 Processing helix chain 'H' and resid 2025 through 2044 removed outlier: 3.951A pdb=" N ARG H2029 " --> pdb=" O PRO H2025 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP H2031 " --> pdb=" O GLU H2027 " (cutoff:3.500A) Processing helix chain 'H' and resid 2094 through 2110 removed outlier: 4.205A pdb=" N ASP H2110 " --> pdb=" O TRP H2106 " (cutoff:3.500A) Processing helix chain 'H' and resid 2114 through 2130 Processing helix chain 'H' and resid 2131 through 2138 Processing helix chain 'H' and resid 2149 through 2169 Processing helix chain 'H' and resid 2172 through 2188 removed outlier: 3.555A pdb=" N MET H2187 " --> pdb=" O ILE H2183 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN H2188 " --> pdb=" O GLY H2184 " (cutoff:3.500A) Processing helix chain 'H' and resid 2189 through 2194 removed outlier: 3.861A pdb=" N PHE H2192 " --> pdb=" O ASN H2189 " (cutoff:3.500A) Processing helix chain 'H' and resid 2195 through 2203 Processing helix chain 'H' and resid 2203 through 2216 Processing helix chain 'H' and resid 2226 through 2242 removed outlier: 3.638A pdb=" N ARG H2242 " --> pdb=" O CYS H2238 " (cutoff:3.500A) Processing helix chain 'H' and resid 2244 through 2252 Processing helix chain 'H' and resid 2254 through 2263 removed outlier: 3.653A pdb=" N GLY H2263 " --> pdb=" O LEU H2259 " (cutoff:3.500A) Processing helix chain 'H' and resid 2272 through 2282 removed outlier: 3.575A pdb=" N VAL H2276 " --> pdb=" O THR H2272 " (cutoff:3.500A) Processing helix chain 'H' and resid 2285 through 2290 Processing helix chain 'H' and resid 2292 through 2307 removed outlier: 4.189A pdb=" N LEU H2296 " --> pdb=" O GLN H2292 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY H2307 " --> pdb=" O LEU H2303 " (cutoff:3.500A) Processing helix chain 'H' and resid 2311 through 2317 removed outlier: 3.531A pdb=" N ALA H2316 " --> pdb=" O PRO H2312 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS H2317 " --> pdb=" O MET H2313 " (cutoff:3.500A) Processing helix chain 'H' and resid 2325 through 2341 removed outlier: 4.134A pdb=" N PHE H2335 " --> pdb=" O ARG H2331 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU H2336 " --> pdb=" O TYR H2332 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE H2341 " --> pdb=" O ARG H2337 " (cutoff:3.500A) Processing helix chain 'H' and resid 2347 through 2360 Processing helix chain 'H' and resid 2361 through 2365 removed outlier: 3.544A pdb=" N CYS H2364 " --> pdb=" O LYS H2361 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE H2365 " --> pdb=" O PRO H2362 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2361 through 2365' Processing helix chain 'H' and resid 2378 through 2385 Processing helix chain 'H' and resid 2423 through 2437 Processing helix chain 'H' and resid 2441 through 2446 Processing helix chain 'H' and resid 2449 through 2462 removed outlier: 4.303A pdb=" N ARG H2453 " --> pdb=" O GLY H2449 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE H2454 " --> pdb=" O GLU H2450 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H2461 " --> pdb=" O ILE H2457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL H2462 " --> pdb=" O LEU H2458 " (cutoff:3.500A) Processing helix chain 'H' and resid 2463 through 2472 removed outlier: 3.611A pdb=" N LEU H2467 " --> pdb=" O PRO H2463 " (cutoff:3.500A) Processing helix chain 'H' and resid 2496 through 2511 removed outlier: 4.355A pdb=" N LYS H2500 " --> pdb=" O VAL H2496 " (cutoff:3.500A) Processing helix chain 'H' and resid 2519 through 2527 Processing helix chain 'H' and resid 2549 through 2558 removed outlier: 3.657A pdb=" N LEU H2555 " --> pdb=" O LEU H2551 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS H2556 " --> pdb=" O ASN H2552 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA H2558 " --> pdb=" O TYR H2554 " (cutoff:3.500A) Processing helix chain 'H' and resid 2558 through 2566 Processing helix chain 'H' and resid 2580 through 2593 removed outlier: 3.704A pdb=" N LEU H2584 " --> pdb=" O VAL H2580 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS H2585 " --> pdb=" O ASP H2581 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR H2586 " --> pdb=" O SER H2582 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H2587 " --> pdb=" O MET H2583 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR H2588 " --> pdb=" O LEU H2584 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY H2593 " --> pdb=" O ARG H2589 " (cutoff:3.500A) Processing helix chain 'H' and resid 2597 through 2611 removed outlier: 3.839A pdb=" N ASP H2602 " --> pdb=" O LYS H2598 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL H2603 " --> pdb=" O ALA H2599 " (cutoff:3.500A) Processing helix chain 'H' and resid 2618 through 2629 removed outlier: 3.501A pdb=" N HIS H2622 " --> pdb=" O SER H2618 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H2627 " --> pdb=" O LEU H2623 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H2628 " --> pdb=" O LEU H2624 " (cutoff:3.500A) Processing helix chain 'H' and resid 2644 through 2653 removed outlier: 3.572A pdb=" N UNK H2650 " --> pdb=" O UNK H2646 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N UNK H2652 " --> pdb=" O UNK H2648 " (cutoff:3.500A) Processing helix chain 'H' and resid 2665 through 2683 removed outlier: 3.836A pdb=" N UNK H2677 " --> pdb=" O UNK H2673 " (cutoff:3.500A) Processing helix chain 'H' and resid 2689 through 2697 Processing helix chain 'H' and resid 2698 through 2700 No H-bonds generated for 'chain 'H' and resid 2698 through 2700' Processing helix chain 'H' and resid 2748 through 2750 No H-bonds generated for 'chain 'H' and resid 2748 through 2750' Processing helix chain 'H' and resid 2751 through 2772 Processing helix chain 'H' and resid 2793 through 2797 Processing helix chain 'H' and resid 2798 through 2819 removed outlier: 3.758A pdb=" N ILE H2804 " --> pdb=" O LYS H2800 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR H2805 " --> pdb=" O ASP H2801 " (cutoff:3.500A) Proline residue: H2808 - end of helix removed outlier: 3.542A pdb=" N TRP H2819 " --> pdb=" O ALA H2815 " (cutoff:3.500A) Processing helix chain 'H' and resid 2868 through 2897 removed outlier: 3.533A pdb=" N GLU H2876 " --> pdb=" O GLN H2872 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN H2877 " --> pdb=" O ALA H2873 " (cutoff:3.500A) Processing helix chain 'H' and resid 2912 through 2933 removed outlier: 4.422A pdb=" N ARG H2918 " --> pdb=" O LYS H2914 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP H2919 " --> pdb=" O GLU H2915 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS H2922 " --> pdb=" O ARG H2918 " (cutoff:3.500A) Processing helix chain 'H' and resid 2957 through 2978 removed outlier: 3.565A pdb=" N UNK H2975 " --> pdb=" O UNK H2971 " (cutoff:3.500A) Processing helix chain 'H' and resid 3000 through 3018 removed outlier: 3.590A pdb=" N UNK H3009 " --> pdb=" O UNK H3005 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N UNK H3010 " --> pdb=" O UNK H3006 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK H3015 " --> pdb=" O UNK H3011 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N UNK H3016 " --> pdb=" O UNK H3012 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK H3017 " --> pdb=" O UNK H3013 " (cutoff:3.500A) Processing helix chain 'H' and resid 3033 through 3045 removed outlier: 3.552A pdb=" N UNK H3039 " --> pdb=" O UNK H3035 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N UNK H3043 " --> pdb=" O UNK H3039 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N UNK H3044 " --> pdb=" O UNK H3040 " (cutoff:3.500A) Processing helix chain 'H' and resid 3052 through 3059 removed outlier: 3.572A pdb=" N UNK H3056 " --> pdb=" O UNK H3052 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N UNK H3059 " --> pdb=" O UNK H3055 " (cutoff:3.500A) Processing helix chain 'H' and resid 3147 through 3166 removed outlier: 3.722A pdb=" N UNK H3156 " --> pdb=" O UNK H3152 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK H3163 " --> pdb=" O UNK H3159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK H3166 " --> pdb=" O UNK H3162 " (cutoff:3.500A) Processing helix chain 'H' and resid 3174 through 3187 removed outlier: 3.624A pdb=" N UNK H3179 " --> pdb=" O UNK H3175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK H3182 " --> pdb=" O UNK H3178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK H3185 " --> pdb=" O UNK H3181 " (cutoff:3.500A) Processing helix chain 'H' and resid 3203 through 3217 removed outlier: 3.655A pdb=" N UNK H3212 " --> pdb=" O UNK H3208 " (cutoff:3.500A) Processing helix chain 'H' and resid 3226 through 3237 removed outlier: 3.721A pdb=" N UNK H3230 " --> pdb=" O UNK H3226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK H3237 " --> pdb=" O UNK H3233 " (cutoff:3.500A) Processing helix chain 'H' and resid 3293 through 3308 removed outlier: 3.524A pdb=" N UNK H3301 " --> pdb=" O UNK H3297 " (cutoff:3.500A) Processing helix chain 'H' and resid 3321 through 3334 removed outlier: 3.769A pdb=" N UNK H3325 " --> pdb=" O UNK H3321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK H3328 " --> pdb=" O UNK H3324 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK H3331 " --> pdb=" O UNK H3327 " (cutoff:3.500A) Processing helix chain 'H' and resid 3347 through 3358 removed outlier: 3.501A pdb=" N UNK H3354 " --> pdb=" O UNK H3350 " (cutoff:3.500A) Processing helix chain 'H' and resid 3367 through 3385 Processing helix chain 'H' and resid 3399 through 3427 removed outlier: 3.519A pdb=" N ALA H3408 " --> pdb=" O ARG H3404 " (cutoff:3.500A) Proline residue: H3411 - end of helix removed outlier: 3.864A pdb=" N ASP H3418 " --> pdb=" O ILE H3414 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN H3419 " --> pdb=" O ARG H3415 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG H3421 " --> pdb=" O VAL H3417 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA H3422 " --> pdb=" O ASP H3418 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR H3426 " --> pdb=" O ALA H3422 " (cutoff:3.500A) Processing helix chain 'H' and resid 3429 through 3449 removed outlier: 3.675A pdb=" N ILE H3442 " --> pdb=" O MET H3438 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR H3445 " --> pdb=" O GLU H3441 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER H3447 " --> pdb=" O PHE H3443 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS H3448 " --> pdb=" O ILE H3444 " (cutoff:3.500A) Processing helix chain 'H' and resid 3449 through 3459 removed outlier: 3.576A pdb=" N GLN H3457 " --> pdb=" O LYS H3453 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE H3459 " --> pdb=" O GLU H3455 " (cutoff:3.500A) Processing helix chain 'H' and resid 3510 through 3526 Processing helix chain 'H' and resid 3535 through 3544 removed outlier: 3.527A pdb=" N UNK H3539 " --> pdb=" O UNK H3535 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK H3540 " --> pdb=" O UNK H3536 " (cutoff:3.500A) Processing helix chain 'H' and resid 3549 through 3555 Processing helix chain 'H' and resid 3567 through 3574 Processing helix chain 'H' and resid 3587 through 3606 Processing helix chain 'H' and resid 3641 through 3658 removed outlier: 3.810A pdb=" N ASN H3647 " --> pdb=" O HIS H3643 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE H3649 " --> pdb=" O ALA H3645 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU H3650 " --> pdb=" O CYS H3646 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU H3651 " --> pdb=" O ASN H3647 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER H3652 " --> pdb=" O MET H3648 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS H3654 " --> pdb=" O LEU H3650 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA H3655 " --> pdb=" O GLU H3651 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP H3657 " --> pdb=" O TYR H3653 " (cutoff:3.500A) Processing helix chain 'H' and resid 3665 through 3674 removed outlier: 3.992A pdb=" N ILE H3670 " --> pdb=" O GLU H3666 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP H3671 " --> pdb=" O ASP H3667 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP H3672 " --> pdb=" O ARG H3668 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU H3673 " --> pdb=" O MET H3669 " (cutoff:3.500A) Processing helix chain 'H' and resid 3694 through 3706 removed outlier: 4.198A pdb=" N VAL H3698 " --> pdb=" O LEU H3694 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE H3701 " --> pdb=" O LEU H3697 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER H3702 " --> pdb=" O VAL H3698 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG H3703 " --> pdb=" O LEU H3699 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR H3704 " --> pdb=" O HIS H3700 " (cutoff:3.500A) Processing helix chain 'H' and resid 3715 through 3731 removed outlier: 3.557A pdb=" N MET H3719 " --> pdb=" O ASP H3715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP H3723 " --> pdb=" O MET H3719 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H3724 " --> pdb=" O ALA H3720 " (cutoff:3.500A) Processing helix chain 'H' and resid 3748 through 3767 removed outlier: 3.993A pdb=" N LEU H3765 " --> pdb=" O GLN H3761 " (cutoff:3.500A) Processing helix chain 'H' and resid 3769 through 3781 removed outlier: 3.628A pdb=" N MET H3773 " --> pdb=" O GLY H3769 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H3774 " --> pdb=" O ALA H3770 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU H3775 " --> pdb=" O ALA H3771 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE H3778 " --> pdb=" O VAL H3774 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER H3779 " --> pdb=" O LEU H3775 " (cutoff:3.500A) Processing helix chain 'H' and resid 3786 through 3800 removed outlier: 3.698A pdb=" N SER H3798 " --> pdb=" O LYS H3794 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H3799 " --> pdb=" O LEU H3795 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU H3800 " --> pdb=" O GLY H3796 " (cutoff:3.500A) Processing helix chain 'H' and resid 3808 through 3813 removed outlier: 3.655A pdb=" N ASP H3813 " --> pdb=" O GLN H3809 " (cutoff:3.500A) Processing helix chain 'H' and resid 3813 through 3818 Processing helix chain 'H' and resid 3822 through 3833 removed outlier: 3.683A pdb=" N ILE H3827 " --> pdb=" O PHE H3823 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN H3828 " --> pdb=" O PHE H3824 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA H3829 " --> pdb=" O GLN H3825 " (cutoff:3.500A) Processing helix chain 'H' and resid 3838 through 3850 removed outlier: 3.715A pdb=" N ARG H3844 " --> pdb=" O ASN H3840 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN H3846 " --> pdb=" O PHE H3842 " (cutoff:3.500A) Processing helix chain 'H' and resid 3875 through 3885 removed outlier: 3.667A pdb=" N PHE H3880 " --> pdb=" O THR H3876 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG H3881 " --> pdb=" O GLN H3877 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU H3883 " --> pdb=" O LEU H3879 " (cutoff:3.500A) Processing helix chain 'H' and resid 3886 through 3888 No H-bonds generated for 'chain 'H' and resid 3886 through 3888' Processing helix chain 'H' and resid 3891 through 3900 removed outlier: 3.614A pdb=" N GLN H3895 " --> pdb=" O ASN H3891 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR H3897 " --> pdb=" O ASP H3893 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU H3898 " --> pdb=" O PHE H3894 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG H3899 " --> pdb=" O GLN H3895 " (cutoff:3.500A) Processing helix chain 'H' and resid 3909 through 3933 removed outlier: 3.961A pdb=" N CYS H3913 " --> pdb=" O ASN H3909 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR H3917 " --> pdb=" O CYS H3913 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU H3918 " --> pdb=" O THR H3914 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU H3923 " --> pdb=" O LEU H3919 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE H3928 " --> pdb=" O SER H3924 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H3932 " --> pdb=" O PHE H3928 " (cutoff:3.500A) Processing helix chain 'H' and resid 3939 through 3964 removed outlier: 3.917A pdb=" N PHE H3957 " --> pdb=" O ALA H3953 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU H3962 " --> pdb=" O ASN H3958 " (cutoff:3.500A) Processing helix chain 'H' and resid 3969 through 3978 removed outlier: 3.623A pdb=" N GLN H3973 " --> pdb=" O THR H3969 " (cutoff:3.500A) Processing helix chain 'H' and resid 3979 through 4001 removed outlier: 3.564A pdb=" N VAL H3984 " --> pdb=" O LEU H3980 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL H3985 " --> pdb=" O TRP H3981 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY H3986 " --> pdb=" O ASP H3982 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL H3990 " --> pdb=" O GLY H3986 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS H3993 " --> pdb=" O HIS H3989 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET H3996 " --> pdb=" O ALA H3992 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN H4000 " --> pdb=" O MET H3996 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP H4001 " --> pdb=" O LYS H3997 " (cutoff:3.500A) Processing helix chain 'H' and resid 4004 through 4026 removed outlier: 3.675A pdb=" N LEU H4008 " --> pdb=" O GLN H4004 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H4014 " --> pdb=" O GLU H4010 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN H4015 " --> pdb=" O LEU H4011 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP H4017 " --> pdb=" O ASP H4013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H4020 " --> pdb=" O LYS H4016 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET H4021 " --> pdb=" O ASP H4017 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU H4022 " --> pdb=" O MET H4018 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU H4023 " --> pdb=" O VAL H4019 " (cutoff:3.500A) Processing helix chain 'H' and resid 4035 through 4037 No H-bonds generated for 'chain 'H' and resid 4035 through 4037' Processing helix chain 'H' and resid 4038 through 4046 removed outlier: 3.513A pdb=" N LEU H4043 " --> pdb=" O MET H4039 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL H4044 " --> pdb=" O VAL H4040 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU H4045 " --> pdb=" O ASP H4041 " (cutoff:3.500A) Processing helix chain 'H' and resid 4046 through 4067 removed outlier: 4.083A pdb=" N MET H4052 " --> pdb=" O SER H4048 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE H4053 " --> pdb=" O ASN H4049 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE H4056 " --> pdb=" O MET H4052 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE H4060 " --> pdb=" O PHE H4056 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS H4064 " --> pdb=" O PHE H4060 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP H4065 " --> pdb=" O LEU H4061 " (cutoff:3.500A) Processing helix chain 'H' and resid 4069 through 4076 removed outlier: 3.633A pdb=" N GLN H4073 " --> pdb=" O SER H4069 " (cutoff:3.500A) Processing helix chain 'H' and resid 4127 through 4149 removed outlier: 3.669A pdb=" N ALA H4131 " --> pdb=" O PHE H4127 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP H4133 " --> pdb=" O GLU H4129 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H4134 " --> pdb=" O PRO H4130 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA H4139 " --> pdb=" O GLY H4135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER H4146 " --> pdb=" O LEU H4142 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU H4147 " --> pdb=" O THR H4143 " (cutoff:3.500A) Processing helix chain 'H' and resid 4152 through 4162 Processing helix chain 'H' and resid 4162 through 4169 removed outlier: 3.507A pdb=" N TYR H4168 " --> pdb=" O SER H4164 " (cutoff:3.500A) Processing helix chain 'H' and resid 4193 through 4201 removed outlier: 3.693A pdb=" N GLU H4201 " --> pdb=" O ARG H4197 " (cutoff:3.500A) Processing helix chain 'H' and resid 4202 through 4216 removed outlier: 3.618A pdb=" N PHE H4214 " --> pdb=" O ARG H4210 " (cutoff:3.500A) Processing helix chain 'H' and resid 4221 through 4239 removed outlier: 3.603A pdb=" N MET H4226 " --> pdb=" O GLU H4222 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU H4227 " --> pdb=" O SER H4223 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU H4228 " --> pdb=" O GLU H4224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H4229 " --> pdb=" O LYS H4225 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL H4230 " --> pdb=" O MET H4226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER H4231 " --> pdb=" O GLU H4227 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE H4238 " --> pdb=" O GLU H4234 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU H4239 " --> pdb=" O ASP H4235 " (cutoff:3.500A) Processing helix chain 'H' and resid 4544 through 4556 removed outlier: 3.501A pdb=" N LEU H4550 " --> pdb=" O ARG H4546 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN H4551 " --> pdb=" O VAL H4547 " (cutoff:3.500A) Processing helix chain 'H' and resid 4556 through 4576 removed outlier: 3.529A pdb=" N ARG H4561 " --> pdb=" O PHE H4557 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE H4562 " --> pdb=" O TYR H4558 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU H4563 " --> pdb=" O THR H4559 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA H4564 " --> pdb=" O LEU H4560 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H4565 " --> pdb=" O ARG H4561 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA H4568 " --> pdb=" O ALA H4564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H4569 " --> pdb=" O LEU H4565 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE H4573 " --> pdb=" O PHE H4569 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE H4574 " --> pdb=" O ALA H4570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H4575 " --> pdb=" O ILE H4571 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H4576 " --> pdb=" O ASN H4572 " (cutoff:3.500A) Processing helix chain 'H' and resid 4639 through 4661 removed outlier: 3.645A pdb=" N SER H4645 " --> pdb=" O LEU H4641 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU H4646 " --> pdb=" O ARG H4642 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU H4647 " --> pdb=" O CYS H4643 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H4649 " --> pdb=" O SER H4645 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H4652 " --> pdb=" O HIS H4648 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE H4656 " --> pdb=" O ALA H4652 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE H4657 " --> pdb=" O PHE H4653 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS H4661 " --> pdb=" O ILE H4657 " (cutoff:3.500A) Processing helix chain 'H' and resid 4663 through 4681 removed outlier: 3.795A pdb=" N GLU H4674 " --> pdb=" O LYS H4670 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU H4680 " --> pdb=" O ALA H4676 " (cutoff:3.500A) Processing helix chain 'H' and resid 4696 through 4700 Processing helix chain 'H' and resid 4721 through 4726 removed outlier: 3.798A pdb=" N LYS H4725 " --> pdb=" O LYS H4721 " (cutoff:3.500A) Processing helix chain 'H' and resid 4726 through 4735 removed outlier: 4.481A pdb=" N TYR H4730 " --> pdb=" O HIS H4726 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG H4732 " --> pdb=" O ASP H4728 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLU H4733 " --> pdb=" O ILE H4729 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG H4734 " --> pdb=" O TYR H4730 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE H4735 " --> pdb=" O GLY H4731 " (cutoff:3.500A) Processing helix chain 'H' and resid 4762 through 4767 Processing helix chain 'H' and resid 4770 through 4784 removed outlier: 3.656A pdb=" N TRP H4776 " --> pdb=" O LYS H4772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL H4780 " --> pdb=" O TRP H4776 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H4781 " --> pdb=" O LYS H4777 " (cutoff:3.500A) Processing helix chain 'H' and resid 4784 through 4799 removed outlier: 3.609A pdb=" N TYR H4793 " --> pdb=" O TYR H4789 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET H4794 " --> pdb=" O LEU H4790 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET H4796 " --> pdb=" O TRP H4792 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER H4797 " --> pdb=" O TYR H4793 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H4798 " --> pdb=" O MET H4794 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU H4799 " --> pdb=" O VAL H4795 " (cutoff:3.500A) Processing helix chain 'H' and resid 4800 through 4802 No H-bonds generated for 'chain 'H' and resid 4800 through 4802' Processing helix chain 'H' and resid 4806 through 4815 removed outlier: 3.974A pdb=" N HIS H4810 " --> pdb=" O PHE H4806 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H4812 " --> pdb=" O ALA H4808 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP H4813 " --> pdb=" O ALA H4809 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA H4815 " --> pdb=" O LEU H4811 " (cutoff:3.500A) Processing helix chain 'H' and resid 4821 through 4830 removed outlier: 4.083A pdb=" N LEU H4825 " --> pdb=" O LEU H4821 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR H4829 " --> pdb=" O LEU H4825 " (cutoff:3.500A) Processing helix chain 'H' and resid 4831 through 4856 removed outlier: 3.934A pdb=" N LEU H4835 " --> pdb=" O ASN H4831 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET H4837 " --> pdb=" O LYS H4833 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H4846 " --> pdb=" O LEU H4842 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL H4852 " --> pdb=" O LEU H4848 " (cutoff:3.500A) Processing helix chain 'H' and resid 4872 through 4875 removed outlier: 3.741A pdb=" N ASP H4875 " --> pdb=" O MET H4872 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 4872 through 4875' Processing helix chain 'H' and resid 4876 through 4892 removed outlier: 3.775A pdb=" N TYR H4881 " --> pdb=" O MET H4877 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H4889 " --> pdb=" O MET H4885 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG H4890 " --> pdb=" O TYR H4886 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY H4892 " --> pdb=" O GLY H4888 " (cutoff:3.500A) Processing helix chain 'H' and resid 4894 through 4898 removed outlier: 3.945A pdb=" N ASP H4897 " --> pdb=" O GLY H4894 " (cutoff:3.500A) Processing helix chain 'H' and resid 4907 through 4922 removed outlier: 3.563A pdb=" N VAL H4922 " --> pdb=" O PHE H4918 " (cutoff:3.500A) Processing helix chain 'H' and resid 4924 through 4955 removed outlier: 3.530A pdb=" N ALA H4928 " --> pdb=" O VAL H4924 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H4934 " --> pdb=" O ILE H4930 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU H4953 " --> pdb=" O ARG H4949 " (cutoff:3.500A) Processing helix chain 'H' and resid 4964 through 4968 removed outlier: 4.034A pdb=" N ASP H4967 " --> pdb=" O ASP H4964 " (cutoff:3.500A) Processing helix chain 'H' and resid 4972 through 4977 removed outlier: 4.288A pdb=" N THR H4977 " --> pdb=" O PHE H4973 " (cutoff:3.500A) Processing helix chain 'H' and resid 4986 through 4996 Processing helix chain 'H' and resid 4997 through 5001 removed outlier: 3.547A pdb=" N HIS H5001 " --> pdb=" O GLU H4998 " (cutoff:3.500A) Processing helix chain 'H' and resid 5002 through 5014 removed outlier: 3.610A pdb=" N TYR H5007 " --> pdb=" O GLY H5003 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU H5014 " --> pdb=" O LYS H5010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.597A pdb=" N GLU A 3 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 5 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 71 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 70 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 97 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.530A pdb=" N CYS B 24 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.932A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 68 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 110 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.530A pdb=" N CYS B 24 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.932A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 21 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 203 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 170 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS B 151 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.867A pdb=" N LEU B 73 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.530A pdb=" N SER B 183 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 223 through 224 removed outlier: 5.649A pdb=" N GLU B 229 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS B 230 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 248 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AA9, first strand: chain 'B' and resid 636 through 639 removed outlier: 3.634A pdb=" N ASN B 636 " --> pdb=" O ALA B1638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AB2, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.556A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B 746 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 664 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 748 " --> pdb=" O TRP B 662 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP B 662 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 727 through 729 removed outlier: 4.263A pdb=" N HIS B 720 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 717 " --> pdb=" O HIS B 720 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY B 715 " --> pdb=" O TRP B 722 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 684 " --> pdb=" O PHE B 716 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 768 through 769 Processing sheet with id=AB5, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.704A pdb=" N GLU B1091 " --> pdb=" O ASN B1203 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP B1088 " --> pdb=" O ILE B1153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B1153 " --> pdb=" O TRP B1088 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.983A pdb=" N THR B 892 " --> pdb=" O HIS B 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 939 through 940 Processing sheet with id=AB8, first strand: chain 'B' and resid 1102 through 1105 removed outlier: 4.440A pdb=" N GLY B1103 " --> pdb=" O VAL B1191 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B1191 " --> pdb=" O GLY B1103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B1073 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1123 through 1124 removed outlier: 3.526A pdb=" N TRP B1132 " --> pdb=" O VAL B1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1244 through 1247 removed outlier: 3.826A pdb=" N GLN B1244 " --> pdb=" O MET B1601 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1256 through 1260 removed outlier: 3.656A pdb=" N SER B1258 " --> pdb=" O ARG B1271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B1271 " --> pdb=" O SER B1258 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B1270 " --> pdb=" O GLN B1563 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN B1563 " --> pdb=" O LEU B1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1272 " --> pdb=" O VAL B1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B1565 " --> pdb=" O SER B1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B1436 " --> pdb=" O GLU B1565 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B1437 " --> pdb=" O ILE B1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B1516 " --> pdb=" O VAL B1437 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B1439 " --> pdb=" O LEU B1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B1514 " --> pdb=" O VAL B1439 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET B1527 " --> pdb=" O THR B1538 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1538 " --> pdb=" O MET B1527 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE B1529 " --> pdb=" O SER B1536 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B1536 " --> pdb=" O PHE B1529 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B1534 " --> pdb=" O ALA B1531 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1256 through 1260 removed outlier: 3.656A pdb=" N SER B1258 " --> pdb=" O ARG B1271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B1271 " --> pdb=" O SER B1258 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B1270 " --> pdb=" O GLN B1563 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN B1563 " --> pdb=" O LEU B1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1272 " --> pdb=" O VAL B1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B1565 " --> pdb=" O SER B1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B1436 " --> pdb=" O GLU B1565 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B1437 " --> pdb=" O ILE B1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B1516 " --> pdb=" O VAL B1437 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B1439 " --> pdb=" O LEU B1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B1514 " --> pdb=" O VAL B1439 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B1573 " --> pdb=" O THR B1432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B1434 " --> pdb=" O MET B1573 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1449 through 1453 Processing sheet with id=AC5, first strand: chain 'B' and resid 1734 through 1736 removed outlier: 3.696A pdb=" N TYR B2143 " --> pdb=" O TYR B1734 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 2776 through 2777 removed outlier: 6.693A pdb=" N SER B2776 " --> pdb=" O HIS B2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 2822 through 2825 removed outlier: 3.606A pdb=" N GLU B2824 " --> pdb=" O ALA B2936 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 4173 through 4174 removed outlier: 3.549A pdb=" N GLY B4174 " --> pdb=" O PHE B4190 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 4177 through 4179 removed outlier: 3.830A pdb=" N ILE B4178 " --> pdb=" O GLU B4186 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU B4186 " --> pdb=" O ILE B4178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.596A pdb=" N GLU C 3 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU C 5 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 71 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 70 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU C 97 " --> pdb=" O CYS C 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.530A pdb=" N CYS D 24 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.933A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 68 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG D 110 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.530A pdb=" N CYS D 24 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.933A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 21 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 203 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 170 " --> pdb=" O HIS D 151 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS D 151 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 73 through 74 removed outlier: 3.867A pdb=" N LEU D 73 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 117 through 120 Processing sheet with id=AD6, first strand: chain 'D' and resid 179 through 183 removed outlier: 3.530A pdb=" N SER D 183 " --> pdb=" O GLN D 190 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 223 through 224 removed outlier: 5.649A pdb=" N GLU D 229 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS D 230 " --> pdb=" O GLU D 248 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 248 " --> pdb=" O CYS D 230 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 315 through 316 Processing sheet with id=AD9, first strand: chain 'D' and resid 636 through 639 removed outlier: 3.634A pdb=" N ASN D 636 " --> pdb=" O ALA D1638 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 644 through 645 Processing sheet with id=AE2, first strand: chain 'D' and resid 762 through 763 removed outlier: 3.556A pdb=" N VAL D 666 " --> pdb=" O VAL D 744 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 746 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE D 664 " --> pdb=" O CYS D 746 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU D 748 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP D 662 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 727 through 729 removed outlier: 4.263A pdb=" N HIS D 720 " --> pdb=" O ASP D 717 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP D 717 " --> pdb=" O HIS D 720 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY D 715 " --> pdb=" O TRP D 722 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 684 " --> pdb=" O PHE D 716 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 768 through 769 Processing sheet with id=AE5, first strand: chain 'D' and resid 830 through 831 removed outlier: 3.704A pdb=" N GLU D1091 " --> pdb=" O ASN D1203 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP D1088 " --> pdb=" O ILE D1153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D1153 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 892 through 893 removed outlier: 6.983A pdb=" N THR D 892 " --> pdb=" O HIS D 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 939 through 940 Processing sheet with id=AE8, first strand: chain 'D' and resid 1102 through 1105 removed outlier: 4.438A pdb=" N GLY D1103 " --> pdb=" O VAL D1191 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D1191 " --> pdb=" O GLY D1103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D1073 " --> pdb=" O LEU D1194 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1123 through 1124 removed outlier: 3.526A pdb=" N TRP D1132 " --> pdb=" O VAL D1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1244 through 1247 removed outlier: 3.826A pdb=" N GLN D1244 " --> pdb=" O MET D1601 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1256 through 1260 removed outlier: 3.656A pdb=" N SER D1258 " --> pdb=" O ARG D1271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D1271 " --> pdb=" O SER D1258 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D1270 " --> pdb=" O GLN D1563 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN D1563 " --> pdb=" O LEU D1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU D1272 " --> pdb=" O VAL D1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D1565 " --> pdb=" O SER D1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER D1436 " --> pdb=" O GLU D1565 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D1437 " --> pdb=" O ILE D1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D1516 " --> pdb=" O VAL D1437 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D1439 " --> pdb=" O LEU D1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D1514 " --> pdb=" O VAL D1439 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET D1527 " --> pdb=" O THR D1538 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR D1538 " --> pdb=" O MET D1527 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE D1529 " --> pdb=" O SER D1536 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D1536 " --> pdb=" O PHE D1529 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D1534 " --> pdb=" O ALA D1531 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1256 through 1260 removed outlier: 3.656A pdb=" N SER D1258 " --> pdb=" O ARG D1271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D1271 " --> pdb=" O SER D1258 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D1270 " --> pdb=" O GLN D1563 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN D1563 " --> pdb=" O LEU D1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU D1272 " --> pdb=" O VAL D1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D1565 " --> pdb=" O SER D1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER D1436 " --> pdb=" O GLU D1565 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D1437 " --> pdb=" O ILE D1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D1516 " --> pdb=" O VAL D1437 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D1439 " --> pdb=" O LEU D1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D1514 " --> pdb=" O VAL D1439 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET D1573 " --> pdb=" O THR D1432 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR D1434 " --> pdb=" O MET D1573 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1449 through 1453 Processing sheet with id=AF5, first strand: chain 'D' and resid 1734 through 1736 removed outlier: 3.696A pdb=" N TYR D2143 " --> pdb=" O TYR D1734 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 2776 through 2777 removed outlier: 6.693A pdb=" N SER D2776 " --> pdb=" O HIS D2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'D' and resid 2822 through 2825 removed outlier: 3.605A pdb=" N GLU D2824 " --> pdb=" O ALA D2936 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 4173 through 4174 removed outlier: 3.549A pdb=" N GLY D4174 " --> pdb=" O PHE D4190 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 4177 through 4179 removed outlier: 3.831A pdb=" N ILE D4178 " --> pdb=" O GLU D4186 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU D4186 " --> pdb=" O ILE D4178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.596A pdb=" N GLU E 3 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 5 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN E 70 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU E 97 " --> pdb=" O CYS E 76 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 47 through 51 removed outlier: 3.531A pdb=" N CYS F 24 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 37 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 22 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ALA F 39 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 13.933A pdb=" N VAL F 20 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL F 68 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG F 110 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 47 through 51 removed outlier: 3.531A pdb=" N CYS F 24 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 37 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 22 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ALA F 39 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 13.933A pdb=" N VAL F 20 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU F 19 " --> pdb=" O ILE F 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 21 " --> pdb=" O ASN F 203 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN F 203 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE F 170 " --> pdb=" O HIS F 151 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS F 151 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 73 through 74 removed outlier: 3.867A pdb=" N LEU F 73 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 117 through 120 Processing sheet with id=AG6, first strand: chain 'F' and resid 179 through 183 removed outlier: 3.530A pdb=" N SER F 183 " --> pdb=" O GLN F 190 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 223 through 224 removed outlier: 5.649A pdb=" N GLU F 229 " --> pdb=" O HIS F 224 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS F 230 " --> pdb=" O GLU F 248 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU F 248 " --> pdb=" O CYS F 230 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 315 through 316 Processing sheet with id=AG9, first strand: chain 'F' and resid 636 through 639 removed outlier: 3.635A pdb=" N ASN F 636 " --> pdb=" O ALA F1638 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 644 through 645 Processing sheet with id=AH2, first strand: chain 'F' and resid 762 through 763 removed outlier: 3.556A pdb=" N VAL F 666 " --> pdb=" O VAL F 744 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS F 746 " --> pdb=" O PHE F 664 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE F 664 " --> pdb=" O CYS F 746 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU F 748 " --> pdb=" O TRP F 662 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP F 662 " --> pdb=" O LEU F 748 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS F 788 " --> pdb=" O ASP F 669 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 727 through 729 removed outlier: 4.263A pdb=" N HIS F 720 " --> pdb=" O ASP F 717 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP F 717 " --> pdb=" O HIS F 720 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY F 715 " --> pdb=" O TRP F 722 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL F 684 " --> pdb=" O PHE F 716 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 768 through 769 Processing sheet with id=AH5, first strand: chain 'F' and resid 830 through 831 removed outlier: 3.705A pdb=" N GLU F1091 " --> pdb=" O ASN F1203 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP F1088 " --> pdb=" O ILE F1153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F1153 " --> pdb=" O TRP F1088 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 892 through 893 removed outlier: 6.983A pdb=" N THR F 892 " --> pdb=" O HIS F 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'F' and resid 939 through 940 Processing sheet with id=AH8, first strand: chain 'F' and resid 1102 through 1105 removed outlier: 4.439A pdb=" N GLY F1103 " --> pdb=" O VAL F1191 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F1191 " --> pdb=" O GLY F1103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F1077 " --> pdb=" O PRO F1190 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F1073 " --> pdb=" O LEU F1194 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE F1074 " --> pdb=" O SER F1239 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 1123 through 1124 removed outlier: 3.526A pdb=" N TRP F1132 " --> pdb=" O VAL F1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 1244 through 1247 removed outlier: 3.826A pdb=" N GLN F1244 " --> pdb=" O MET F1601 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 1256 through 1260 removed outlier: 3.657A pdb=" N SER F1258 " --> pdb=" O ARG F1271 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG F1271 " --> pdb=" O SER F1258 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU F1270 " --> pdb=" O GLN F1563 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN F1563 " --> pdb=" O LEU F1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU F1272 " --> pdb=" O VAL F1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F1565 " --> pdb=" O SER F1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER F1436 " --> pdb=" O GLU F1565 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F1437 " --> pdb=" O ILE F1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE F1516 " --> pdb=" O VAL F1437 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL F1439 " --> pdb=" O LEU F1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F1514 " --> pdb=" O VAL F1439 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET F1527 " --> pdb=" O THR F1538 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR F1538 " --> pdb=" O MET F1527 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE F1529 " --> pdb=" O SER F1536 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F1536 " --> pdb=" O PHE F1529 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F1534 " --> pdb=" O ALA F1531 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 1256 through 1260 removed outlier: 3.657A pdb=" N SER F1258 " --> pdb=" O ARG F1271 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG F1271 " --> pdb=" O SER F1258 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU F1270 " --> pdb=" O GLN F1563 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN F1563 " --> pdb=" O LEU F1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU F1272 " --> pdb=" O VAL F1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F1565 " --> pdb=" O SER F1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER F1436 " --> pdb=" O GLU F1565 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F1437 " --> pdb=" O ILE F1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE F1516 " --> pdb=" O VAL F1437 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL F1439 " --> pdb=" O LEU F1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F1514 " --> pdb=" O VAL F1439 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET F1573 " --> pdb=" O THR F1432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR F1434 " --> pdb=" O MET F1573 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 1449 through 1453 Processing sheet with id=AI5, first strand: chain 'F' and resid 1734 through 1736 removed outlier: 3.698A pdb=" N TYR F2143 " --> pdb=" O TYR F1734 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 2776 through 2777 removed outlier: 6.693A pdb=" N SER F2776 " --> pdb=" O HIS F2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 2822 through 2825 removed outlier: 3.606A pdb=" N GLU F2824 " --> pdb=" O ALA F2936 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 4173 through 4174 removed outlier: 3.549A pdb=" N GLY F4174 " --> pdb=" O PHE F4190 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 4177 through 4179 removed outlier: 3.831A pdb=" N ILE F4178 " --> pdb=" O GLU F4186 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU F4186 " --> pdb=" O ILE F4178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.596A pdb=" N GLU G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU G 5 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN G 70 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU G 97 " --> pdb=" O CYS G 76 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 47 through 51 removed outlier: 3.531A pdb=" N CYS H 24 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU H 37 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU H 22 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ALA H 39 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 13.933A pdb=" N VAL H 20 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 68 " --> pdb=" O ARG H 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG H 110 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'H' and resid 47 through 51 removed outlier: 3.531A pdb=" N CYS H 24 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU H 37 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU H 22 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ALA H 39 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 13.933A pdb=" N VAL H 20 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU H 19 " --> pdb=" O ILE H 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 21 " --> pdb=" O ASN H 203 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN H 203 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE H 170 " --> pdb=" O HIS H 151 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS H 151 " --> pdb=" O ILE H 170 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'H' and resid 73 through 74 removed outlier: 3.867A pdb=" N LEU H 73 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 117 through 120 Processing sheet with id=AJ6, first strand: chain 'H' and resid 179 through 183 removed outlier: 3.530A pdb=" N SER H 183 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'H' and resid 223 through 224 removed outlier: 5.649A pdb=" N GLU H 229 " --> pdb=" O HIS H 224 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS H 230 " --> pdb=" O GLU H 248 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU H 248 " --> pdb=" O CYS H 230 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 315 through 316 Processing sheet with id=AJ9, first strand: chain 'H' and resid 636 through 639 removed outlier: 3.634A pdb=" N ASN H 636 " --> pdb=" O ALA H1638 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'H' and resid 644 through 645 Processing sheet with id=AK2, first strand: chain 'H' and resid 762 through 763 removed outlier: 3.555A pdb=" N VAL H 666 " --> pdb=" O VAL H 744 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS H 746 " --> pdb=" O PHE H 664 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE H 664 " --> pdb=" O CYS H 746 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU H 748 " --> pdb=" O TRP H 662 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP H 662 " --> pdb=" O LEU H 748 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS H 788 " --> pdb=" O ASP H 669 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'H' and resid 727 through 729 removed outlier: 4.263A pdb=" N HIS H 720 " --> pdb=" O ASP H 717 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP H 717 " --> pdb=" O HIS H 720 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY H 715 " --> pdb=" O TRP H 722 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL H 684 " --> pdb=" O PHE H 716 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'H' and resid 768 through 769 Processing sheet with id=AK5, first strand: chain 'H' and resid 830 through 831 removed outlier: 3.704A pdb=" N GLU H1091 " --> pdb=" O ASN H1203 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP H1088 " --> pdb=" O ILE H1153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE H1153 " --> pdb=" O TRP H1088 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'H' and resid 892 through 893 removed outlier: 6.983A pdb=" N THR H 892 " --> pdb=" O HIS H 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK6 Processing sheet with id=AK7, first strand: chain 'H' and resid 939 through 940 Processing sheet with id=AK8, first strand: chain 'H' and resid 1102 through 1105 removed outlier: 4.439A pdb=" N GLY H1103 " --> pdb=" O VAL H1191 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL H1191 " --> pdb=" O GLY H1103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA H1077 " --> pdb=" O PRO H1190 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG H1073 " --> pdb=" O LEU H1194 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE H1074 " --> pdb=" O SER H1239 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 1123 through 1124 removed outlier: 3.527A pdb=" N TRP H1132 " --> pdb=" O VAL H1123 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 1244 through 1247 removed outlier: 3.826A pdb=" N GLN H1244 " --> pdb=" O MET H1601 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'H' and resid 1256 through 1260 removed outlier: 3.657A pdb=" N SER H1258 " --> pdb=" O ARG H1271 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG H1271 " --> pdb=" O SER H1258 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU H1270 " --> pdb=" O GLN H1563 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN H1563 " --> pdb=" O LEU H1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU H1272 " --> pdb=" O VAL H1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H1565 " --> pdb=" O SER H1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER H1436 " --> pdb=" O GLU H1565 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL H1437 " --> pdb=" O ILE H1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE H1516 " --> pdb=" O VAL H1437 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H1439 " --> pdb=" O LEU H1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU H1514 " --> pdb=" O VAL H1439 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET H1527 " --> pdb=" O THR H1538 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR H1538 " --> pdb=" O MET H1527 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE H1529 " --> pdb=" O SER H1536 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER H1536 " --> pdb=" O PHE H1529 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS H1534 " --> pdb=" O ALA H1531 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'H' and resid 1256 through 1260 removed outlier: 3.657A pdb=" N SER H1258 " --> pdb=" O ARG H1271 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG H1271 " --> pdb=" O SER H1258 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU H1270 " --> pdb=" O GLN H1563 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN H1563 " --> pdb=" O LEU H1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU H1272 " --> pdb=" O VAL H1561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H1565 " --> pdb=" O SER H1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER H1436 " --> pdb=" O GLU H1565 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL H1437 " --> pdb=" O ILE H1516 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE H1516 " --> pdb=" O VAL H1437 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H1439 " --> pdb=" O LEU H1514 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU H1514 " --> pdb=" O VAL H1439 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET H1573 " --> pdb=" O THR H1432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR H1434 " --> pdb=" O MET H1573 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 1449 through 1453 Processing sheet with id=AL5, first strand: chain 'H' and resid 1734 through 1736 removed outlier: 3.696A pdb=" N TYR H2143 " --> pdb=" O TYR H1734 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 2776 through 2777 removed outlier: 6.693A pdb=" N SER H2776 " --> pdb=" O HIS H2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'H' and resid 2822 through 2825 removed outlier: 3.605A pdb=" N GLU H2824 " --> pdb=" O ALA H2936 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'H' and resid 4173 through 4174 removed outlier: 3.549A pdb=" N GLY H4174 " --> pdb=" O PHE H4190 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'H' and resid 4177 through 4179 removed outlier: 3.830A pdb=" N ILE H4178 " --> pdb=" O GLU H4186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU H4186 " --> pdb=" O ILE H4178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL9 5346 hydrogen bonds defined for protein. 15510 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: 73.96 Time building geometry restraints manager: 30.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 33240 1.35 - 1.46: 23828 1.46 - 1.58: 42088 1.58 - 1.70: 0 1.70 - 1.82: 524 Bond restraints: 99680 Sorted by residual: bond pdb=" CB GLN B3756 " pdb=" CG GLN B3756 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CB GLN H3756 " pdb=" CG GLN H3756 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB GLN F3756 " pdb=" CG GLN F3756 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CA PRO B 454 " pdb=" C PRO B 454 " ideal model delta sigma weight residual 1.517 1.509 0.008 6.70e-03 2.23e+04 1.45e+00 bond pdb=" CB GLN D3756 " pdb=" CG GLN D3756 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 ... (remaining 99675 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 2802 106.99 - 113.74: 55984 113.74 - 120.50: 38159 120.50 - 127.26: 39235 127.26 - 134.02: 988 Bond angle restraints: 137168 Sorted by residual: angle pdb=" CB GLN F3756 " pdb=" CG GLN F3756 " pdb=" CD GLN F3756 " ideal model delta sigma weight residual 112.60 116.72 -4.12 1.70e+00 3.46e-01 5.86e+00 angle pdb=" CB GLN H3756 " pdb=" CG GLN H3756 " pdb=" CD GLN H3756 " ideal model delta sigma weight residual 112.60 116.72 -4.12 1.70e+00 3.46e-01 5.86e+00 angle pdb=" CB GLN D3756 " pdb=" CG GLN D3756 " pdb=" CD GLN D3756 " ideal model delta sigma weight residual 112.60 116.71 -4.11 1.70e+00 3.46e-01 5.84e+00 angle pdb=" CB GLN B3756 " pdb=" CG GLN B3756 " pdb=" CD GLN B3756 " ideal model delta sigma weight residual 112.60 116.70 -4.10 1.70e+00 3.46e-01 5.82e+00 angle pdb=" C ILE B4686 " pdb=" N THR B4687 " pdb=" CA THR B4687 " ideal model delta sigma weight residual 120.38 123.27 -2.89 1.37e+00 5.33e-01 4.45e+00 ... (remaining 137163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 55444 17.29 - 34.59: 1714 34.59 - 51.88: 318 51.88 - 69.17: 40 69.17 - 86.47: 12 Dihedral angle restraints: 57528 sinusoidal: 13260 harmonic: 44268 Sorted by residual: dihedral pdb=" CB GLU F3661 " pdb=" CG GLU F3661 " pdb=" CD GLU F3661 " pdb=" OE1 GLU F3661 " ideal model delta sinusoidal sigma weight residual 0.00 -86.47 86.47 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU D3661 " pdb=" CG GLU D3661 " pdb=" CD GLU D3661 " pdb=" OE1 GLU D3661 " ideal model delta sinusoidal sigma weight residual 0.00 -86.40 86.40 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU H3661 " pdb=" CG GLU H3661 " pdb=" CD GLU H3661 " pdb=" OE1 GLU H3661 " ideal model delta sinusoidal sigma weight residual 0.00 -86.39 86.39 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 57525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 11644 0.029 - 0.058: 3956 0.058 - 0.088: 895 0.088 - 0.117: 574 0.117 - 0.146: 39 Chirality restraints: 17108 Sorted by residual: chirality pdb=" CB ILE B 648 " pdb=" CA ILE B 648 " pdb=" CG1 ILE B 648 " pdb=" CG2 ILE B 648 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB ILE F 648 " pdb=" CA ILE F 648 " pdb=" CG1 ILE F 648 " pdb=" CG2 ILE F 648 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CB ILE D 648 " pdb=" CA ILE D 648 " pdb=" CG1 ILE D 648 " pdb=" CG2 ILE D 648 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 17105 not shown) Planarity restraints: 17952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B2496 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B2497 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B2497 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B2497 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D2496 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO D2497 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D2497 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D2497 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H2496 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO H2497 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H2497 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H2497 " 0.022 5.00e-02 4.00e+02 ... (remaining 17949 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 25868 2.79 - 3.31: 88634 3.31 - 3.84: 149267 3.84 - 4.37: 153926 4.37 - 4.90: 271181 Nonbonded interactions: 688876 Sorted by model distance: nonbonded pdb=" O VAL B3956 " pdb=" OG SER B3959 " model vdw 2.258 2.440 nonbonded pdb=" O VAL F3956 " pdb=" OG SER F3959 " model vdw 2.258 2.440 nonbonded pdb=" O VAL H3956 " pdb=" OG SER H3959 " model vdw 2.258 2.440 nonbonded pdb=" O VAL D3956 " pdb=" OG SER D3959 " model vdw 2.258 2.440 nonbonded pdb=" OG SER C 67 " pdb=" OE1 GLN C 70 " model vdw 2.287 2.440 ... (remaining 688871 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 13 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 3448 or resid 3450 through 5029 or resid 5101 \ )) selection = (chain 'D' and (resid 13 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 3448 or resid 3450 through 5029 or resid 5101 \ )) selection = (chain 'F' and (resid 13 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 3448 or resid 3450 through 5029 or resid 5101 \ )) selection = (chain 'H' and (resid 13 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 3448 or resid 3450 through 5029 or resid 5101 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 25.500 Check model and map are aligned: 1.050 Set scattering table: 0.660 Process input model: 298.490 Find NCS groups from input model: 7.530 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 343.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 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 : 0.001 0.037 99680 Z= 0.097 Angle : 0.411 7.162 137168 Z= 0.214 Chirality : 0.034 0.146 17108 Planarity : 0.002 0.040 17952 Dihedral : 9.382 86.469 28680 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.61 % Allowed : 3.16 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.06), residues: 13668 helix: -1.86 (0.05), residues: 6096 sheet: -1.92 (0.14), residues: 1104 loop : -2.02 (0.07), residues: 6468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.000 TRP F3930 HIS 0.002 0.000 HIS F2205 PHE 0.010 0.001 PHE B4973 TYR 0.004 0.000 TYR B2257 ARG 0.001 0.000 ARG B1110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1959 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1919 time to evaluate : 7.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 215 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7484 (t) REVERT: B 407 THR cc_start: 0.8729 (t) cc_final: 0.7024 (p) REVERT: B 625 LEU cc_start: 0.8165 (tt) cc_final: 0.7950 (mm) REVERT: B 2102 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 2103 VAL cc_start: 0.9004 (m) cc_final: 0.8687 (p) REVERT: B 2118 VAL cc_start: 0.8801 (p) cc_final: 0.7799 (p) REVERT: B 2347 VAL cc_start: 0.8292 (t) cc_final: 0.7953 (t) REVERT: B 2500 LYS cc_start: 0.8179 (tttt) cc_final: 0.7175 (tptt) REVERT: B 2505 LEU cc_start: 0.9662 (mt) cc_final: 0.9389 (pp) REVERT: B 3882 PHE cc_start: 0.7387 (t80) cc_final: 0.7172 (t80) REVERT: B 4841 LEU cc_start: 0.9109 (mt) cc_final: 0.8793 (mt) REVERT: D 215 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7512 (t) REVERT: D 407 THR cc_start: 0.8784 (t) cc_final: 0.7146 (p) REVERT: D 485 SER cc_start: 0.9090 (m) cc_final: 0.8860 (p) REVERT: D 2102 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8698 (p) REVERT: D 2103 VAL cc_start: 0.8989 (m) cc_final: 0.8678 (p) REVERT: D 2118 VAL cc_start: 0.8801 (p) cc_final: 0.7826 (p) REVERT: D 2500 LYS cc_start: 0.8173 (tttt) cc_final: 0.7140 (tptt) REVERT: D 2505 LEU cc_start: 0.9658 (mt) cc_final: 0.9393 (pp) REVERT: D 3880 PHE cc_start: 0.7244 (m-80) cc_final: 0.7025 (m-80) REVERT: D 4841 LEU cc_start: 0.9111 (mt) cc_final: 0.8805 (mt) REVERT: E 37 ASP cc_start: 0.6393 (p0) cc_final: 0.5064 (p0) REVERT: F 215 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7440 (t) REVERT: F 404 ILE cc_start: 0.9540 (pt) cc_final: 0.9330 (pt) REVERT: F 407 THR cc_start: 0.8773 (t) cc_final: 0.6999 (p) REVERT: F 414 PHE cc_start: 0.8825 (t80) cc_final: 0.8609 (t80) REVERT: F 521 LEU cc_start: 0.9176 (mm) cc_final: 0.8853 (pp) REVERT: F 625 LEU cc_start: 0.8199 (tt) cc_final: 0.7990 (mm) REVERT: F 2102 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8701 (p) REVERT: F 2103 VAL cc_start: 0.8969 (m) cc_final: 0.8637 (p) REVERT: F 2118 VAL cc_start: 0.8824 (p) cc_final: 0.8466 (p) REVERT: F 2500 LYS cc_start: 0.8141 (tttt) cc_final: 0.7181 (tptt) REVERT: F 2505 LEU cc_start: 0.9664 (mt) cc_final: 0.9402 (pp) REVERT: F 3880 PHE cc_start: 0.7272 (m-80) cc_final: 0.7034 (m-80) REVERT: F 4841 LEU cc_start: 0.9114 (mt) cc_final: 0.8810 (mt) REVERT: G 37 ASP cc_start: 0.6468 (p0) cc_final: 0.5136 (p0) REVERT: H 215 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7458 (t) REVERT: H 404 ILE cc_start: 0.9534 (pt) cc_final: 0.9328 (pt) REVERT: H 407 THR cc_start: 0.8728 (t) cc_final: 0.7022 (p) REVERT: H 414 PHE cc_start: 0.8835 (t80) cc_final: 0.8631 (t80) REVERT: H 521 LEU cc_start: 0.9182 (mm) cc_final: 0.8877 (pp) REVERT: H 625 LEU cc_start: 0.8214 (tt) cc_final: 0.7978 (mm) REVERT: H 2007 ILE cc_start: 0.9208 (mm) cc_final: 0.8944 (tt) REVERT: H 2102 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8692 (p) REVERT: H 2103 VAL cc_start: 0.9038 (m) cc_final: 0.8719 (p) REVERT: H 2118 VAL cc_start: 0.8823 (p) cc_final: 0.8463 (p) REVERT: H 2347 VAL cc_start: 0.8303 (t) cc_final: 0.7953 (t) REVERT: H 2500 LYS cc_start: 0.8154 (tttt) cc_final: 0.7113 (tptt) REVERT: H 2505 LEU cc_start: 0.9668 (mt) cc_final: 0.9391 (pp) REVERT: H 3882 PHE cc_start: 0.7375 (t80) cc_final: 0.7105 (t80) REVERT: H 4841 LEU cc_start: 0.9108 (mt) cc_final: 0.8822 (mt) outliers start: 40 outliers final: 8 residues processed: 1943 average time/residue: 0.8094 time to fit residues: 2801.1553 Evaluate side-chains 1389 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1373 time to evaluate : 7.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1286 optimal weight: 2.9990 chunk 1155 optimal weight: 40.0000 chunk 640 optimal weight: 20.0000 chunk 394 optimal weight: 0.0070 chunk 779 optimal weight: 8.9990 chunk 617 optimal weight: 50.0000 chunk 1194 optimal weight: 8.9990 chunk 462 optimal weight: 20.0000 chunk 726 optimal weight: 0.9980 chunk 889 optimal weight: 0.8980 chunk 1383 optimal weight: 30.0000 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 350 HIS B 379 HIS B 596 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 HIS B 848 HIS ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1460 HIS B1661 GLN B1696 HIS B1702 HIS ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2006 GLN B2036 HIS B2101 HIS B2181 GLN B2194 GLN ** B3766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3972 GLN ** B4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4038 GLN B4810 HIS B4884 HIS B4931 GLN D 57 ASN D 350 HIS D 379 HIS D 596 ASN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 838 HIS D 848 HIS ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1460 HIS D1661 GLN D1696 HIS D1702 HIS ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2006 GLN D2036 HIS D2101 HIS D2181 GLN D2194 GLN ** D3766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3972 GLN ** D4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4038 GLN D4144 ASN D4810 HIS D4884 HIS D4931 GLN F 57 ASN F 350 HIS F 379 HIS F 596 ASN ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 838 HIS F 848 HIS ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1460 HIS F1661 GLN F1696 HIS F1702 HIS ** F1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2006 GLN F2036 HIS F2101 HIS F2181 GLN F2194 GLN ** F3766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3972 GLN ** F4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4038 GLN F4884 HIS F4931 GLN H 57 ASN H 350 HIS H 379 HIS H 596 ASN ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 838 HIS H 848 HIS ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1460 HIS H1661 GLN H1696 HIS H1702 HIS ** H1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2006 GLN H2036 HIS H2101 HIS H2181 GLN H2194 GLN ** H3766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H3972 GLN ** H4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H4038 GLN H4884 HIS H4931 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 99680 Z= 0.220 Angle : 0.567 10.432 137168 Z= 0.294 Chirality : 0.037 0.348 17108 Planarity : 0.004 0.043 17952 Dihedral : 2.896 13.983 15704 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.12 % Allowed : 3.97 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.95 (0.07), residues: 13668 helix: 0.20 (0.06), residues: 6411 sheet: -1.60 (0.14), residues: 1202 loop : -1.26 (0.08), residues: 6055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F4714 HIS 0.015 0.001 HIS B4884 PHE 0.038 0.002 PHE H4549 TYR 0.032 0.002 TYR H3963 ARG 0.010 0.001 ARG F 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1484 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1476 time to evaluate : 7.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6694 (p0) cc_final: 0.5604 (p0) REVERT: A 59 PHE cc_start: 0.8219 (t80) cc_final: 0.7974 (t80) REVERT: A 99 PHE cc_start: 0.8422 (m-80) cc_final: 0.7996 (m-10) REVERT: B 407 THR cc_start: 0.8438 (t) cc_final: 0.7378 (p) REVERT: B 471 LEU cc_start: 0.8882 (tp) cc_final: 0.8632 (tt) REVERT: B 1433 TYR cc_start: 0.8499 (m-80) cc_final: 0.7588 (m-80) REVERT: B 2126 HIS cc_start: 0.6976 (t-90) cc_final: 0.6745 (t-90) REVERT: B 2127 ARG cc_start: 0.7895 (ptp-110) cc_final: 0.7596 (ptp-110) REVERT: B 2179 MET cc_start: 0.8697 (mmp) cc_final: 0.8046 (mmm) REVERT: B 2212 MET cc_start: 0.7198 (tmm) cc_final: 0.6652 (tmm) REVERT: B 2500 LYS cc_start: 0.8362 (tttt) cc_final: 0.7263 (tptt) REVERT: B 3919 LEU cc_start: 0.9088 (mt) cc_final: 0.8842 (mt) REVERT: B 4232 PHE cc_start: 0.8481 (t80) cc_final: 0.8243 (t80) REVERT: B 4781 ILE cc_start: 0.9259 (pt) cc_final: 0.9043 (pt) REVERT: C 37 ASP cc_start: 0.6635 (p0) cc_final: 0.5501 (p0) REVERT: D 407 THR cc_start: 0.8631 (t) cc_final: 0.7544 (p) REVERT: D 471 LEU cc_start: 0.8930 (tp) cc_final: 0.8729 (tt) REVERT: D 525 ILE cc_start: 0.8865 (tp) cc_final: 0.8492 (mt) REVERT: D 2126 HIS cc_start: 0.7005 (t-90) cc_final: 0.6626 (t-90) REVERT: D 2179 MET cc_start: 0.8742 (mmp) cc_final: 0.8159 (mmm) REVERT: D 2211 VAL cc_start: 0.9127 (t) cc_final: 0.8913 (t) REVERT: D 2212 MET cc_start: 0.7037 (tmm) cc_final: 0.6535 (tmm) REVERT: D 2500 LYS cc_start: 0.8310 (tttt) cc_final: 0.7435 (tptt) REVERT: D 2505 LEU cc_start: 0.9642 (mt) cc_final: 0.9437 (pp) REVERT: D 3831 MET cc_start: 0.7863 (mtm) cc_final: 0.7638 (mtp) REVERT: D 3919 LEU cc_start: 0.9098 (mt) cc_final: 0.8812 (mt) REVERT: D 4781 ILE cc_start: 0.9294 (pt) cc_final: 0.9079 (pt) REVERT: E 37 ASP cc_start: 0.6750 (p0) cc_final: 0.5597 (p0) REVERT: F 407 THR cc_start: 0.8519 (t) cc_final: 0.7342 (p) REVERT: F 414 PHE cc_start: 0.8864 (t80) cc_final: 0.8631 (t80) REVERT: F 2122 PHE cc_start: 0.7657 (m-10) cc_final: 0.7419 (m-80) REVERT: F 2126 HIS cc_start: 0.6931 (t-90) cc_final: 0.6691 (t-90) REVERT: F 2179 MET cc_start: 0.8721 (mmp) cc_final: 0.8174 (mmm) REVERT: F 2211 VAL cc_start: 0.9105 (t) cc_final: 0.8884 (t) REVERT: F 2212 MET cc_start: 0.7105 (tmm) cc_final: 0.6639 (tmm) REVERT: F 2500 LYS cc_start: 0.8330 (tttt) cc_final: 0.7348 (tptt) REVERT: F 3919 LEU cc_start: 0.9088 (mt) cc_final: 0.8836 (mt) REVERT: F 4781 ILE cc_start: 0.9299 (pt) cc_final: 0.9079 (pt) REVERT: G 37 ASP cc_start: 0.6760 (p0) cc_final: 0.5649 (p0) REVERT: G 59 PHE cc_start: 0.8254 (t80) cc_final: 0.8044 (t80) REVERT: G 99 PHE cc_start: 0.8446 (m-80) cc_final: 0.8009 (m-10) REVERT: H 22 LEU cc_start: 0.8731 (tp) cc_final: 0.8526 (tp) REVERT: H 407 THR cc_start: 0.8426 (t) cc_final: 0.7367 (p) REVERT: H 414 PHE cc_start: 0.8871 (t80) cc_final: 0.8622 (t80) REVERT: H 471 LEU cc_start: 0.8925 (tp) cc_final: 0.8708 (tt) REVERT: H 525 ILE cc_start: 0.8861 (tp) cc_final: 0.8465 (mt) REVERT: H 1433 TYR cc_start: 0.8448 (m-80) cc_final: 0.7533 (m-80) REVERT: H 2127 ARG cc_start: 0.7861 (ptp-110) cc_final: 0.6829 (mtm-85) REVERT: H 2179 MET cc_start: 0.8669 (mmp) cc_final: 0.8049 (mmm) REVERT: H 2211 VAL cc_start: 0.9114 (t) cc_final: 0.8739 (t) REVERT: H 2212 MET cc_start: 0.7066 (tmm) cc_final: 0.6513 (tmm) REVERT: H 2500 LYS cc_start: 0.8295 (tttt) cc_final: 0.7372 (tptt) REVERT: H 2505 LEU cc_start: 0.9642 (mt) cc_final: 0.9424 (pp) REVERT: H 3919 LEU cc_start: 0.9085 (mt) cc_final: 0.8856 (mt) REVERT: H 4232 PHE cc_start: 0.8518 (t80) cc_final: 0.8294 (t80) REVERT: H 4781 ILE cc_start: 0.9302 (pt) cc_final: 0.9086 (pt) outliers start: 8 outliers final: 4 residues processed: 1480 average time/residue: 0.8045 time to fit residues: 2174.3566 Evaluate side-chains 1217 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1213 time to evaluate : 7.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 769 optimal weight: 6.9990 chunk 429 optimal weight: 10.0000 chunk 1151 optimal weight: 0.4980 chunk 942 optimal weight: 0.0970 chunk 381 optimal weight: 20.0000 chunk 1386 optimal weight: 0.0020 chunk 1497 optimal weight: 0.0060 chunk 1234 optimal weight: 0.0270 chunk 1374 optimal weight: 20.0000 chunk 472 optimal weight: 0.0570 chunk 1112 optimal weight: 9.9990 overall best weight: 0.0378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN B1661 GLN B1696 HIS ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3663 HIS ** B4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4144 ASN B4801 HIS ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1231 GLN D1661 GLN D1696 HIS ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3663 HIS D4015 GLN D4801 HIS ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1231 GLN F1661 GLN ** F1663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1696 HIS ** F1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3663 HIS F4015 GLN F4144 ASN ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1231 GLN H1661 GLN ** H1663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1696 HIS ** H1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1950 GLN ** H2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3663 HIS H4015 GLN H4144 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 99680 Z= 0.127 Angle : 0.521 14.687 137168 Z= 0.244 Chirality : 0.037 0.169 17108 Planarity : 0.003 0.054 17952 Dihedral : 2.709 14.188 15704 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.27 (0.07), residues: 13668 helix: 0.85 (0.07), residues: 6413 sheet: -1.35 (0.14), residues: 1265 loop : -1.00 (0.08), residues: 5990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F4714 HIS 0.007 0.001 HIS F2205 PHE 0.037 0.001 PHE F4573 TYR 0.030 0.001 TYR H4881 ARG 0.018 0.001 ARG B1680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1490 time to evaluate : 7.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6714 (p0) cc_final: 0.5092 (p0) REVERT: A 59 PHE cc_start: 0.8180 (t80) cc_final: 0.7971 (t80) REVERT: A 99 PHE cc_start: 0.8125 (m-80) cc_final: 0.7793 (m-10) REVERT: B 407 THR cc_start: 0.8483 (t) cc_final: 0.7310 (p) REVERT: B 2121 MET cc_start: 0.7705 (ptp) cc_final: 0.7208 (ptp) REVERT: B 2122 PHE cc_start: 0.7686 (m-10) cc_final: 0.7188 (m-80) REVERT: B 2127 ARG cc_start: 0.7573 (ptp-110) cc_final: 0.6955 (mtm110) REVERT: B 2500 LYS cc_start: 0.8269 (tttt) cc_final: 0.7363 (tptt) REVERT: B 2505 LEU cc_start: 0.9695 (mt) cc_final: 0.9482 (pp) REVERT: B 2507 LEU cc_start: 0.9024 (mt) cc_final: 0.8440 (mt) REVERT: B 3788 MET cc_start: 0.8403 (mmm) cc_final: 0.7835 (mmm) REVERT: B 3919 LEU cc_start: 0.9103 (mt) cc_final: 0.8792 (mt) REVERT: B 4781 ILE cc_start: 0.9214 (pt) cc_final: 0.8796 (pt) REVERT: C 37 ASP cc_start: 0.6461 (p0) cc_final: 0.5303 (p0) REVERT: C 59 PHE cc_start: 0.8262 (t80) cc_final: 0.7996 (t80) REVERT: C 99 PHE cc_start: 0.7983 (m-80) cc_final: 0.7511 (m-10) REVERT: D 407 THR cc_start: 0.8605 (t) cc_final: 0.7266 (p) REVERT: D 625 LEU cc_start: 0.8257 (mm) cc_final: 0.8012 (mm) REVERT: D 1241 SER cc_start: 0.8232 (m) cc_final: 0.7935 (p) REVERT: D 2121 MET cc_start: 0.7623 (ptp) cc_final: 0.7094 (ptp) REVERT: D 2122 PHE cc_start: 0.7652 (m-10) cc_final: 0.7180 (m-10) REVERT: D 2126 HIS cc_start: 0.6550 (t-90) cc_final: 0.6211 (t-90) REVERT: D 2127 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7443 (ptp-110) REVERT: D 2500 LYS cc_start: 0.8220 (tttt) cc_final: 0.7372 (tptt) REVERT: D 3912 ILE cc_start: 0.8869 (pt) cc_final: 0.8644 (mp) REVERT: D 3919 LEU cc_start: 0.9060 (mt) cc_final: 0.8795 (mt) REVERT: D 4781 ILE cc_start: 0.9172 (pt) cc_final: 0.8732 (pt) REVERT: E 37 ASP cc_start: 0.6569 (p0) cc_final: 0.5391 (p0) REVERT: E 59 PHE cc_start: 0.8252 (t80) cc_final: 0.8020 (t80) REVERT: E 99 PHE cc_start: 0.7943 (m-80) cc_final: 0.7465 (m-10) REVERT: F 407 THR cc_start: 0.8508 (t) cc_final: 0.7030 (p) REVERT: F 1241 SER cc_start: 0.8100 (m) cc_final: 0.7851 (p) REVERT: F 2121 MET cc_start: 0.7650 (ptp) cc_final: 0.7128 (ptp) REVERT: F 2122 PHE cc_start: 0.7588 (m-10) cc_final: 0.6996 (m-80) REVERT: F 2126 HIS cc_start: 0.6804 (t-90) cc_final: 0.6329 (t-90) REVERT: F 2500 LYS cc_start: 0.8199 (tttt) cc_final: 0.7376 (tptt) REVERT: F 3788 MET cc_start: 0.8451 (mmm) cc_final: 0.7866 (mmm) REVERT: F 3919 LEU cc_start: 0.9050 (mt) cc_final: 0.8756 (mt) REVERT: F 4781 ILE cc_start: 0.9252 (pt) cc_final: 0.8845 (pt) REVERT: G 37 ASP cc_start: 0.6658 (p0) cc_final: 0.5469 (p0) REVERT: G 99 PHE cc_start: 0.8214 (m-80) cc_final: 0.7809 (m-10) REVERT: H 22 LEU cc_start: 0.8572 (tp) cc_final: 0.8334 (tp) REVERT: H 407 THR cc_start: 0.8468 (t) cc_final: 0.7249 (p) REVERT: H 471 LEU cc_start: 0.8832 (tp) cc_final: 0.8508 (tt) REVERT: H 2121 MET cc_start: 0.7691 (ptp) cc_final: 0.7139 (ptp) REVERT: H 2122 PHE cc_start: 0.7711 (m-10) cc_final: 0.7221 (m-80) REVERT: H 2127 ARG cc_start: 0.7508 (ptp-110) cc_final: 0.6962 (mtm110) REVERT: H 2500 LYS cc_start: 0.8177 (tttt) cc_final: 0.7319 (tptt) REVERT: H 3788 MET cc_start: 0.8446 (mmm) cc_final: 0.7900 (mmm) REVERT: H 3919 LEU cc_start: 0.9030 (mt) cc_final: 0.8787 (mt) REVERT: H 4781 ILE cc_start: 0.9221 (pt) cc_final: 0.8944 (pt) outliers start: 4 outliers final: 0 residues processed: 1494 average time/residue: 0.7838 time to fit residues: 2125.9368 Evaluate side-chains 1240 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1240 time to evaluate : 8.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1369 optimal weight: 9.9990 chunk 1042 optimal weight: 30.0000 chunk 719 optimal weight: 6.9990 chunk 153 optimal weight: 0.0670 chunk 661 optimal weight: 30.0000 chunk 930 optimal weight: 9.9990 chunk 1391 optimal weight: 50.0000 chunk 1473 optimal weight: 5.9990 chunk 726 optimal weight: 6.9990 chunk 1318 optimal weight: 9.9990 chunk 396 optimal weight: 20.0000 overall best weight: 6.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 HIS B 489 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1611 HIS B1661 GLN ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1953 GLN ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2552 ASN B3958 ASN ** B4004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4971 HIS D 218 HIS D 489 ASN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1611 HIS D1661 GLN ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2552 ASN ** D3832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3958 ASN ** D4004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4144 ASN D4148 HIS ** D4931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4971 HIS F 218 HIS F 489 ASN ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1611 HIS F1661 GLN ** F1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2552 ASN F3958 ASN F3993 HIS ** F4004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4971 HIS H 218 HIS H 489 ASN ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1611 HIS H1661 GLN ** H1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2552 ASN ** H3832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3958 ASN H3993 HIS ** H4004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H4971 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 99680 Z= 0.429 Angle : 0.790 15.661 137168 Z= 0.428 Chirality : 0.042 0.302 17108 Planarity : 0.005 0.062 17952 Dihedral : 4.146 17.865 15704 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.45 (0.07), residues: 13668 helix: 0.62 (0.06), residues: 6508 sheet: -1.48 (0.14), residues: 1226 loop : -0.99 (0.08), residues: 5934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP F 276 HIS 0.014 0.003 HIS F2012 PHE 0.031 0.003 PHE B 778 TYR 0.033 0.003 TYR D4793 ARG 0.029 0.002 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1220 time to evaluate : 8.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7160 (p0) cc_final: 0.5725 (p0) REVERT: B 151 HIS cc_start: 0.8123 (m-70) cc_final: 0.7896 (m-70) REVERT: B 1433 TYR cc_start: 0.9056 (m-80) cc_final: 0.8244 (m-80) REVERT: B 2121 MET cc_start: 0.7765 (ptp) cc_final: 0.7259 (ptm) REVERT: B 2122 PHE cc_start: 0.7669 (m-10) cc_final: 0.7415 (m-10) REVERT: B 2126 HIS cc_start: 0.7010 (t-90) cc_final: 0.6782 (t-90) REVERT: B 2179 MET cc_start: 0.8553 (mmp) cc_final: 0.8334 (mmm) REVERT: B 2212 MET cc_start: 0.7844 (tmm) cc_final: 0.7229 (tmm) REVERT: B 2464 LEU cc_start: 0.9207 (mt) cc_final: 0.8913 (mp) REVERT: B 2500 LYS cc_start: 0.8467 (tttt) cc_final: 0.7910 (mmtp) REVERT: B 3716 TYR cc_start: 0.8239 (p90) cc_final: 0.7910 (p90) REVERT: B 3788 MET cc_start: 0.8702 (mmm) cc_final: 0.8266 (mmm) REVERT: B 3919 LEU cc_start: 0.9153 (mt) cc_final: 0.8943 (mt) REVERT: B 4781 ILE cc_start: 0.9572 (pt) cc_final: 0.9323 (pt) REVERT: C 37 ASP cc_start: 0.7335 (p0) cc_final: 0.6231 (p0) REVERT: D 151 HIS cc_start: 0.8158 (m-70) cc_final: 0.7902 (m-70) REVERT: D 1852 MET cc_start: 0.8842 (mmp) cc_final: 0.8609 (mmm) REVERT: D 2121 MET cc_start: 0.7747 (ptp) cc_final: 0.7138 (ptm) REVERT: D 2126 HIS cc_start: 0.7146 (t-90) cc_final: 0.6788 (t-90) REVERT: D 2212 MET cc_start: 0.7470 (tmm) cc_final: 0.6804 (tmm) REVERT: D 2500 LYS cc_start: 0.8412 (tttt) cc_final: 0.7814 (mmtm) REVERT: D 3716 TYR cc_start: 0.8348 (p90) cc_final: 0.7973 (p90) REVERT: D 3912 ILE cc_start: 0.8850 (pt) cc_final: 0.8636 (mp) REVERT: D 3919 LEU cc_start: 0.9145 (mt) cc_final: 0.8933 (mt) REVERT: D 3927 ASP cc_start: 0.8927 (m-30) cc_final: 0.8725 (p0) REVERT: D 4026 LEU cc_start: 0.8664 (mt) cc_final: 0.8131 (mp) REVERT: D 4034 MET cc_start: 0.8759 (tpt) cc_final: 0.8457 (tpp) REVERT: D 4781 ILE cc_start: 0.9569 (pt) cc_final: 0.9315 (pt) REVERT: E 37 ASP cc_start: 0.7425 (p0) cc_final: 0.6243 (p0) REVERT: F 151 HIS cc_start: 0.8148 (m-70) cc_final: 0.7901 (m-70) REVERT: F 1852 MET cc_start: 0.8849 (mmp) cc_final: 0.8615 (mmm) REVERT: F 2121 MET cc_start: 0.7704 (ptp) cc_final: 0.7243 (ptm) REVERT: F 2122 PHE cc_start: 0.7547 (m-10) cc_final: 0.7249 (m-10) REVERT: F 2126 HIS cc_start: 0.7214 (t-90) cc_final: 0.6865 (t-90) REVERT: F 2212 MET cc_start: 0.7475 (tmm) cc_final: 0.6844 (tmm) REVERT: F 2500 LYS cc_start: 0.8375 (tttt) cc_final: 0.7855 (mmtp) REVERT: F 3716 TYR cc_start: 0.8203 (p90) cc_final: 0.7848 (p90) REVERT: F 3788 MET cc_start: 0.8755 (mmm) cc_final: 0.8348 (mmm) REVERT: F 3912 ILE cc_start: 0.8969 (pt) cc_final: 0.8748 (mp) REVERT: F 3919 LEU cc_start: 0.9167 (mt) cc_final: 0.8940 (mt) REVERT: F 4781 ILE cc_start: 0.9558 (pt) cc_final: 0.9312 (pt) REVERT: G 37 ASP cc_start: 0.7199 (p0) cc_final: 0.5729 (p0) REVERT: G 68 LEU cc_start: 0.8006 (pt) cc_final: 0.7759 (tp) REVERT: H 151 HIS cc_start: 0.8126 (m-70) cc_final: 0.7872 (m-70) REVERT: H 1433 TYR cc_start: 0.8923 (m-80) cc_final: 0.8121 (m-80) REVERT: H 2121 MET cc_start: 0.7864 (ptp) cc_final: 0.7371 (ptm) REVERT: H 2122 PHE cc_start: 0.7569 (m-10) cc_final: 0.7221 (m-80) REVERT: H 2126 HIS cc_start: 0.7087 (t-90) cc_final: 0.6870 (t-90) REVERT: H 2179 MET cc_start: 0.8597 (mmp) cc_final: 0.8346 (mmm) REVERT: H 2212 MET cc_start: 0.7314 (tmm) cc_final: 0.6861 (tmm) REVERT: H 2500 LYS cc_start: 0.8282 (tttt) cc_final: 0.7885 (tptt) REVERT: H 3716 TYR cc_start: 0.8230 (p90) cc_final: 0.7917 (p90) REVERT: H 3788 MET cc_start: 0.8710 (mmm) cc_final: 0.8290 (mmm) REVERT: H 3912 ILE cc_start: 0.8949 (pt) cc_final: 0.8737 (mp) REVERT: H 3919 LEU cc_start: 0.9172 (mt) cc_final: 0.8943 (mt) REVERT: H 4781 ILE cc_start: 0.9561 (pt) cc_final: 0.9321 (pt) outliers start: 0 outliers final: 0 residues processed: 1220 average time/residue: 0.7548 time to fit residues: 1684.4075 Evaluate side-chains 985 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 985 time to evaluate : 7.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1226 optimal weight: 10.0000 chunk 836 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 1096 optimal weight: 9.9990 chunk 607 optimal weight: 9.9990 chunk 1257 optimal weight: 2.9990 chunk 1018 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 752 optimal weight: 0.7980 chunk 1322 optimal weight: 0.0020 chunk 371 optimal weight: 0.6980 overall best weight: 2.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1679 ASN B1696 HIS ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1950 GLN ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3958 ASN B4015 GLN ** B4810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1661 GLN D1696 HIS ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1950 GLN D1953 GLN ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3958 ASN D3993 HIS ** D4004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1950 GLN F1953 GLN ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3958 ASN ** F4004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4801 HIS ** H 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1696 HIS ** H1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3695 HIS H3958 ASN H4801 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 99680 Z= 0.179 Angle : 0.535 12.479 137168 Z= 0.271 Chirality : 0.037 0.188 17108 Planarity : 0.003 0.060 17952 Dihedral : 3.536 17.435 15704 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.19 (0.07), residues: 13668 helix: 1.27 (0.06), residues: 6457 sheet: -1.19 (0.14), residues: 1217 loop : -0.80 (0.08), residues: 5994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 260 HIS 0.010 0.001 HIS F2205 PHE 0.016 0.001 PHE H 778 TYR 0.043 0.002 TYR F4881 ARG 0.010 0.001 ARG D2127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1277 time to evaluate : 7.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7406 (p0) cc_final: 0.5535 (p0) REVERT: A 59 PHE cc_start: 0.8430 (t80) cc_final: 0.8118 (t80) REVERT: B 414 PHE cc_start: 0.8554 (t80) cc_final: 0.8273 (t80) REVERT: B 1433 TYR cc_start: 0.8948 (m-80) cc_final: 0.8303 (m-80) REVERT: B 2121 MET cc_start: 0.7717 (ptp) cc_final: 0.7055 (ptm) REVERT: B 2122 PHE cc_start: 0.7652 (m-10) cc_final: 0.7111 (m-10) REVERT: B 2237 LEU cc_start: 0.9149 (mt) cc_final: 0.8870 (mt) REVERT: B 2500 LYS cc_start: 0.8257 (tttt) cc_final: 0.7396 (tptt) REVERT: B 2503 MET cc_start: 0.8643 (ttp) cc_final: 0.8177 (ttp) REVERT: B 3716 TYR cc_start: 0.8054 (p90) cc_final: 0.7695 (p90) REVERT: B 3774 VAL cc_start: 0.9326 (m) cc_final: 0.9112 (p) REVERT: B 4931 GLN cc_start: 0.8764 (mp-120) cc_final: 0.8432 (mm-40) REVERT: C 37 ASP cc_start: 0.7769 (p0) cc_final: 0.6611 (p0) REVERT: D 1241 SER cc_start: 0.8372 (m) cc_final: 0.8093 (p) REVERT: D 1947 PHE cc_start: 0.7787 (m-80) cc_final: 0.7587 (m-80) REVERT: D 2121 MET cc_start: 0.7657 (ptp) cc_final: 0.7059 (ptm) REVERT: D 2122 PHE cc_start: 0.7645 (m-10) cc_final: 0.7060 (m-10) REVERT: D 2126 HIS cc_start: 0.6946 (t-90) cc_final: 0.6560 (t-90) REVERT: D 2179 MET cc_start: 0.8523 (mmp) cc_final: 0.8250 (mmm) REVERT: D 2237 LEU cc_start: 0.9189 (mt) cc_final: 0.8977 (mt) REVERT: D 2500 LYS cc_start: 0.8243 (tttt) cc_final: 0.7650 (mmtm) REVERT: D 2505 LEU cc_start: 0.9696 (mt) cc_final: 0.9468 (pp) REVERT: D 3716 TYR cc_start: 0.8100 (p90) cc_final: 0.7732 (p90) REVERT: D 4034 MET cc_start: 0.8737 (tpt) cc_final: 0.8436 (tpp) REVERT: D 4781 ILE cc_start: 0.9478 (pt) cc_final: 0.9276 (pt) REVERT: E 37 ASP cc_start: 0.7578 (p0) cc_final: 0.6209 (p0) REVERT: E 59 PHE cc_start: 0.8410 (t80) cc_final: 0.8095 (t80) REVERT: E 99 PHE cc_start: 0.7731 (m-10) cc_final: 0.7299 (m-10) REVERT: F 1241 SER cc_start: 0.8401 (m) cc_final: 0.8125 (p) REVERT: F 2121 MET cc_start: 0.7600 (ptp) cc_final: 0.7034 (ptm) REVERT: F 2122 PHE cc_start: 0.7660 (m-10) cc_final: 0.7147 (m-10) REVERT: F 2126 HIS cc_start: 0.6853 (t-90) cc_final: 0.6502 (t-90) REVERT: F 2179 MET cc_start: 0.8517 (mmp) cc_final: 0.8256 (mmm) REVERT: F 2237 LEU cc_start: 0.9108 (mt) cc_final: 0.8860 (mt) REVERT: F 2500 LYS cc_start: 0.8267 (tttt) cc_final: 0.7761 (mmtp) REVERT: F 3716 TYR cc_start: 0.8059 (p90) cc_final: 0.7689 (p90) REVERT: F 3879 LEU cc_start: 0.8801 (tt) cc_final: 0.8553 (tt) REVERT: F 3919 LEU cc_start: 0.9097 (mt) cc_final: 0.8895 (mt) REVERT: F 4781 ILE cc_start: 0.9473 (pt) cc_final: 0.9195 (pt) REVERT: F 4931 GLN cc_start: 0.8759 (mp-120) cc_final: 0.8451 (mm-40) REVERT: G 37 ASP cc_start: 0.7534 (p0) cc_final: 0.6238 (p0) REVERT: G 59 PHE cc_start: 0.8407 (t80) cc_final: 0.8142 (t80) REVERT: G 68 LEU cc_start: 0.8187 (pt) cc_final: 0.7887 (tp) REVERT: H 414 PHE cc_start: 0.8698 (t80) cc_final: 0.8432 (t80) REVERT: H 1433 TYR cc_start: 0.8993 (m-80) cc_final: 0.8365 (m-80) REVERT: H 2121 MET cc_start: 0.7691 (ptp) cc_final: 0.7059 (ptm) REVERT: H 2122 PHE cc_start: 0.7603 (m-10) cc_final: 0.7067 (m-10) REVERT: H 2179 MET cc_start: 0.8528 (mmp) cc_final: 0.8318 (mmm) REVERT: H 2237 LEU cc_start: 0.9189 (mt) cc_final: 0.8917 (mt) REVERT: H 2500 LYS cc_start: 0.8217 (tttt) cc_final: 0.7729 (mmtt) REVERT: H 3716 TYR cc_start: 0.8023 (p90) cc_final: 0.7626 (p90) REVERT: H 3880 PHE cc_start: 0.8089 (m-80) cc_final: 0.7791 (m-80) REVERT: H 3919 LEU cc_start: 0.9104 (mt) cc_final: 0.8899 (mt) REVERT: H 4781 ILE cc_start: 0.9476 (pt) cc_final: 0.9200 (pt) REVERT: H 4931 GLN cc_start: 0.8750 (mp-120) cc_final: 0.8424 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1277 average time/residue: 0.7830 time to fit residues: 1826.9560 Evaluate side-chains 1024 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1024 time to evaluate : 7.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 495 optimal weight: 4.9990 chunk 1326 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 864 optimal weight: 40.0000 chunk 363 optimal weight: 4.9990 chunk 1474 optimal weight: 9.9990 chunk 1224 optimal weight: 8.9990 chunk 682 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 487 optimal weight: 40.0000 chunk 774 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2261 ASN B2285 ASN B3695 HIS B4144 ASN B4148 HIS D 576 ASN D1203 ASN ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1661 GLN ** D1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2261 ASN D2285 ASN D3695 HIS ** D3832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 HIS ** F 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1203 ASN ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2261 ASN F2285 ASN F3695 HIS F3989 HIS F4144 ASN F4148 HIS ** H 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 576 ASN H1203 ASN ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1679 ASN ** H1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2261 ASN H2285 ASN H3989 HIS H4144 ASN H4148 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 99680 Z= 0.396 Angle : 0.750 13.660 137168 Z= 0.401 Chirality : 0.041 0.248 17108 Planarity : 0.005 0.079 17952 Dihedral : 4.508 18.394 15704 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.49 (0.07), residues: 13668 helix: 0.53 (0.06), residues: 6513 sheet: -1.40 (0.14), residues: 1130 loop : -0.99 (0.08), residues: 6025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 148 HIS 0.013 0.003 HIS D4884 PHE 0.027 0.003 PHE B4805 TYR 0.028 0.003 TYR D4881 ARG 0.014 0.001 ARG H 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1110 time to evaluate : 7.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7425 (p0) cc_final: 0.5899 (p0) REVERT: B 1433 TYR cc_start: 0.8978 (m-80) cc_final: 0.8336 (m-80) REVERT: B 2121 MET cc_start: 0.7727 (ptp) cc_final: 0.7159 (ptm) REVERT: B 2126 HIS cc_start: 0.7450 (t-90) cc_final: 0.7135 (t-90) REVERT: B 2154 MET cc_start: 0.8510 (mmp) cc_final: 0.8261 (mmm) REVERT: B 2500 LYS cc_start: 0.8410 (tttt) cc_final: 0.8097 (mmtp) REVERT: B 3716 TYR cc_start: 0.8223 (p90) cc_final: 0.7920 (p90) REVERT: B 3774 VAL cc_start: 0.9389 (m) cc_final: 0.9121 (p) REVERT: C 37 ASP cc_start: 0.7541 (p0) cc_final: 0.6108 (p0) REVERT: D 2121 MET cc_start: 0.7721 (ptp) cc_final: 0.7240 (ptm) REVERT: D 2126 HIS cc_start: 0.7506 (t-90) cc_final: 0.7218 (t-90) REVERT: D 3716 TYR cc_start: 0.8153 (p90) cc_final: 0.7821 (p90) REVERT: D 3774 VAL cc_start: 0.9374 (m) cc_final: 0.9137 (p) REVERT: D 4034 MET cc_start: 0.8956 (tpt) cc_final: 0.8535 (tmm) REVERT: E 37 ASP cc_start: 0.7665 (p0) cc_final: 0.6029 (p0) REVERT: F 485 SER cc_start: 0.9498 (m) cc_final: 0.9277 (p) REVERT: F 1707 LEU cc_start: 0.8075 (mt) cc_final: 0.7866 (mt) REVERT: F 2121 MET cc_start: 0.7769 (ptp) cc_final: 0.7221 (ptp) REVERT: F 2126 HIS cc_start: 0.7444 (t-90) cc_final: 0.7063 (t-90) REVERT: F 2500 LYS cc_start: 0.8756 (tttt) cc_final: 0.8129 (mmtp) REVERT: F 3716 TYR cc_start: 0.8261 (p90) cc_final: 0.7979 (p90) REVERT: F 3879 LEU cc_start: 0.8950 (tt) cc_final: 0.8714 (tt) REVERT: F 3880 PHE cc_start: 0.8337 (m-80) cc_final: 0.8076 (m-80) REVERT: G 37 ASP cc_start: 0.7395 (p0) cc_final: 0.5908 (p0) REVERT: G 68 LEU cc_start: 0.8381 (pt) cc_final: 0.8140 (tp) REVERT: H 1433 TYR cc_start: 0.8983 (m-80) cc_final: 0.8351 (m-80) REVERT: H 1707 LEU cc_start: 0.8063 (mt) cc_final: 0.7861 (mt) REVERT: H 2121 MET cc_start: 0.7790 (ptp) cc_final: 0.7335 (ptm) REVERT: H 2126 HIS cc_start: 0.7462 (t-90) cc_final: 0.7172 (t-90) REVERT: H 2500 LYS cc_start: 0.8435 (tttt) cc_final: 0.7864 (mmtt) REVERT: H 3716 TYR cc_start: 0.8235 (p90) cc_final: 0.7932 (p90) REVERT: H 3774 VAL cc_start: 0.9382 (m) cc_final: 0.9136 (p) outliers start: 0 outliers final: 0 residues processed: 1110 average time/residue: 0.7708 time to fit residues: 1570.7582 Evaluate side-chains 914 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 914 time to evaluate : 8.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1421 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 840 optimal weight: 4.9990 chunk 1076 optimal weight: 2.9990 chunk 834 optimal weight: 8.9990 chunk 1241 optimal weight: 30.0000 chunk 823 optimal weight: 8.9990 chunk 1468 optimal weight: 30.0000 chunk 919 optimal weight: 0.8980 chunk 895 optimal weight: 9.9990 chunk 678 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1719 HIS B1971 GLN ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4712 ASN ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1661 GLN D1719 HIS D1950 GLN ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4712 ASN ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1719 HIS ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4712 ASN ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1719 HIS H1953 GLN ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4712 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 99680 Z= 0.306 Angle : 0.647 12.320 137168 Z= 0.341 Chirality : 0.039 0.253 17108 Planarity : 0.004 0.076 17952 Dihedral : 4.387 19.189 15704 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.34 (0.07), residues: 13668 helix: 0.74 (0.06), residues: 6461 sheet: -1.37 (0.14), residues: 1157 loop : -1.00 (0.08), residues: 6050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D5009 HIS 0.013 0.002 HIS B4810 PHE 0.036 0.002 PHE H 800 TYR 0.029 0.002 TYR B1122 ARG 0.011 0.001 ARG D4858 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1119 time to evaluate : 7.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7524 (p0) cc_final: 0.6127 (p0) REVERT: B 1433 TYR cc_start: 0.9201 (m-80) cc_final: 0.8506 (m-80) REVERT: B 1669 LEU cc_start: 0.8811 (mt) cc_final: 0.8532 (mt) REVERT: B 1707 LEU cc_start: 0.7759 (mt) cc_final: 0.7418 (mt) REVERT: B 1947 PHE cc_start: 0.7514 (m-80) cc_final: 0.7276 (m-80) REVERT: B 2121 MET cc_start: 0.7860 (ptp) cc_final: 0.7251 (ptm) REVERT: B 2122 PHE cc_start: 0.7977 (m-10) cc_final: 0.7423 (m-10) REVERT: B 2500 LYS cc_start: 0.8575 (tttt) cc_final: 0.8200 (mmtp) REVERT: B 3716 TYR cc_start: 0.7888 (p90) cc_final: 0.7598 (p90) REVERT: B 3774 VAL cc_start: 0.9378 (m) cc_final: 0.9132 (p) REVERT: C 37 ASP cc_start: 0.7661 (p0) cc_final: 0.6012 (p0) REVERT: D 485 SER cc_start: 0.9457 (m) cc_final: 0.9238 (p) REVERT: D 1433 TYR cc_start: 0.9049 (m-80) cc_final: 0.8104 (m-80) REVERT: D 1669 LEU cc_start: 0.8921 (mt) cc_final: 0.8631 (mt) REVERT: D 1707 LEU cc_start: 0.7747 (mt) cc_final: 0.7412 (mt) REVERT: D 2121 MET cc_start: 0.7871 (ptp) cc_final: 0.7339 (ptm) REVERT: D 2122 PHE cc_start: 0.7827 (m-10) cc_final: 0.7108 (m-10) REVERT: D 2237 LEU cc_start: 0.9251 (mt) cc_final: 0.8950 (mt) REVERT: D 2500 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8054 (tptt) REVERT: D 3716 TYR cc_start: 0.7897 (p90) cc_final: 0.7628 (p90) REVERT: D 3774 VAL cc_start: 0.9368 (m) cc_final: 0.9103 (p) REVERT: D 4034 MET cc_start: 0.8969 (tpt) cc_final: 0.8547 (tmm) REVERT: D 4035 ILE cc_start: 0.9130 (tp) cc_final: 0.8794 (tt) REVERT: D 4781 ILE cc_start: 0.9575 (pt) cc_final: 0.9374 (pt) REVERT: E 99 PHE cc_start: 0.7889 (m-10) cc_final: 0.7492 (m-10) REVERT: F 485 SER cc_start: 0.9557 (m) cc_final: 0.9296 (p) REVERT: F 1433 TYR cc_start: 0.9029 (m-80) cc_final: 0.8094 (m-80) REVERT: F 1669 LEU cc_start: 0.8853 (mt) cc_final: 0.8586 (mt) REVERT: F 1947 PHE cc_start: 0.7503 (m-80) cc_final: 0.7290 (m-80) REVERT: F 2121 MET cc_start: 0.7782 (ptp) cc_final: 0.7227 (ptm) REVERT: F 2126 HIS cc_start: 0.7426 (t-90) cc_final: 0.7173 (t-90) REVERT: F 2237 LEU cc_start: 0.9260 (mt) cc_final: 0.8925 (mt) REVERT: F 2500 LYS cc_start: 0.8894 (tttt) cc_final: 0.8371 (mmtp) REVERT: F 3716 TYR cc_start: 0.7908 (p90) cc_final: 0.7642 (p90) REVERT: F 3774 VAL cc_start: 0.9379 (m) cc_final: 0.9161 (p) REVERT: F 3879 LEU cc_start: 0.8899 (tt) cc_final: 0.8664 (tt) REVERT: F 3880 PHE cc_start: 0.8319 (m-80) cc_final: 0.8035 (m-80) REVERT: F 4781 ILE cc_start: 0.9572 (pt) cc_final: 0.9367 (pt) REVERT: G 37 ASP cc_start: 0.7530 (p0) cc_final: 0.6058 (p0) REVERT: G 68 LEU cc_start: 0.8161 (pt) cc_final: 0.7952 (tp) REVERT: H 1433 TYR cc_start: 0.9064 (m-80) cc_final: 0.8522 (m-80) REVERT: H 1669 LEU cc_start: 0.8835 (mt) cc_final: 0.8574 (mt) REVERT: H 1947 PHE cc_start: 0.7504 (m-80) cc_final: 0.7294 (m-80) REVERT: H 2121 MET cc_start: 0.7866 (ptp) cc_final: 0.7322 (ptm) REVERT: H 2122 PHE cc_start: 0.7730 (m-10) cc_final: 0.7064 (m-10) REVERT: H 2126 HIS cc_start: 0.7172 (t-90) cc_final: 0.6920 (t-90) REVERT: H 2500 LYS cc_start: 0.8892 (tttt) cc_final: 0.8390 (mmtp) REVERT: H 2503 MET cc_start: 0.8847 (ttt) cc_final: 0.8643 (ttt) REVERT: H 3716 TYR cc_start: 0.7880 (p90) cc_final: 0.7600 (p90) REVERT: H 3788 MET cc_start: 0.8785 (mmm) cc_final: 0.8576 (mmt) outliers start: 0 outliers final: 0 residues processed: 1119 average time/residue: 0.7536 time to fit residues: 1547.5217 Evaluate side-chains 938 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 938 time to evaluate : 7.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 908 optimal weight: 0.7980 chunk 586 optimal weight: 7.9990 chunk 877 optimal weight: 20.0000 chunk 442 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 chunk 933 optimal weight: 0.9980 chunk 1000 optimal weight: 40.0000 chunk 726 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 1154 optimal weight: 8.9990 overall best weight: 2.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1971 GLN ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4712 ASN ** H 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 99680 Z= 0.176 Angle : 0.545 10.368 137168 Z= 0.276 Chirality : 0.038 0.194 17108 Planarity : 0.003 0.074 17952 Dihedral : 3.899 16.391 15704 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.18 (0.07), residues: 13668 helix: 1.23 (0.07), residues: 6543 sheet: -1.13 (0.14), residues: 1188 loop : -0.84 (0.08), residues: 5937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 269 HIS 0.013 0.001 HIS F1133 PHE 0.027 0.001 PHE B 800 TYR 0.028 0.001 TYR F 411 ARG 0.007 0.001 ARG D4858 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1168 time to evaluate : 7.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7758 (p0) cc_final: 0.6238 (p0) REVERT: B 37 LEU cc_start: 0.9118 (tp) cc_final: 0.8752 (tt) REVERT: B 1433 TYR cc_start: 0.9175 (m-80) cc_final: 0.8484 (m-80) REVERT: B 1669 LEU cc_start: 0.8793 (mt) cc_final: 0.8516 (mt) REVERT: B 1707 LEU cc_start: 0.7722 (mt) cc_final: 0.7296 (mt) REVERT: B 2121 MET cc_start: 0.7739 (ptp) cc_final: 0.7277 (ptm) REVERT: B 2122 PHE cc_start: 0.7717 (m-10) cc_final: 0.7172 (m-10) REVERT: B 2179 MET cc_start: 0.8520 (mmp) cc_final: 0.8257 (mmm) REVERT: B 3716 TYR cc_start: 0.7651 (p90) cc_final: 0.7337 (p90) REVERT: B 3774 VAL cc_start: 0.9414 (m) cc_final: 0.9131 (p) REVERT: C 37 ASP cc_start: 0.7825 (p0) cc_final: 0.6076 (p0) REVERT: D 37 LEU cc_start: 0.9124 (tp) cc_final: 0.8794 (tt) REVERT: D 485 SER cc_start: 0.9416 (m) cc_final: 0.9198 (p) REVERT: D 1433 TYR cc_start: 0.9045 (m-80) cc_final: 0.8162 (m-80) REVERT: D 1669 LEU cc_start: 0.8840 (mt) cc_final: 0.8529 (mt) REVERT: D 2121 MET cc_start: 0.7751 (ptp) cc_final: 0.7238 (ptm) REVERT: D 2122 PHE cc_start: 0.7701 (m-10) cc_final: 0.7160 (m-10) REVERT: D 2126 HIS cc_start: 0.7117 (t-90) cc_final: 0.6655 (t-90) REVERT: D 2179 MET cc_start: 0.8523 (mmp) cc_final: 0.8257 (mmm) REVERT: D 2237 LEU cc_start: 0.9166 (mt) cc_final: 0.8906 (mt) REVERT: D 2500 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8019 (mmtt) REVERT: D 3716 TYR cc_start: 0.7610 (p90) cc_final: 0.7332 (p90) REVERT: D 3774 VAL cc_start: 0.9390 (m) cc_final: 0.9121 (p) REVERT: D 3880 PHE cc_start: 0.8128 (m-80) cc_final: 0.7927 (m-10) REVERT: D 4026 LEU cc_start: 0.8750 (mt) cc_final: 0.8269 (mp) REVERT: D 4034 MET cc_start: 0.8901 (tpt) cc_final: 0.8526 (tpp) REVERT: E 37 ASP cc_start: 0.7892 (p0) cc_final: 0.6014 (p0) REVERT: E 99 PHE cc_start: 0.7687 (m-10) cc_final: 0.7322 (m-10) REVERT: F 37 LEU cc_start: 0.9125 (tp) cc_final: 0.8774 (tt) REVERT: F 485 SER cc_start: 0.9526 (m) cc_final: 0.9312 (p) REVERT: F 1433 TYR cc_start: 0.9057 (m-80) cc_final: 0.8176 (m-80) REVERT: F 1669 LEU cc_start: 0.8802 (mt) cc_final: 0.8538 (mt) REVERT: F 1707 LEU cc_start: 0.7571 (mt) cc_final: 0.7175 (mt) REVERT: F 2121 MET cc_start: 0.7776 (ptp) cc_final: 0.7245 (ptm) REVERT: F 2122 PHE cc_start: 0.7844 (m-10) cc_final: 0.7117 (m-10) REVERT: F 2179 MET cc_start: 0.8438 (mmp) cc_final: 0.8204 (mmm) REVERT: F 2237 LEU cc_start: 0.9163 (mt) cc_final: 0.8910 (mt) REVERT: F 2500 LYS cc_start: 0.8755 (tttt) cc_final: 0.7319 (mmtp) REVERT: F 3716 TYR cc_start: 0.7572 (p90) cc_final: 0.7229 (p90) REVERT: F 3774 VAL cc_start: 0.9415 (m) cc_final: 0.9142 (p) REVERT: F 3879 LEU cc_start: 0.8830 (tt) cc_final: 0.8586 (tt) REVERT: F 3880 PHE cc_start: 0.8228 (m-80) cc_final: 0.7986 (m-80) REVERT: F 4666 LEU cc_start: 0.8855 (mt) cc_final: 0.8649 (mt) REVERT: F 4781 ILE cc_start: 0.9474 (pt) cc_final: 0.9271 (pt) REVERT: G 37 ASP cc_start: 0.7929 (p0) cc_final: 0.5949 (p0) REVERT: G 68 LEU cc_start: 0.8094 (pt) cc_final: 0.7861 (tp) REVERT: H 37 LEU cc_start: 0.9114 (tp) cc_final: 0.8751 (tt) REVERT: H 1433 TYR cc_start: 0.9010 (m-80) cc_final: 0.8501 (m-80) REVERT: H 1669 LEU cc_start: 0.8788 (mt) cc_final: 0.8542 (mt) REVERT: H 2121 MET cc_start: 0.7786 (ptp) cc_final: 0.7296 (ptm) REVERT: H 2122 PHE cc_start: 0.7724 (m-10) cc_final: 0.7077 (m-10) REVERT: H 2179 MET cc_start: 0.8508 (mmp) cc_final: 0.8236 (mmm) REVERT: H 2237 LEU cc_start: 0.9169 (mt) cc_final: 0.8816 (mt) REVERT: H 2500 LYS cc_start: 0.8837 (tttt) cc_final: 0.7592 (mmtp) REVERT: H 3716 TYR cc_start: 0.7641 (p90) cc_final: 0.7348 (p90) outliers start: 0 outliers final: 0 residues processed: 1168 average time/residue: 0.7740 time to fit residues: 1647.8063 Evaluate side-chains 980 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 7.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1336 optimal weight: 4.9990 chunk 1407 optimal weight: 20.0000 chunk 1283 optimal weight: 8.9990 chunk 1368 optimal weight: 20.0000 chunk 1406 optimal weight: 20.0000 chunk 823 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 chunk 1074 optimal weight: 0.9990 chunk 420 optimal weight: 3.9990 chunk 1236 optimal weight: 6.9990 chunk 1294 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1950 GLN B1971 GLN ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2214 ASN B3993 HIS ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1661 GLN D1971 GLN ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1950 GLN F1971 GLN ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1971 GLN ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 99680 Z= 0.294 Angle : 0.640 12.532 137168 Z= 0.336 Chirality : 0.039 0.207 17108 Planarity : 0.004 0.072 17952 Dihedral : 4.280 19.048 15704 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.02 % Allowed : 0.59 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.15 (0.07), residues: 13668 helix: 0.94 (0.06), residues: 6530 sheet: -1.47 (0.14), residues: 1190 loop : -0.91 (0.08), residues: 5948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H5009 HIS 0.011 0.002 HIS B4810 PHE 0.026 0.002 PHE B2341 TYR 0.026 0.002 TYR F 411 ARG 0.015 0.001 ARG D 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1116 time to evaluate : 8.061 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: A 37 ASP cc_start: 0.8167 (p0) cc_final: 0.6533 (p0) REVERT: B 1433 TYR cc_start: 0.9240 (m-80) cc_final: 0.8563 (m-80) REVERT: B 1669 LEU cc_start: 0.8804 (mt) cc_final: 0.8557 (mt) REVERT: B 1707 LEU cc_start: 0.7938 (mt) cc_final: 0.7578 (mt) REVERT: B 2121 MET cc_start: 0.7864 (ptp) cc_final: 0.7358 (ptm) REVERT: B 2122 PHE cc_start: 0.7835 (m-10) cc_final: 0.7388 (m-10) REVERT: B 2154 MET cc_start: 0.8570 (mmp) cc_final: 0.8356 (mmm) REVERT: B 2237 LEU cc_start: 0.9159 (mt) cc_final: 0.8878 (mt) REVERT: B 2500 LYS cc_start: 0.8736 (mmtp) cc_final: 0.7989 (tptt) REVERT: B 3716 TYR cc_start: 0.7833 (p90) cc_final: 0.7510 (p90) REVERT: B 3725 MET cc_start: 0.8386 (ptp) cc_final: 0.8151 (ptp) REVERT: B 3774 VAL cc_start: 0.9411 (m) cc_final: 0.9157 (p) REVERT: B 3812 LEU cc_start: 0.8834 (mt) cc_final: 0.8510 (mp) REVERT: B 4921 PHE cc_start: 0.7433 (m-10) cc_final: 0.7181 (m-10) REVERT: C 37 ASP cc_start: 0.8100 (p0) cc_final: 0.6388 (p0) REVERT: D 485 SER cc_start: 0.9495 (m) cc_final: 0.9229 (p) REVERT: D 1433 TYR cc_start: 0.9102 (m-80) cc_final: 0.8201 (m-80) REVERT: D 1669 LEU cc_start: 0.8876 (mt) cc_final: 0.8572 (mt) REVERT: D 1707 LEU cc_start: 0.7779 (mt) cc_final: 0.7395 (mt) REVERT: D 2121 MET cc_start: 0.7905 (ptp) cc_final: 0.7436 (ptm) REVERT: D 2122 PHE cc_start: 0.7736 (m-10) cc_final: 0.7166 (m-10) REVERT: D 2126 HIS cc_start: 0.7188 (t-90) cc_final: 0.6861 (t-90) REVERT: D 2500 LYS cc_start: 0.8659 (mmtm) cc_final: 0.7934 (tptt) REVERT: D 3716 TYR cc_start: 0.7960 (p90) cc_final: 0.7729 (p90) REVERT: D 3774 VAL cc_start: 0.9395 (m) cc_final: 0.9145 (p) REVERT: D 3812 LEU cc_start: 0.8847 (mt) cc_final: 0.8515 (mp) REVERT: D 3880 PHE cc_start: 0.8206 (m-80) cc_final: 0.8003 (m-10) REVERT: D 4034 MET cc_start: 0.9027 (tpt) cc_final: 0.8790 (tmm) REVERT: D 4035 ILE cc_start: 0.9215 (tt) cc_final: 0.8744 (tt) REVERT: E 37 ASP cc_start: 0.8159 (p0) cc_final: 0.6470 (p0) REVERT: F 485 SER cc_start: 0.9543 (m) cc_final: 0.9328 (p) REVERT: F 1433 TYR cc_start: 0.9121 (m-80) cc_final: 0.8181 (m-80) REVERT: F 1669 LEU cc_start: 0.8812 (mt) cc_final: 0.8559 (mt) REVERT: F 1707 LEU cc_start: 0.7927 (mt) cc_final: 0.7451 (mt) REVERT: F 2121 MET cc_start: 0.7891 (ptp) cc_final: 0.7435 (ptm) REVERT: F 2126 HIS cc_start: 0.7157 (t-90) cc_final: 0.6905 (t-90) REVERT: F 2500 LYS cc_start: 0.8542 (tttt) cc_final: 0.7220 (mmtp) REVERT: F 2503 MET cc_start: 0.8173 (ppp) cc_final: 0.7950 (ppp) REVERT: F 3716 TYR cc_start: 0.7863 (p90) cc_final: 0.7575 (p90) REVERT: F 3774 VAL cc_start: 0.9412 (m) cc_final: 0.9165 (p) REVERT: F 3812 LEU cc_start: 0.8848 (mt) cc_final: 0.8503 (mp) REVERT: F 3879 LEU cc_start: 0.8893 (tt) cc_final: 0.8631 (tt) REVERT: F 3880 PHE cc_start: 0.8379 (m-80) cc_final: 0.8100 (m-80) REVERT: G 68 LEU cc_start: 0.8178 (pt) cc_final: 0.7968 (tp) REVERT: H 1433 TYR cc_start: 0.9213 (m-80) cc_final: 0.8550 (m-80) REVERT: H 1669 LEU cc_start: 0.8802 (mt) cc_final: 0.8498 (mt) REVERT: H 1707 LEU cc_start: 0.7922 (mt) cc_final: 0.7471 (mt) REVERT: H 2121 MET cc_start: 0.7999 (ptp) cc_final: 0.7465 (ptm) REVERT: H 2122 PHE cc_start: 0.7661 (m-10) cc_final: 0.7077 (m-10) REVERT: H 2500 LYS cc_start: 0.8647 (tttt) cc_final: 0.7505 (mmtp) REVERT: H 2503 MET cc_start: 0.8166 (ppp) cc_final: 0.7865 (ppp) REVERT: H 3716 TYR cc_start: 0.7957 (p90) cc_final: 0.7704 (p90) REVERT: H 3788 MET cc_start: 0.8325 (mmp) cc_final: 0.8122 (mmp) REVERT: H 3812 LEU cc_start: 0.8853 (mt) cc_final: 0.8520 (mp) REVERT: H 4921 PHE cc_start: 0.7483 (m-10) cc_final: 0.7198 (m-10) outliers start: 1 outliers final: 0 residues processed: 1117 average time/residue: 0.7496 time to fit residues: 1531.3590 Evaluate side-chains 930 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 930 time to evaluate : 7.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 1364 optimal weight: 7.9990 chunk 898 optimal weight: 0.0770 chunk 1447 optimal weight: 2.9990 chunk 883 optimal weight: 8.9990 chunk 686 optimal weight: 0.7980 chunk 1006 optimal weight: 50.0000 chunk 1518 optimal weight: 10.0000 chunk 1397 optimal weight: 40.0000 chunk 1209 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 933 optimal weight: 8.9990 overall best weight: 3.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1971 GLN ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2126 HIS ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1661 GLN D1971 GLN ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1971 GLN ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1971 GLN ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 99680 Z= 0.224 Angle : 0.579 12.021 137168 Z= 0.299 Chirality : 0.038 0.197 17108 Planarity : 0.004 0.073 17952 Dihedral : 4.097 21.360 15704 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.05 (0.07), residues: 13668 helix: 1.16 (0.06), residues: 6549 sheet: -1.39 (0.14), residues: 1187 loop : -0.90 (0.08), residues: 5932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 148 HIS 0.013 0.002 HIS D 350 PHE 0.024 0.002 PHE H2341 TYR 0.028 0.002 TYR F 411 ARG 0.013 0.001 ARG B4037 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27336 Ramachandran restraints generated. 13668 Oldfield, 0 Emsley, 13668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1121 time to evaluate : 7.855 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: A 37 ASP cc_start: 0.8183 (p0) cc_final: 0.6445 (p0) REVERT: B 37 LEU cc_start: 0.9096 (tp) cc_final: 0.8755 (tt) REVERT: B 1433 TYR cc_start: 0.9219 (m-80) cc_final: 0.8542 (m-80) REVERT: B 1669 LEU cc_start: 0.8864 (mt) cc_final: 0.8569 (mt) REVERT: B 1707 LEU cc_start: 0.7863 (mt) cc_final: 0.7442 (mt) REVERT: B 2121 MET cc_start: 0.7770 (ptp) cc_final: 0.7230 (ptm) REVERT: B 2122 PHE cc_start: 0.7950 (m-10) cc_final: 0.7488 (m-10) REVERT: B 2179 MET cc_start: 0.8451 (mmp) cc_final: 0.8204 (mmm) REVERT: B 2237 LEU cc_start: 0.9070 (mt) cc_final: 0.8827 (mt) REVERT: B 2500 LYS cc_start: 0.8533 (mmtp) cc_final: 0.7720 (tptt) REVERT: B 3716 TYR cc_start: 0.7747 (p90) cc_final: 0.7414 (p90) REVERT: B 3725 MET cc_start: 0.8403 (ptp) cc_final: 0.8187 (ptp) REVERT: B 3774 VAL cc_start: 0.9459 (m) cc_final: 0.9199 (p) REVERT: B 4921 PHE cc_start: 0.7175 (m-10) cc_final: 0.6959 (m-10) REVERT: C 37 ASP cc_start: 0.8108 (p0) cc_final: 0.6292 (p0) REVERT: D 37 LEU cc_start: 0.9132 (tp) cc_final: 0.8785 (tt) REVERT: D 485 SER cc_start: 0.9441 (m) cc_final: 0.9218 (p) REVERT: D 1433 TYR cc_start: 0.9029 (m-80) cc_final: 0.8228 (m-80) REVERT: D 1669 LEU cc_start: 0.8932 (mt) cc_final: 0.8586 (mt) REVERT: D 1707 LEU cc_start: 0.7682 (mt) cc_final: 0.7262 (mt) REVERT: D 2121 MET cc_start: 0.7865 (ptp) cc_final: 0.7144 (ptm) REVERT: D 2122 PHE cc_start: 0.7765 (m-10) cc_final: 0.7191 (m-10) REVERT: D 2126 HIS cc_start: 0.7093 (t-90) cc_final: 0.6830 (t-90) REVERT: D 2179 MET cc_start: 0.8431 (mmp) cc_final: 0.8197 (mmm) REVERT: D 2500 LYS cc_start: 0.8735 (mmtm) cc_final: 0.7969 (tptt) REVERT: D 2503 MET cc_start: 0.8063 (ppp) cc_final: 0.7841 (ppp) REVERT: D 3716 TYR cc_start: 0.7974 (p90) cc_final: 0.7701 (p90) REVERT: D 3725 MET cc_start: 0.8387 (ptp) cc_final: 0.8119 (ptp) REVERT: D 3774 VAL cc_start: 0.9449 (m) cc_final: 0.9191 (p) REVERT: D 4026 LEU cc_start: 0.8589 (mt) cc_final: 0.7963 (mp) REVERT: D 4034 MET cc_start: 0.8980 (tpt) cc_final: 0.8749 (tmm) REVERT: D 4035 ILE cc_start: 0.9206 (tt) cc_final: 0.8768 (tt) REVERT: E 37 ASP cc_start: 0.8109 (p0) cc_final: 0.6211 (p0) REVERT: E 99 PHE cc_start: 0.7745 (m-10) cc_final: 0.7503 (m-10) REVERT: F 37 LEU cc_start: 0.9111 (tp) cc_final: 0.8767 (tt) REVERT: F 485 SER cc_start: 0.9548 (m) cc_final: 0.9330 (p) REVERT: F 1433 TYR cc_start: 0.9032 (m-80) cc_final: 0.8221 (m-80) REVERT: F 1669 LEU cc_start: 0.8862 (mt) cc_final: 0.8582 (mt) REVERT: F 1707 LEU cc_start: 0.7779 (mt) cc_final: 0.7282 (mt) REVERT: F 2121 MET cc_start: 0.7809 (ptp) cc_final: 0.7312 (ptm) REVERT: F 2126 HIS cc_start: 0.7216 (t-90) cc_final: 0.6846 (t-90) REVERT: F 2179 MET cc_start: 0.8341 (mmp) cc_final: 0.8043 (mmm) REVERT: F 2500 LYS cc_start: 0.8587 (tttt) cc_final: 0.7251 (mmtp) REVERT: F 2503 MET cc_start: 0.8092 (ppp) cc_final: 0.7789 (ppp) REVERT: F 3716 TYR cc_start: 0.7748 (p90) cc_final: 0.7474 (p90) REVERT: F 3774 VAL cc_start: 0.9462 (m) cc_final: 0.9220 (p) REVERT: F 3879 LEU cc_start: 0.8871 (tt) cc_final: 0.8664 (tt) REVERT: F 3880 PHE cc_start: 0.8313 (m-80) cc_final: 0.8091 (m-80) REVERT: H 37 LEU cc_start: 0.9087 (tp) cc_final: 0.8755 (tt) REVERT: H 1433 TYR cc_start: 0.9228 (m-80) cc_final: 0.8572 (m-80) REVERT: H 1669 LEU cc_start: 0.8849 (mt) cc_final: 0.8567 (mt) REVERT: H 1707 LEU cc_start: 0.7750 (mt) cc_final: 0.7313 (mt) REVERT: H 2121 MET cc_start: 0.7905 (ptp) cc_final: 0.7286 (ptm) REVERT: H 2122 PHE cc_start: 0.7629 (m-10) cc_final: 0.7000 (m-10) REVERT: H 2179 MET cc_start: 0.8380 (mmp) cc_final: 0.8053 (mmm) REVERT: H 2500 LYS cc_start: 0.8694 (tttt) cc_final: 0.7468 (mmtp) REVERT: H 2503 MET cc_start: 0.8181 (ppp) cc_final: 0.7899 (ppp) REVERT: H 3716 TYR cc_start: 0.7784 (p90) cc_final: 0.7537 (p90) REVERT: H 3788 MET cc_start: 0.8359 (mmp) cc_final: 0.8043 (mmp) outliers start: 0 outliers final: 0 residues processed: 1121 average time/residue: 0.7493 time to fit residues: 1548.1360 Evaluate side-chains 942 residues out of total 12184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 942 time to evaluate : 7.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1524 random chunks: chunk 741 optimal weight: 7.9990 chunk 960 optimal weight: 0.0270 chunk 1287 optimal weight: 20.0000 chunk 370 optimal weight: 3.9990 chunk 1114 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 1210 optimal weight: 0.8980 chunk 506 optimal weight: 7.9990 chunk 1243 optimal weight: 40.0000 chunk 153 optimal weight: 10.0000 overall best weight: 3.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1971 GLN ** B2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1971 GLN ** D2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1971 GLN ** F2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1971 GLN ** H2008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049865 restraints weight = 1567712.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051406 restraints weight = 783179.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.052162 restraints weight = 464206.377| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 99680 Z= 0.233 Angle : 0.591 12.157 137168 Z= 0.306 Chirality : 0.038 0.207 17108 Planarity : 0.004 0.076 17952 Dihedral : 4.096 18.819 15704 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.02 (0.07), residues: 13668 helix: 1.15 (0.07), residues: 6555 sheet: -1.47 (0.14), residues: 1148 loop : -0.93 (0.08), residues: 5965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D5009 HIS 0.012 0.002 HIS F2205 PHE 0.027 0.002 PHE H4569 TYR 0.027 0.002 TYR F 411 ARG 0.007 0.001 ARG H2127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26594.97 seconds wall clock time: 466 minutes 26.08 seconds (27986.08 seconds total)