Starting phenix.real_space_refine on Sat Apr 6 12:32:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3f_32278/04_2024/7w3f_32278_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3f_32278/04_2024/7w3f_32278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3f_32278/04_2024/7w3f_32278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3f_32278/04_2024/7w3f_32278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3f_32278/04_2024/7w3f_32278_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3f_32278/04_2024/7w3f_32278_updated.pdb" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 S 640 5.16 5 C 70008 2.51 5 N 19011 2.21 5 O 21077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "W TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 110751 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 389} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3207 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 389} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3105 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 379} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3097 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 19, 'TRANS': 369} Chain: "F" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1867 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1933 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1813 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1890 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1521 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "O" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6828 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 31, 'TRANS': 840} Chain breaks: 1 Chain: "X" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 369} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "f" Number of atoms: 6866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6866 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 34, 'TRANS': 854} Chain: "g" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1879 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "h" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1782 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1861 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "m" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "n" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "p" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "q" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1549 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "s" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "t" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "v" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "x" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3929 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "y" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "W" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3635 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 437} Chain: "V" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3612 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 15, 'TRANS': 428} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N ALA K 120 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA K 120 " occ=0.50 residue: pdb=" N LYS P 17 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS P 17 " occ=0.50 residue: pdb=" N ALA X 359 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.50 residue: pdb=" N GLN X 380 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.50 residue: pdb=" N GLY Z 30 " occ=0.38 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.38 residue: pdb=" N ILE b 90 " occ=0.46 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.46 residue: pdb=" N SER b 115 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.70 residue: pdb=" N ILE b 140 " occ=0.39 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.39 residue: pdb=" N VAL b 173 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.89 residue: pdb=" N GLY b 191 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.50 residue: pdb=" N ILE d 63 " occ=0.78 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.78 residue: pdb=" N SER d 70 " occ=0.95 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.95 ... (remaining 9 not shown) Time building chain proxies: 42.07, per 1000 atoms: 0.38 Number of scatterers: 110751 At special positions: 0 Unit cell: (326.745, 225.365, 226.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 640 16.00 P 14 15.00 O 21077 8.00 N 19011 7.00 C 70008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 270 " distance=2.04 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.03 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: 30.68 Conformation dependent library (CDL) restraints added in 15.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26382 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 511 helices and 91 sheets defined 54.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 59.63 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.561A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 64 removed outlier: 4.690A pdb=" N GLY A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.593A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 91 removed outlier: 4.882A pdb=" N SER A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 4.673A pdb=" N ILE A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 156 through 162 removed outlier: 5.960A pdb=" N VAL A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.198A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 180 through 197 removed outlier: 4.427A pdb=" N ILE A 184 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.829A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 241 through 246 removed outlier: 4.600A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 246' Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 289 through 310 removed outlier: 6.499A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.488A pdb=" N ARG A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 removed outlier: 5.797A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 4.956A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.595A pdb=" N PHE A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 86 removed outlier: 3.735A pdb=" N LYS B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 5.103A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.521A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.539A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.886A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.618A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 318 removed outlier: 3.623A pdb=" N ARG B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.835A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 4.394A pdb=" N LYS B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 387 removed outlier: 3.508A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.785A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 428 removed outlier: 3.778A pdb=" N TYR B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 68 removed outlier: 3.961A pdb=" N LYS C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 removed outlier: 4.347A pdb=" N ILE C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLY C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 152' Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.390A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.622A pdb=" N ARG C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 231 " --> pdb=" O GLY C 227 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 281 removed outlier: 6.715A pdb=" N GLN C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.925A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASP C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 302' Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.816A pdb=" N ASP C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.810A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.740A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 6.813A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.712A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 405 removed outlier: 6.060A pdb=" N LYS C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 85 removed outlier: 4.004A pdb=" N LYS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 5.121A pdb=" N LEU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 125' Processing helix chain 'D' and resid 163 through 168 removed outlier: 4.199A pdb=" N ILE D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 168' Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.814A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 removed outlier: 4.019A pdb=" N ILE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 241 through 258 removed outlier: 4.969A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 5.015A pdb=" N THR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 297 removed outlier: 3.658A pdb=" N ARG D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 removed outlier: 4.606A pdb=" N LEU D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASP D 318 " --> pdb=" O ALA D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 318' Processing helix chain 'D' and resid 338 through 350 removed outlier: 6.824A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 4.222A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 390 removed outlier: 3.507A pdb=" N ASN D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 408 removed outlier: 3.853A pdb=" N LYS D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 52 removed outlier: 3.722A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.826A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 124 Processing helix chain 'E' and resid 138 through 155 removed outlier: 4.241A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 163 removed outlier: 4.189A pdb=" N VAL E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 removed outlier: 3.546A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 7.159A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.986A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS E 225 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 266 Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 305 through 318 removed outlier: 6.135A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.940A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 382 removed outlier: 3.728A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 35 removed outlier: 3.715A pdb=" N ILE F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 85 removed outlier: 4.534A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.605A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 167 through 172 removed outlier: 4.929A pdb=" N ARG F 171 " --> pdb=" O GLU F 167 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL F 172 " --> pdb=" O TYR F 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 167 through 172' Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.884A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLY F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 191 through 208 removed outlier: 5.103A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 removed outlier: 5.603A pdb=" N GLU F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 252 through 258 removed outlier: 5.278A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.874A pdb=" N LYS F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 297 removed outlier: 4.613A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS F 294 " --> pdb=" O ALA F 290 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 319 removed outlier: 4.454A pdb=" N ARG F 308 " --> pdb=" O ARG F 304 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 348 removed outlier: 4.463A pdb=" N SER F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU F 348 " --> pdb=" O ARG F 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 341 through 348' Processing helix chain 'F' and resid 359 through 373 removed outlier: 3.722A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 3.777A pdb=" N LEU F 384 " --> pdb=" O ASN F 380 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.530A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.243A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N THR G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 67' Processing helix chain 'G' and resid 83 through 105 Processing helix chain 'G' and resid 110 through 129 removed outlier: 3.809A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.298A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.604A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.756A pdb=" N GLU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 12 removed outlier: 6.268A pdb=" N ASP G 10 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG G 11 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N HIS G 12 " --> pdb=" O PHE G 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 7 through 12' Processing helix chain 'H' and resid 19 through 33 removed outlier: 4.853A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 4.013A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU H 86 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 123 removed outlier: 4.003A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.269A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 removed outlier: 3.820A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 209' Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.782A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.685A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 58 through 63' Processing helix chain 'h' and resid 79 through 102 removed outlier: 3.625A pdb=" N TYR h 83 " --> pdb=" O MET h 79 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG h 84 " --> pdb=" O GLY h 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU h 86 " --> pdb=" O ASP h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 removed outlier: 3.791A pdb=" N TYR h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN h 123 " --> pdb=" O GLN h 119 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER h 124 " --> pdb=" O GLU h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 4.174A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 234 Processing helix chain 'I' and resid 18 through 29 removed outlier: 3.829A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY I 29 " --> pdb=" O MET I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.569A pdb=" N LEU I 110 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.700A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 202 removed outlier: 5.792A pdb=" N ASP I 202 " --> pdb=" O ASN I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 4.021A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 251 removed outlier: 3.575A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.667A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 98 removed outlier: 4.332A pdb=" N ALA J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.658A pdb=" N TYR J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.697A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 removed outlier: 3.686A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 200 removed outlier: 3.755A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN J 200 " --> pdb=" O LEU J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 removed outlier: 3.802A pdb=" N GLU J 226 " --> pdb=" O PRO J 222 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 30 removed outlier: 3.559A pdb=" N LYS j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.650A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG j 60 " --> pdb=" O GLU j 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 55 through 60' Processing helix chain 'j' and resid 76 through 98 Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.634A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 3.631A pdb=" N VAL j 168 " --> pdb=" O GLY j 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 183 removed outlier: 3.554A pdb=" N ILE j 181 " --> pdb=" O THR j 177 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR j 183 " --> pdb=" O GLU j 179 " (cutoff:3.500A) Processing helix chain 'j' and resid 184 through 199 removed outlier: 4.346A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 4 through 9 removed outlier: 4.229A pdb=" N TYR K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 34 removed outlier: 3.653A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.243A pdb=" N ILE K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 65' Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.599A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 122 removed outlier: 4.200A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.724A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 230 through 241 removed outlier: 3.738A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 130 removed outlier: 3.714A pdb=" N ALA K 128 " --> pdb=" O GLU K 125 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP K 129 " --> pdb=" O GLU K 126 " (cutoff:3.500A) Proline residue: K 130 - end of helix No H-bonds generated for 'chain 'K' and resid 125 through 130' Processing helix chain 'L' and resid 2 through 8 removed outlier: 4.541A pdb=" N TYR L 6 " --> pdb=" O PHE L 2 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 8' Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.509A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 122 removed outlier: 4.251A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 165 through 180 removed outlier: 5.568A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.918A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 234 removed outlier: 4.500A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.751A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.902A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 3.973A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 202 removed outlier: 4.165A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 removed outlier: 3.520A pdb=" N LYS M 244 " --> pdb=" O LYS M 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 91 removed outlier: 3.586A pdb=" N TYR N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.729A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.699A pdb=" N ARG N 166 " --> pdb=" O LEU N 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.874A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 141 removed outlier: 3.775A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.626A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG o 89 " --> pdb=" O GLN o 85 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 141 removed outlier: 3.775A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 Processing helix chain 'P' and resid 2 through 8 removed outlier: 4.629A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 8' Processing helix chain 'P' and resid 56 through 79 Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.491A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 4.082A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 4.236A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 5.099A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 79 Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.287A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 3.895A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.155A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 72 removed outlier: 3.669A pdb=" N THR Q 53 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 95 removed outlier: 4.281A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG Q 95 " --> pdb=" O CYS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.458A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 171 Processing helix chain 'q' and resid 49 through 72 removed outlier: 3.783A pdb=" N THR q 53 " --> pdb=" O GLU q 49 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 95 removed outlier: 3.718A pdb=" N CYS q 91 " --> pdb=" O ASN q 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU q 92 " --> pdb=" O LEU q 88 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG q 95 " --> pdb=" O CYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.623A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 171 removed outlier: 3.846A pdb=" N VAL q 157 " --> pdb=" O ARG q 153 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU q 158 " --> pdb=" O GLU q 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 71 Processing helix chain 'R' and resid 75 through 91 removed outlier: 4.004A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.819A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 201 removed outlier: 3.682A pdb=" N GLY R 201 " --> pdb=" O GLU R 197 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 91 removed outlier: 3.850A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.838A pdb=" N GLY r 137 " --> pdb=" O VAL r 133 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL r 138 " --> pdb=" O TYR r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 201 Processing helix chain 'S' and resid 57 through 80 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.946A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.906A pdb=" N GLU S 184 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 80 Processing helix chain 's' and resid 84 through 100 removed outlier: 4.018A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 Processing helix chain 'T' and resid 56 through 78 removed outlier: 4.042A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.706A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 158 removed outlier: 4.144A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.712A pdb=" N LYS T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) Proline residue: T 158 - end of helix Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 4.926A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 209 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.841A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.875A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 158 removed outlier: 4.416A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Proline residue: t 158 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 4.917A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'U' and resid 8 through 15 removed outlier: 3.552A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP U 15 " --> pdb=" O LEU U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 35 removed outlier: 5.536A pdb=" N ASN U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 42 removed outlier: 4.635A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL U 42 " --> pdb=" O ILE U 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 36 through 42' Processing helix chain 'U' and resid 43 through 52 removed outlier: 5.423A pdb=" N GLU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 removed outlier: 4.012A pdb=" N GLY U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 119 Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 Processing helix chain 'U' and resid 146 through 158 removed outlier: 4.239A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 3.964A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 187 removed outlier: 4.681A pdb=" N ALA U 178 " --> pdb=" O PRO U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 209 removed outlier: 3.630A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU U 209 " --> pdb=" O TYR U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 224 removed outlier: 4.226A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE U 222 " --> pdb=" O GLN U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 Processing helix chain 'U' and resid 241 through 256 Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.579A pdb=" N LEU U 261 " --> pdb=" O SER U 257 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 Processing helix chain 'U' and resid 332 through 346 removed outlier: 4.321A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 4.676A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 3.720A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 390 removed outlier: 4.593A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU U 390 " --> pdb=" O LEU U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 391 through 396 removed outlier: 4.676A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 413 removed outlier: 5.740A pdb=" N LYS U 401 " --> pdb=" O THR U 397 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS U 413 " --> pdb=" O GLY U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 418 through 427 Processing helix chain 'U' and resid 435 through 451 removed outlier: 3.947A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS U 450 " --> pdb=" O LEU U 446 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 3.930A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 486 removed outlier: 3.534A pdb=" N MET U 486 " --> pdb=" O GLY U 482 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 4.281A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 521 removed outlier: 4.408A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET U 520 " --> pdb=" O LEU U 516 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU U 521 " --> pdb=" O GLY U 517 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 Processing helix chain 'U' and resid 541 through 557 removed outlier: 4.877A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 573 removed outlier: 3.586A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.859A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.519A pdb=" N ARG U 615 " --> pdb=" O ASN U 611 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE U 627 " --> pdb=" O GLY U 623 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 643 removed outlier: 4.456A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 4.791A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 3.948A pdb=" N CYS U 660 " --> pdb=" O LEU U 656 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 677 removed outlier: 6.203A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN U 670 " --> pdb=" O LYS U 666 " (cutoff:3.500A) Proline residue: U 674 - end of helix removed outlier: 4.952A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.864A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 719 Processing helix chain 'U' and resid 723 through 739 removed outlier: 4.018A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 773 removed outlier: 3.858A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP U 770 " --> pdb=" O PHE U 766 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE U 771 " --> pdb=" O THR U 767 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP U 772 " --> pdb=" O GLN U 768 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE U 773 " --> pdb=" O PHE U 769 " (cutoff:3.500A) Processing helix chain 'U' and resid 774 through 783 removed outlier: 5.412A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 774 through 783' Processing helix chain 'U' and resid 834 through 852 Processing helix chain 'U' and resid 863 through 869 removed outlier: 4.883A pdb=" N LYS U 867 " --> pdb=" O GLU U 863 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS U 868 " --> pdb=" O GLU U 864 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS U 869 " --> pdb=" O LYS U 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 863 through 869' Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.509A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 61 Processing helix chain 'X' and resid 63 through 77 Proline residue: X 75 - end of helix Processing helix chain 'X' and resid 81 through 100 Processing helix chain 'X' and resid 102 through 121 removed outlier: 3.670A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 Processing helix chain 'X' and resid 143 through 161 removed outlier: 4.622A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 4.944A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 199 removed outlier: 4.603A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 222 removed outlier: 5.636A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 3.503A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 3.930A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 273 Processing helix chain 'X' and resid 274 through 280 removed outlier: 4.366A pdb=" N ARG X 278 " --> pdb=" O LYS X 274 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR X 279 " --> pdb=" O LEU X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.711A pdb=" N TYR X 309 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 340 removed outlier: 5.101A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 Processing helix chain 'X' and resid 357 through 372 Processing helix chain 'X' and resid 394 through 422 removed outlier: 3.656A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU X 402 " --> pdb=" O GLU X 398 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 29 Proline residue: Y 29 - end of helix Processing helix chain 'Y' and resid 33 through 48 removed outlier: 4.905A pdb=" N VAL Y 37 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA Y 43 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN Y 48 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 60 removed outlier: 3.601A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 92 removed outlier: 3.574A pdb=" N LEU Y 70 " --> pdb=" O ASP Y 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 115 Processing helix chain 'Y' and resid 116 through 132 removed outlier: 3.507A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 131 " --> pdb=" O THR Y 127 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL Y 132 " --> pdb=" O TYR Y 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 3.521A pdb=" N TYR Y 151 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 167 Processing helix chain 'Y' and resid 174 through 191 removed outlier: 5.234A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE Y 191 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 202 removed outlier: 4.284A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU Y 202 " --> pdb=" O ALA Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.619A pdb=" N PHE Y 219 " --> pdb=" O ASP Y 215 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA Y 230 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 Processing helix chain 'Y' and resid 243 through 254 removed outlier: 3.660A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.591A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 284 removed outlier: 4.322A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 292 through 310 removed outlier: 3.807A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 324 Processing helix chain 'Y' and resid 326 through 341 Processing helix chain 'Y' and resid 360 through 389 removed outlier: 4.999A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N MET Y 389 " --> pdb=" O ARG Y 385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 removed outlier: 4.354A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 102 through 117 removed outlier: 4.740A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS Z 116 " --> pdb=" O MET Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix Processing helix chain 'Z' and resid 165 through 177 removed outlier: 3.754A pdb=" N GLU Z 169 " --> pdb=" O GLU Z 165 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG Z 177 " --> pdb=" O GLU Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 218 removed outlier: 3.562A pdb=" N THR Z 217 " --> pdb=" O GLU Z 213 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY Z 218 " --> pdb=" O LYS Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 237 removed outlier: 3.831A pdb=" N ILE Z 227 " --> pdb=" O ASN Z 223 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR Z 228 " --> pdb=" O HIS Z 224 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 260 removed outlier: 4.232A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) Processing helix chain 'Z' and resid 262 through 290 removed outlier: 4.098A pdb=" N ILE Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 Processing helix chain 'a' and resid 20 through 32 removed outlier: 5.070A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS a 32 " --> pdb=" O LEU a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 4.277A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 68 removed outlier: 3.784A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 Processing helix chain 'a' and resid 90 through 105 removed outlier: 4.450A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 123 removed outlier: 4.501A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 142 removed outlier: 4.479A pdb=" N VAL a 130 " --> pdb=" O GLY a 126 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR a 131 " --> pdb=" O ASP a 127 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS a 132 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU a 133 " --> pdb=" O GLN a 129 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU a 142 " --> pdb=" O VAL a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 164 removed outlier: 4.396A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 4.148A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 Processing helix chain 'a' and resid 219 through 226 removed outlier: 3.557A pdb=" N GLU a 223 " --> pdb=" O HIS a 219 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER a 224 " --> pdb=" O PRO a 220 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.041A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 4.201A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 265 removed outlier: 6.697A pdb=" N ALA a 263 " --> pdb=" O PRO a 259 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU a 265 " --> pdb=" O LEU a 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 259 through 265' Processing helix chain 'a' and resid 266 through 285 removed outlier: 4.190A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) Proline residue: a 285 - end of helix Processing helix chain 'a' and resid 292 through 301 removed outlier: 3.747A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 318 removed outlier: 3.848A pdb=" N VAL a 307 " --> pdb=" O THR a 303 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 376 removed outlier: 3.642A pdb=" N ILE a 346 " --> pdb=" O ASP a 342 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 218 removed outlier: 3.669A pdb=" N LEU a 216 " --> pdb=" O PHE a 213 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU a 217 " --> pdb=" O GLY a 214 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET a 218 " --> pdb=" O GLU a 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 213 through 218' Processing helix chain 'b' and resid 13 through 18 removed outlier: 4.733A pdb=" N ASN b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 removed outlier: 3.962A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 76 removed outlier: 4.741A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 4.263A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 Processing helix chain 'b' and resid 150 through 162 removed outlier: 3.719A pdb=" N GLY b 162 " --> pdb=" O ASN b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 191 Proline residue: b 187 - end of helix removed outlier: 3.628A pdb=" N ALA b 190 " --> pdb=" O SER b 186 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY b 191 " --> pdb=" O PRO b 187 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.659A pdb=" N GLY c 48 " --> pdb=" O HIS c 44 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 103 removed outlier: 4.459A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR c 102 " --> pdb=" O MET c 98 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 146 through 151 removed outlier: 5.633A pdb=" N VAL c 151 " --> pdb=" O PRO c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 195 removed outlier: 4.245A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 223 removed outlier: 6.479A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS c 223 " --> pdb=" O ASN c 219 " (cutoff:3.500A) Processing helix chain 'c' and resid 235 through 262 removed outlier: 5.458A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS c 246 " --> pdb=" O GLU c 242 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU c 247 " --> pdb=" O SER c 243 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 275 removed outlier: 4.444A pdb=" N LEU c 270 " --> pdb=" O THR c 266 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN c 274 " --> pdb=" O LEU c 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL c 275 " --> pdb=" O ALA c 271 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 310 removed outlier: 4.712A pdb=" N GLU c 286 " --> pdb=" O ARG c 282 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL c 290 " --> pdb=" O GLU c 286 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE c 309 " --> pdb=" O ASP c 305 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 32 removed outlier: 4.767A pdb=" N CYS d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY d 20 " --> pdb=" O LEU d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 removed outlier: 3.615A pdb=" N GLN d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 84 removed outlier: 3.589A pdb=" N ASP d 84 " --> pdb=" O CYS d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 110 Processing helix chain 'd' and resid 111 through 123 removed outlier: 3.510A pdb=" N LEU d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Proline residue: d 123 - end of helix Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 3.759A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.624A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 186 removed outlier: 3.780A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA d 185 " --> pdb=" O CYS d 181 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR d 186 " --> pdb=" O ILE d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 199 Processing helix chain 'd' and resid 203 through 214 removed outlier: 5.426A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY d 214 " --> pdb=" O ALA d 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 238 through 254 removed outlier: 4.614A pdb=" N LEU d 242 " --> pdb=" O PRO d 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 7 through 27 removed outlier: 4.862A pdb=" N VAL f 11 " --> pdb=" O ASP f 7 " (cutoff:3.500A) Proline residue: f 13 - end of helix Proline residue: f 17 - end of helix Proline residue: f 21 - end of helix removed outlier: 3.732A pdb=" N ASP f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU f 26 " --> pdb=" O GLY f 22 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS f 27 " --> pdb=" O GLY f 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 47 Processing helix chain 'f' and resid 54 through 64 removed outlier: 3.679A pdb=" N MET f 58 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU f 59 " --> pdb=" O GLU f 55 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU f 61 " --> pdb=" O GLU f 57 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG f 62 " --> pdb=" O MET f 58 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU f 63 " --> pdb=" O LEU f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 72 Processing helix chain 'f' and resid 79 through 99 removed outlier: 4.435A pdb=" N SER f 84 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR f 87 " --> pdb=" O ARG f 83 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER f 88 " --> pdb=" O SER f 84 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N MET f 89 " --> pdb=" O SER f 85 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL f 92 " --> pdb=" O SER f 88 " (cutoff:3.500A) Proline residue: f 93 - end of helix removed outlier: 3.743A pdb=" N LEU f 96 " --> pdb=" O VAL f 92 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU f 99 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 108 removed outlier: 4.888A pdb=" N LYS f 107 " --> pdb=" O TYR f 103 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU f 108 " --> pdb=" O GLY f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 109 through 114 removed outlier: 5.676A pdb=" N MET f 113 " --> pdb=" O ILE f 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA f 114 " --> pdb=" O TYR f 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 109 through 114' Processing helix chain 'f' and resid 118 through 123 removed outlier: 4.472A pdb=" N ALA f 122 " --> pdb=" O ASN f 118 " (cutoff:3.500A) Processing helix chain 'f' and resid 129 through 149 removed outlier: 4.842A pdb=" N MET f 133 " --> pdb=" O LEU f 129 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU f 140 " --> pdb=" O GLU f 136 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 173 removed outlier: 4.150A pdb=" N GLU f 157 " --> pdb=" O SER f 153 " (cutoff:3.500A) Processing helix chain 'f' and resid 176 through 191 removed outlier: 4.198A pdb=" N GLN f 180 " --> pdb=" O ALA f 176 " (cutoff:3.500A) Proline residue: f 183 - end of helix removed outlier: 5.008A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE f 191 " --> pdb=" O LEU f 187 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 209 Processing helix chain 'f' and resid 210 through 227 removed outlier: 4.586A pdb=" N VAL f 214 " --> pdb=" O GLU f 210 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP f 215 " --> pdb=" O ILE f 211 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA f 227 " --> pdb=" O GLU f 223 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 247 removed outlier: 3.833A pdb=" N THR f 234 " --> pdb=" O CYS f 230 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS f 236 " --> pdb=" O TYR f 232 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL f 237 " --> pdb=" O LEU f 233 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 3.683A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER f 246 " --> pdb=" O GLU f 242 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) Processing helix chain 'f' and resid 254 through 263 removed outlier: 4.165A pdb=" N LYS f 258 " --> pdb=" O GLY f 254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG f 261 " --> pdb=" O ARG f 257 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE f 262 " --> pdb=" O LYS f 258 " (cutoff:3.500A) Proline residue: f 263 - end of helix Processing helix chain 'f' and resid 269 through 276 removed outlier: 5.136A pdb=" N ASN f 273 " --> pdb=" O ALA f 269 " (cutoff:3.500A) Processing helix chain 'f' and resid 284 through 294 removed outlier: 4.227A pdb=" N VAL f 288 " --> pdb=" O SER f 284 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL f 290 " --> pdb=" O LYS f 286 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN f 291 " --> pdb=" O ASP f 287 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 297 through 304 removed outlier: 4.743A pdb=" N HIS f 301 " --> pdb=" O MET f 297 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY f 302 " --> pdb=" O LEU f 298 " (cutoff:3.500A) Processing helix chain 'f' and resid 307 through 312 removed outlier: 6.615A pdb=" N VAL f 311 " --> pdb=" O LEU f 307 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU f 312 " --> pdb=" O SER f 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 307 through 312' Processing helix chain 'f' and resid 313 through 323 removed outlier: 3.869A pdb=" N ASN f 323 " --> pdb=" O GLU f 319 " (cutoff:3.500A) Processing helix chain 'f' and resid 324 through 336 removed outlier: 4.317A pdb=" N SER f 328 " --> pdb=" O VAL f 324 " (cutoff:3.500A) Processing helix chain 'f' and resid 345 through 351 removed outlier: 4.397A pdb=" N TYR f 349 " --> pdb=" O PRO f 345 " (cutoff:3.500A) Processing helix chain 'f' and resid 354 through 360 removed outlier: 3.737A pdb=" N PHE f 358 " --> pdb=" O GLU f 354 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLY f 359 " --> pdb=" O ASN f 355 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY f 360 " --> pdb=" O ASN f 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 354 through 360' Processing helix chain 'f' and resid 367 through 383 removed outlier: 3.525A pdb=" N ALA f 373 " --> pdb=" O ARG f 369 " (cutoff:3.500A) Processing helix chain 'f' and resid 390 through 395 removed outlier: 4.866A pdb=" N ASP f 394 " --> pdb=" O LEU f 390 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY f 395 " --> pdb=" O LEU f 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 390 through 395' Processing helix chain 'f' and resid 396 through 402 removed outlier: 5.099A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 419 removed outlier: 4.592A pdb=" N SER f 409 " --> pdb=" O HIS f 405 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 423 through 434 removed outlier: 4.152A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 4.179A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 471 removed outlier: 4.007A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR f 469 " --> pdb=" O LEU f 465 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL f 470 " --> pdb=" O LEU f 466 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 3.523A pdb=" N TYR f 489 " --> pdb=" O LEU f 485 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 507 removed outlier: 3.617A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix removed outlier: 4.662A pdb=" N GLY f 506 " --> pdb=" O LEU f 502 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP f 507 " --> pdb=" O PRO f 503 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.578A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 3.522A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 552 removed outlier: 4.060A pdb=" N LYS f 551 " --> pdb=" O GLU f 547 " (cutoff:3.500A) Processing helix chain 'f' and resid 555 through 567 Proline residue: f 559 - end of helix removed outlier: 3.697A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS f 566 " --> pdb=" O LEU f 562 " (cutoff:3.500A) Processing helix chain 'f' and resid 571 through 582 removed outlier: 4.992A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU f 577 " --> pdb=" O ILE f 573 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 585 through 601 removed outlier: 4.182A pdb=" N SER f 589 " --> pdb=" O GLU f 585 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE f 590 " --> pdb=" O PRO f 586 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA f 599 " --> pdb=" O VAL f 595 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 616 removed outlier: 4.302A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS f 616 " --> pdb=" O LEU f 612 " (cutoff:3.500A) Processing helix chain 'f' and resid 618 through 623 removed outlier: 3.843A pdb=" N SER f 622 " --> pdb=" O GLU f 618 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS f 623 " --> pdb=" O HIS f 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 618 through 623' Processing helix chain 'f' and resid 626 through 641 removed outlier: 6.572A pdb=" N ASP f 630 " --> pdb=" O GLU f 626 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS f 632 " --> pdb=" O ASP f 628 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS f 634 " --> pdb=" O ASP f 630 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS f 637 " --> pdb=" O GLU f 633 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP f 638 " --> pdb=" O LYS f 634 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS f 639 " --> pdb=" O LYS f 635 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS f 640 " --> pdb=" O ASP f 636 " (cutoff:3.500A) Processing helix chain 'f' and resid 645 through 659 removed outlier: 4.304A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) Processing helix chain 'f' and resid 666 through 680 removed outlier: 5.559A pdb=" N MET f 670 " --> pdb=" O ILE f 666 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA f 671 " --> pdb=" O GLY f 667 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU f 672 " --> pdb=" O ALA f 668 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR f 674 " --> pdb=" O MET f 670 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU f 679 " --> pdb=" O PHE f 675 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG f 680 " --> pdb=" O GLY f 676 " (cutoff:3.500A) Processing helix chain 'f' and resid 690 through 699 removed outlier: 3.971A pdb=" N LEU f 694 " --> pdb=" O VAL f 690 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA f 695 " --> pdb=" O PRO f 691 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU f 696 " --> pdb=" O LEU f 692 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL f 699 " --> pdb=" O ALA f 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 690 through 699' Processing helix chain 'f' and resid 701 through 717 removed outlier: 3.663A pdb=" N PHE f 713 " --> pdb=" O THR f 709 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER f 714 " --> pdb=" O LEU f 710 " (cutoff:3.500A) Processing helix chain 'f' and resid 721 through 733 removed outlier: 4.603A pdb=" N SER f 725 " --> pdb=" O VAL f 721 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE f 726 " --> pdb=" O SER f 722 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE f 727 " --> pdb=" O TYR f 723 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY f 733 " --> pdb=" O MET f 729 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 755 removed outlier: 3.718A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR f 751 " --> pdb=" O GLN f 747 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS f 754 " --> pdb=" O GLN f 750 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP f 755 " --> pdb=" O TYR f 751 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 787 removed outlier: 4.217A pdb=" N LEU f 776 " --> pdb=" O GLY f 772 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR f 777 " --> pdb=" O LYS f 773 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N CYS f 779 " --> pdb=" O THR f 775 " (cutoff:3.500A) Proline residue: f 780 - end of helix removed outlier: 4.409A pdb=" N SER f 783 " --> pdb=" O CYS f 779 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP f 784 " --> pdb=" O PRO f 780 " (cutoff:3.500A) Processing helix chain 'f' and resid 797 through 803 removed outlier: 3.579A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.983A pdb=" N ALA g 28 " --> pdb=" O GLN g 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE g 29 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.189A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N THR g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 67' Processing helix chain 'g' and resid 83 through 105 Processing helix chain 'g' and resid 110 through 129 removed outlier: 5.332A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 3.944A pdb=" N LYS g 184 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 Processing helix chain 'g' and resid 211 through 216 removed outlier: 4.311A pdb=" N ILE g 215 " --> pdb=" O LYS g 211 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLU g 216 " --> pdb=" O PRO g 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 211 through 216' Processing helix chain 'g' and resid 231 through 245 removed outlier: 3.680A pdb=" N ARG g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 32 removed outlier: 3.726A pdb=" N ALA i 24 " --> pdb=" O GLN i 20 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.652A pdb=" N ALA i 83 " --> pdb=" O ILE i 79 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN i 84 " --> pdb=" O THR i 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.538A pdb=" N LEU i 110 " --> pdb=" O PRO i 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR i 122 " --> pdb=" O LYS i 118 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 removed outlier: 3.659A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 202 removed outlier: 4.021A pdb=" N ASP i 202 " --> pdb=" O ASN i 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 212 removed outlier: 3.817A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLU i 212 " --> pdb=" O ALA i 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 207 through 212' Processing helix chain 'i' and resid 229 through 251 Processing helix chain 'k' and resid 21 through 35 removed outlier: 3.727A pdb=" N ILE k 31 " --> pdb=" O ALA k 27 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER k 35 " --> pdb=" O ILE k 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 65 removed outlier: 4.117A pdb=" N ILE k 64 " --> pdb=" O GLU k 60 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU k 65 " --> pdb=" O PRO k 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 60 through 65' Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.728A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 3.983A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.968A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 211 through 216 removed outlier: 4.144A pdb=" N ILE k 215 " --> pdb=" O ASN k 211 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU k 216 " --> pdb=" O ALA k 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 211 through 216' Processing helix chain 'k' and resid 230 through 241 removed outlier: 4.085A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.669A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 Processing helix chain 'l' and resid 104 through 123 removed outlier: 4.066A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 3.521A pdb=" N ARG l 122 " --> pdb=" O ILE l 118 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TYR l 123 " --> pdb=" O PRO l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 180 removed outlier: 5.685A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 199 removed outlier: 3.977A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU l 199 " --> pdb=" O LEU l 195 " (cutoff:3.500A) Processing helix chain 'l' and resid 225 through 234 removed outlier: 4.339A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 3.875A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 4.751A pdb=" N ASP l 7 " --> pdb=" O ASN l 4 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN l 8 " --> pdb=" O GLN l 5 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP l 9 " --> pdb=" O TYR l 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 9' Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.592A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU m 31 " --> pdb=" O MET m 27 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 Processing helix chain 'm' and resid 107 through 125 removed outlier: 4.038A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR m 125 " --> pdb=" O ALA m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 4.069A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 180 through 185 removed outlier: 4.008A pdb=" N MET m 184 " --> pdb=" O GLN m 180 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR m 185 " --> pdb=" O MET m 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 180 through 185' Processing helix chain 'm' and resid 186 through 201 removed outlier: 3.848A pdb=" N VAL m 190 " --> pdb=" O CYS m 186 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 removed outlier: 3.679A pdb=" N LYS m 244 " --> pdb=" O LYS m 240 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 10 removed outlier: 5.347A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER m 10 " --> pdb=" O TYR m 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 5 through 10' Processing helix chain 'n' and resid 48 through 71 Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.700A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.595A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 removed outlier: 3.669A pdb=" N ARG n 166 " --> pdb=" O LEU n 162 " (cutoff:3.500A) Processing helix chain 'x' and resid 25 through 38 Processing helix chain 'x' and resid 94 through 103 removed outlier: 3.797A pdb=" N ALA x 98 " --> pdb=" O GLU x 94 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET x 101 " --> pdb=" O LEU x 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU x 102 " --> pdb=" O ALA x 98 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU x 103 " --> pdb=" O SER x 99 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 126 removed outlier: 3.829A pdb=" N ASN x 117 " --> pdb=" O THR x 113 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL x 126 " --> pdb=" O CYS x 122 " (cutoff:3.500A) Processing helix chain 'x' and resid 127 through 137 removed outlier: 4.327A pdb=" N ALA x 137 " --> pdb=" O LEU x 133 " (cutoff:3.500A) Processing helix chain 'x' and resid 146 through 167 removed outlier: 4.667A pdb=" N GLN x 150 " --> pdb=" O MET x 146 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER x 167 " --> pdb=" O MET x 163 " (cutoff:3.500A) Processing helix chain 'x' and resid 172 through 184 Proline residue: x 184 - end of helix Processing helix chain 'x' and resid 199 through 215 Processing helix chain 'x' and resid 220 through 226 Processing helix chain 'x' and resid 241 through 248 Processing helix chain 'x' and resid 285 through 296 removed outlier: 3.904A pdb=" N GLN x 295 " --> pdb=" O LYS x 291 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU x 296 " --> pdb=" O LEU x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 355 through 360 removed outlier: 4.105A pdb=" N CYS x 359 " --> pdb=" O MET x 355 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR x 360 " --> pdb=" O TYR x 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 355 through 360' Processing helix chain 'x' and resid 361 through 369 removed outlier: 5.107A pdb=" N SER x 369 " --> pdb=" O GLU x 365 " (cutoff:3.500A) Processing helix chain 'x' and resid 370 through 380 Processing helix chain 'x' and resid 459 through 467 removed outlier: 3.616A pdb=" N ILE x 463 " --> pdb=" O THR x 459 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER x 467 " --> pdb=" O ILE x 463 " (cutoff:3.500A) Processing helix chain 'y' and resid 22 through 34 removed outlier: 4.185A pdb=" N VAL y 26 " --> pdb=" O THR y 22 " (cutoff:3.500A) Processing helix chain 'y' and resid 55 through 60 removed outlier: 3.544A pdb=" N TYR y 59 " --> pdb=" O THR y 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 35 Proline residue: W 29 - end of helix removed outlier: 3.889A pdb=" N ALA W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS W 33 " --> pdb=" O PRO W 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA W 35 " --> pdb=" O CYS W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 57 removed outlier: 4.247A pdb=" N THR W 46 " --> pdb=" O GLU W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 78 removed outlier: 3.709A pdb=" N THR W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU W 67 " --> pdb=" O THR W 63 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL W 68 " --> pdb=" O SER W 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS W 78 " --> pdb=" O CYS W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 93 Processing helix chain 'W' and resid 97 through 116 removed outlier: 3.662A pdb=" N THR W 116 " --> pdb=" O VAL W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 140 through 156 removed outlier: 5.226A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR W 148 " --> pdb=" O ARG W 144 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 removed outlier: 4.399A pdb=" N ALA W 163 " --> pdb=" O VAL W 159 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER W 164 " --> pdb=" O LYS W 160 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE W 165 " --> pdb=" O GLU W 161 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 169 through 177 removed outlier: 4.568A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY W 175 " --> pdb=" O VAL W 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET W 177 " --> pdb=" O THR W 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 169 through 177' Processing helix chain 'W' and resid 178 through 197 Processing helix chain 'W' and resid 198 through 213 removed outlier: 4.247A pdb=" N LYS W 207 " --> pdb=" O GLN W 203 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS W 208 " --> pdb=" O ILE W 204 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE W 209 " --> pdb=" O ILE W 205 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS W 212 " --> pdb=" O LYS W 208 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE W 213 " --> pdb=" O ILE W 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 238 removed outlier: 4.044A pdb=" N LYS W 223 " --> pdb=" O THR W 219 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU W 224 " --> pdb=" O GLU W 220 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS W 225 " --> pdb=" O LYS W 221 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE W 231 " --> pdb=" O TYR W 227 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 4.941A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 259 through 278 removed outlier: 3.565A pdb=" N VAL W 271 " --> pdb=" O LEU W 267 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU W 272 " --> pdb=" O LYS W 268 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA W 277 " --> pdb=" O TYR W 273 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 292 removed outlier: 4.211A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE W 290 " --> pdb=" O LEU W 286 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 300 removed outlier: 4.316A pdb=" N GLU W 297 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU W 298 " --> pdb=" O LYS W 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE W 299 " --> pdb=" O LYS W 295 " (cutoff:3.500A) Proline residue: W 300 - end of helix No H-bonds generated for 'chain 'W' and resid 293 through 300' Processing helix chain 'W' and resid 301 through 307 Processing helix chain 'W' and resid 316 through 324 Processing helix chain 'W' and resid 325 through 330 removed outlier: 3.507A pdb=" N ARG W 329 " --> pdb=" O GLY W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 removed outlier: 4.300A pdb=" N ASP W 339 " --> pdb=" O SER W 335 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 370 removed outlier: 4.081A pdb=" N GLU W 348 " --> pdb=" O THR W 344 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS W 368 " --> pdb=" O ARG W 364 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 removed outlier: 3.684A pdb=" N ASP W 383 " --> pdb=" O ALA W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 400 Processing helix chain 'W' and resid 420 through 454 removed outlier: 3.560A pdb=" N LEU W 424 " --> pdb=" O ASP W 420 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 91 through 105 Proline residue: V 102 - end of helix Processing helix chain 'V' and resid 109 through 121 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.710A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 5.060A pdb=" N GLU V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 158 Proline residue: V 158 - end of helix Processing helix chain 'V' and resid 160 through 179 Processing helix chain 'V' and resid 180 through 199 removed outlier: 3.867A pdb=" N ALA V 184 " --> pdb=" O ARG V 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 204 through 222 removed outlier: 3.886A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP V 222 " --> pdb=" O TYR V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.495A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.706A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 removed outlier: 3.525A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.563A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 345 through 350 removed outlier: 3.731A pdb=" N ARG V 349 " --> pdb=" O ARG V 345 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN V 350 " --> pdb=" O LEU V 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 345 through 350' Processing helix chain 'V' and resid 353 through 370 Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 383 removed outlier: 3.515A pdb=" N PHE V 375 " --> pdb=" O ASN V 371 " (cutoff:3.500A) Processing helix chain 'V' and resid 384 through 390 Processing helix chain 'V' and resid 391 through 402 removed outlier: 4.215A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 403 through 415 removed outlier: 5.350A pdb=" N SER V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 Processing helix chain 'V' and resid 430 through 445 Processing helix chain 'V' and resid 470 through 494 removed outlier: 4.110A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET V 494 " --> pdb=" O SER V 490 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 4.527A pdb=" N ASP e 46 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN e 47 " --> pdb=" O TRP e 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 42 through 47' Processing helix chain 'e' and resid 51 through 64 removed outlier: 5.059A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.353A pdb=" N ARG A 139 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id= 3, first strand: chain 'A' and resid 235 through 240 removed outlier: 4.098A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 270 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 318 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 212 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A 339 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 114 through 117 removed outlier: 3.941A pdb=" N GLU B 114 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 122 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS B 148 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER B 149 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 246 through 251 removed outlier: 4.171A pdb=" N THR B 246 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 280 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 330 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 120 through 125 removed outlier: 4.756A pdb=" N SER B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 71 through 75 removed outlier: 4.387A pdb=" N ARG C 113 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 83 through 87 removed outlier: 7.572A pdb=" N LYS C 83 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 99 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 209 through 215 removed outlier: 4.088A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 102 through 105 removed outlier: 6.567A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA D 128 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N SER D 129 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 226 through 231 removed outlier: 3.653A pdb=" N ALA D 310 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG D 200 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 76 through 81 removed outlier: 6.826A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR E 74 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N VAL E 57 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 194 through 198 removed outlier: 4.207A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS E 228 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS E 274 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS E 170 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 95 through 98 removed outlier: 6.698A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 247 through 251 removed outlier: 5.145A pdb=" N THR F 247 " --> pdb=" O PRO F 280 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER F 281 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE F 283 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LYS F 221 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 350 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 224 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE F 352 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 121 through 126 removed outlier: 4.134A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.502A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.326A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.517A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS H 71 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 160 through 164 removed outlier: 5.418A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.548A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS h 71 " --> pdb=" O TRP h 139 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY h 138 " --> pdb=" O TYR h 145 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'h' and resid 160 through 164 removed outlier: 3.782A pdb=" N GLU h 49 " --> pdb=" O PRO h 34 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN h 207 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 64 through 68 removed outlier: 6.277A pdb=" N LYS I 64 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP I 71 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP I 139 " --> pdb=" O ASP I 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 161 through 165 removed outlier: 5.031A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.515A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA J 131 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 158 through 162 removed outlier: 4.742A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'j' and resid 62 through 65 removed outlier: 6.562A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA j 131 " --> pdb=" O THR j 147 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY j 135 " --> pdb=" O ARG j 143 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.746A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.722A pdb=" N LYS K 66 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N HIS K 73 " --> pdb=" O VAL K 146 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU K 153 " --> pdb=" O CYS K 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL K 163 " --> pdb=" O HIS K 155 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 167 through 171 removed outlier: 5.565A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU K 216 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASN K 214 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.479A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 158 through 162 removed outlier: 4.891A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'M' and resid 65 through 68 removed outlier: 6.450A pdb=" N ARG M 65 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL M 77 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP M 152 " --> pdb=" O VAL M 156 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL M 156 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.864A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.534A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER N 46 " --> pdb=" O GLY N 97 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.526A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.410A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.199A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.395A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.600A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'P' and resid 42 through 45 removed outlier: 5.742A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 136 through 140 removed outlier: 5.861A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.593A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.409A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.550A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 129 through 132 removed outlier: 4.093A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.441A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'q' and resid 129 through 132 removed outlier: 6.434A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R' and resid 34 through 37 removed outlier: 6.321A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.288A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.927A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR r 44 " --> pdb=" O MET r 100 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.222A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER r 18 " --> pdb=" O ALA r 173 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.615A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN S 108 " --> pdb=" O PHE S 124 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'S' and resid 135 through 139 removed outlier: 6.170A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP S 26 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY S 202 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 's' and resid 43 through 46 removed outlier: 6.674A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN s 108 " --> pdb=" O PHE s 124 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 's' and resid 135 through 139 removed outlier: 5.554A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.602A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL T 130 " --> pdb=" O ASP T 126 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.199A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 't' and resid 42 through 45 removed outlier: 6.885A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR t 132 " --> pdb=" O TYR t 124 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL t 130 " --> pdb=" O ASP t 126 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 't' and resid 136 through 139 removed outlier: 4.195A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA t 23 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 801 through 806 removed outlier: 4.676A pdb=" N CYS U 806 " --> pdb=" O ASN U 874 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN U 874 " --> pdb=" O CYS U 806 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'X' and resid 376 through 380 Processing sheet with id= 63, first strand: chain 'Y' and resid 344 through 347 removed outlier: 5.927A pdb=" N HIS Y 344 " --> pdb=" O ASN Y 357 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU Y 355 " --> pdb=" O LYS Y 346 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Z' and resid 35 through 40 removed outlier: 4.526A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N SER Z 119 " --> pdb=" O SER Z 140 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER Z 140 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR Z 135 " --> pdb=" O SER Z 160 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER Z 160 " --> pdb=" O THR Z 135 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL Z 141 " --> pdb=" O THR Z 154 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR Z 154 " --> pdb=" O VAL Z 141 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLN Z 7 " --> pdb=" O HIS Z 157 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR Z 159 " --> pdb=" O GLN Z 7 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'a' and resid 320 through 326 removed outlier: 4.360A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'b' and resid 46 through 54 removed outlier: 4.239A pdb=" N GLU b 4 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY b 50 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL b 10 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET b 7 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP b 11 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY b 114 " --> pdb=" O ASP b 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'c' and resid 65 through 69 removed outlier: 3.534A pdb=" N GLN c 30 " --> pdb=" O TYR c 65 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLU c 29 " --> pdb=" O SER c 202 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU c 162 " --> pdb=" O ALA c 140 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ALA c 140 " --> pdb=" O LEU c 162 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL c 141 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP c 111 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL c 145 " --> pdb=" O HIS c 113 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'f' and resid 812 through 815 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'f' and resid 824 through 829 removed outlier: 6.200A pdb=" N ALA f 824 " --> pdb=" O PHE f 865 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE f 865 " --> pdb=" O ALA f 824 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG f 828 " --> pdb=" O THR f 861 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.455A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET g 80 " --> pdb=" O HIS g 68 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR g 81 " --> pdb=" O CYS g 137 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'g' and resid 165 through 169 removed outlier: 5.363A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.564A pdb=" N LYS i 64 " --> pdb=" O VAL i 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL i 76 " --> pdb=" O LYS i 64 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP i 71 " --> pdb=" O TRP i 139 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP i 151 " --> pdb=" O ASN i 155 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN i 155 " --> pdb=" O ASP i 151 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'i' and resid 161 through 165 removed outlier: 5.126A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY i 42 " --> pdb=" O ALA i 39 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'k' and resid 66 through 70 removed outlier: 6.611A pdb=" N LYS k 66 " --> pdb=" O MET k 78 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS k 73 " --> pdb=" O VAL k 146 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU k 153 " --> pdb=" O CYS k 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL k 163 " --> pdb=" O HIS k 155 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'k' and resid 167 through 171 removed outlier: 5.455A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.389A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU l 132 " --> pdb=" O THR l 147 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'l' and resid 158 through 162 removed outlier: 4.653A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'm' and resid 66 through 69 removed outlier: 6.427A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'm' and resid 162 through 166 removed outlier: 5.157A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU m 50 " --> pdb=" O THR m 35 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.570A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.178A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'x' and resid 6 through 9 removed outlier: 3.589A pdb=" N MET x 71 " --> pdb=" O LYS x 9 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'x' and resid 265 through 272 removed outlier: 3.676A pdb=" N THR x 266 " --> pdb=" O MET x 255 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU x 310 " --> pdb=" O THR x 258 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'x' and resid 274 through 278 removed outlier: 5.774A pdb=" N ARG x 330 " --> pdb=" O VAL x 343 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'x' and resid 417 through 420 removed outlier: 6.413A pdb=" N TYR x 417 " --> pdb=" O ARG x 483 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'x' and resid 454 through 458 removed outlier: 6.482A pdb=" N GLU x 446 " --> pdb=" O ARG x 442 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU x 424 " --> pdb=" O TYR x 476 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'x' and resid 323 through 327 Processing sheet with id= 88, first strand: chain 'y' and resid 2 through 7 removed outlier: 4.668A pdb=" N LYS y 11 " --> pdb=" O THR y 7 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'y' and resid 41 through 44 Processing sheet with id= 90, first strand: chain 'W' and resid 404 through 408 Processing sheet with id= 91, first strand: chain 'V' and resid 449 through 452 5895 hydrogen bonds defined for protein. 17604 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: 47.48 Time building geometry restraints manager: 34.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 36516 1.34 - 1.46: 23265 1.46 - 1.58: 51794 1.58 - 1.71: 14 1.71 - 1.83: 1071 Bond restraints: 112660 Sorted by residual: bond pdb=" CA MET x 92 " pdb=" CB MET x 92 " ideal model delta sigma weight residual 1.526 1.597 -0.071 1.53e-02 4.27e+03 2.16e+01 bond pdb=" C ARG f 72 " pdb=" N PRO f 73 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 8.77e+00 bond pdb=" N LEU K 121 " pdb=" CA LEU K 121 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.40e+00 bond pdb=" N PHE d 200 " pdb=" CA PHE d 200 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.68e+00 bond pdb=" N CYS C 112 " pdb=" CA CYS C 112 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.54e+00 ... (remaining 112655 not shown) Histogram of bond angle deviations from ideal: 94.64 - 103.68: 1411 103.68 - 112.72: 59986 112.72 - 121.75: 66629 121.75 - 130.79: 23720 130.79 - 139.83: 447 Bond angle restraints: 152193 Sorted by residual: angle pdb=" N VAL F 326 " pdb=" CA VAL F 326 " pdb=" C VAL F 326 " ideal model delta sigma weight residual 112.43 106.14 6.29 9.20e-01 1.18e+00 4.67e+01 angle pdb=" C ALA e 28 " pdb=" CA ALA e 28 " pdb=" CB ALA e 28 " ideal model delta sigma weight residual 116.54 109.39 7.15 1.15e+00 7.56e-01 3.87e+01 angle pdb=" C ILE A 157 " pdb=" N ASP A 158 " pdb=" CA ASP A 158 " ideal model delta sigma weight residual 121.80 136.40 -14.60 2.44e+00 1.68e-01 3.58e+01 angle pdb=" N VAL a 130 " pdb=" CA VAL a 130 " pdb=" C VAL a 130 " ideal model delta sigma weight residual 113.47 107.61 5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" N THR W 116 " pdb=" CA THR W 116 " pdb=" C THR W 116 " ideal model delta sigma weight residual 108.26 117.14 -8.88 1.66e+00 3.63e-01 2.86e+01 ... (remaining 152188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 63456 20.01 - 40.03: 4733 40.03 - 60.04: 565 60.04 - 80.05: 111 80.05 - 100.07: 31 Dihedral angle restraints: 68896 sinusoidal: 27913 harmonic: 40983 Sorted by residual: dihedral pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -22.39 -63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CA PRO E 166 " pdb=" C PRO E 166 " pdb=" N PRO E 167 " pdb=" CA PRO E 167 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE I 52 " pdb=" C ILE I 52 " pdb=" N HIS I 53 " pdb=" CA HIS I 53 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 68893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 14359 0.062 - 0.124: 2603 0.124 - 0.185: 242 0.185 - 0.247: 16 0.247 - 0.309: 10 Chirality restraints: 17230 Sorted by residual: chirality pdb=" CB ILE X 318 " pdb=" CA ILE X 318 " pdb=" CG1 ILE X 318 " pdb=" CG2 ILE X 318 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE V 466 " pdb=" CA ILE V 466 " pdb=" CG1 ILE V 466 " pdb=" CG2 ILE V 466 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE f 666 " pdb=" CA ILE f 666 " pdb=" CG1 ILE f 666 " pdb=" CG2 ILE f 666 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 17227 not shown) Planarity restraints: 19623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP m 215 " 0.027 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP m 215 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP m 215 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP m 215 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP m 215 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP m 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP m 215 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 215 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP m 215 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 109 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO C 110 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR d 202 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO d 203 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO d 203 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO d 203 " -0.042 5.00e-02 4.00e+02 ... (remaining 19620 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 5826 2.73 - 3.27: 107302 3.27 - 3.82: 180862 3.82 - 4.36: 209370 4.36 - 4.90: 366793 Nonbonded interactions: 870153 Sorted by model distance: nonbonded pdb=" CG HIS c 115 " pdb="ZN ZN c 401 " model vdw 2.190 1.960 nonbonded pdb=" OG SER C 217 " pdb=" OE1 GLU D 291 " model vdw 2.209 2.440 nonbonded pdb=" O LEU W 128 " pdb=" OG1 THR W 132 " model vdw 2.214 2.440 nonbonded pdb=" O PRO U 634 " pdb=" OG SER U 638 " model vdw 2.225 2.440 nonbonded pdb=" O MET W 60 " pdb=" OG SER W 64 " model vdw 2.234 2.440 ... (remaining 870148 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 'G' and (resid 6 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 195 or (resid 196 and (n \ ame N or name CA or name C or name O or name CB )) or resid 197 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 245)) selection = (chain 'g' and resid 6 through 245) } ncs_group { reference = (chain 'H' and (resid 3 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB )) or resid 201 through 234)) selection = (chain 'h' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 234)) } ncs_group { reference = (chain 'I' and (resid 4 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB )) or resid 200 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 251)) selection = (chain 'i' and (resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 228 or (resid 229 and (name N or na \ me CA or name C or name O or name CB )) or resid 230 or (resid 231 and (name N o \ r name CA or name C or name O or name CB )) or resid 232 through 238 or (resid 2 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 251)) } ncs_group { reference = (chain 'J' and (resid 2 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 223 or (resid 22 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or re \ sid 233 through 238 or (resid 239 through 240 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'j' and (resid 2 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 173 or (resid 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 188 \ or (resid 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 217 or (resid 218 and (name N or name CA or name C or name O or nam \ e CB )) or resid 219 through 240)) } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)))) selection = (chain 'k' and (resid 8 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 207 or (resid 208 an \ d (name N or name CA or name C or name O or name CB )) or resid 209 through 241) \ ) } ncs_group { reference = (chain 'L' and (resid 4 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 241)) selection = (chain 'l' and (resid 4 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 241)) } ncs_group { reference = (chain 'M' and resid 5 through 244) selection = (chain 'm' and (resid 5 through 187 or (resid 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 244)) } ncs_group { reference = (chain 'N' and (resid 1 through 149 or (resid 150 and (name N or name CA or name \ C or name O or name CB )) or resid 151 through 202)) selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and (resid 1 through 179 or (resid 180 and (name N or name CA or name \ C or name O or name CB )) or resid 181 through 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 202 or (resid 20 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 204 through \ 220)) } ncs_group { reference = chain 'P' selection = (chain 'p' and (resid 2 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 205)) } ncs_group { reference = (chain 'Q' and (resid 1 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 199)) selection = chain 'q' } ncs_group { reference = (chain 'R' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 88 or (resid 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 through 201)) selection = chain 'r' } ncs_group { reference = (chain 'S' and (resid 1 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 213)) selection = (chain 's' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 213)) } ncs_group { reference = chain 'T' selection = (chain 't' and (resid 1 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 216)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 9.090 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: 0.080 Extract box with map and model: 51.490 Check model and map are aligned: 1.670 Set scattering table: 0.860 Process input model: 291.160 Find NCS groups from input model: 6.720 Set up NCS constraints: 0.560 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 363.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.003 0.071 112660 Z= 0.208 Angle : 0.742 14.856 152193 Z= 0.387 Chirality : 0.047 0.309 17230 Planarity : 0.005 0.078 19623 Dihedral : 13.773 100.066 42508 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 0.15 % Allowed : 0.41 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: -0.80 (0.07), residues: 13974 helix: 0.45 (0.06), residues: 6415 sheet: 0.06 (0.11), residues: 2124 loop : -1.97 (0.08), residues: 5435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP m 215 HIS 0.016 0.001 HIS U 70 PHE 0.044 0.002 PHE Y 201 TYR 0.037 0.001 TYR y 59 ARG 0.009 0.000 ARG Q 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 474 time to evaluate : 9.967 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: A 332 MET cc_start: 0.8472 (mmm) cc_final: 0.7804 (mmm) REVERT: B 214 MET cc_start: 0.8029 (mmm) cc_final: 0.7796 (tpp) REVERT: E 258 MET cc_start: 0.8640 (ttm) cc_final: 0.8162 (tmm) REVERT: F 175 MET cc_start: 0.4682 (mmt) cc_final: 0.3794 (mmm) REVERT: F 356 MET cc_start: 0.7310 (mmm) cc_final: 0.6765 (tpp) REVERT: F 373 MET cc_start: 0.6923 (ptt) cc_final: 0.5781 (tpp) REVERT: F 405 MET cc_start: 0.9347 (tpt) cc_final: 0.9116 (tpp) REVERT: d 205 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7825 (pttm) REVERT: j 211 MET cc_start: 0.8341 (ttt) cc_final: 0.8092 (ttt) REVERT: n 116 MET cc_start: 0.8761 (mtt) cc_final: 0.8532 (ttm) REVERT: x 47 MET cc_start: 0.5260 (tpt) cc_final: 0.4782 (tpp) REVERT: x 163 MET cc_start: 0.6787 (ppp) cc_final: 0.6431 (ppp) REVERT: x 352 MET cc_start: 0.7176 (tpt) cc_final: 0.6016 (mmm) REVERT: y 1 MET cc_start: 0.6327 (tmm) cc_final: 0.5552 (tpt) REVERT: W 120 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6790 (mt) REVERT: W 230 MET cc_start: 0.8587 (pmm) cc_final: 0.8322 (pmm) REVERT: V 139 MET cc_start: 0.6827 (pmm) cc_final: 0.4839 (ptt) outliers start: 18 outliers final: 2 residues processed: 492 average time/residue: 0.9091 time to fit residues: 801.8770 Evaluate side-chains 450 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 446 time to evaluate : 9.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain W residue 120 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1174 optimal weight: 9.9990 chunk 1054 optimal weight: 3.9990 chunk 585 optimal weight: 30.0000 chunk 360 optimal weight: 20.0000 chunk 711 optimal weight: 40.0000 chunk 563 optimal weight: 7.9990 chunk 1090 optimal weight: 9.9990 chunk 421 optimal weight: 8.9990 chunk 662 optimal weight: 10.0000 chunk 811 optimal weight: 20.0000 chunk 1263 optimal weight: 40.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 HIS C 270 GLN D 412 GLN ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN O 193 ASN U 373 ASN U 398 ASN U 801 GLN ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 HIS ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 264 GLN W 399 ASN W 422 ASN ** W 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS V 118 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 112660 Z= 0.277 Angle : 0.580 16.777 152193 Z= 0.303 Chirality : 0.041 0.169 17230 Planarity : 0.004 0.069 19623 Dihedral : 5.676 106.651 15523 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 0.27 % Allowed : 5.57 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.22 (0.07), residues: 13974 helix: 1.62 (0.07), residues: 6530 sheet: 0.07 (0.11), residues: 2146 loop : -1.75 (0.08), residues: 5298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP m 215 HIS 0.011 0.001 HIS f 677 PHE 0.024 0.001 PHE f 713 TYR 0.020 0.001 TYR U 246 ARG 0.008 0.000 ARG Y 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 446 time to evaluate : 9.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6297 (tpt) cc_final: 0.5446 (mpp) REVERT: A 263 MET cc_start: 0.8055 (tmm) cc_final: 0.7749 (ppp) REVERT: A 332 MET cc_start: 0.8477 (mmm) cc_final: 0.7805 (mmm) REVERT: E 232 MET cc_start: 0.8746 (mpp) cc_final: 0.8524 (mpp) REVERT: E 258 MET cc_start: 0.8714 (ttm) cc_final: 0.8286 (tmm) REVERT: F 69 MET cc_start: 0.7744 (ppp) cc_final: 0.7524 (ttt) REVERT: F 175 MET cc_start: 0.4925 (mmt) cc_final: 0.3841 (mmm) REVERT: F 310 MET cc_start: 0.4999 (mmt) cc_final: 0.3257 (mmm) REVERT: F 356 MET cc_start: 0.7359 (mmm) cc_final: 0.6764 (tpp) REVERT: F 373 MET cc_start: 0.7503 (ptt) cc_final: 0.6025 (tpp) REVERT: F 405 MET cc_start: 0.9344 (tpt) cc_final: 0.9114 (tpp) REVERT: U 188 MET cc_start: 0.8453 (ppp) cc_final: 0.8113 (ppp) REVERT: U 556 MET cc_start: 0.7865 (tpp) cc_final: 0.7410 (mtt) REVERT: U 588 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8091 (tmm) REVERT: X 160 MET cc_start: 0.7357 (tmm) cc_final: 0.7143 (tmm) REVERT: a 349 MET cc_start: 0.8916 (pmm) cc_final: 0.8600 (pmm) REVERT: c 51 MET cc_start: 0.7499 (tmm) cc_final: 0.7256 (tmm) REVERT: d 205 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8335 (pptt) REVERT: f 729 MET cc_start: 0.9326 (mpp) cc_final: 0.9054 (mpp) REVERT: j 211 MET cc_start: 0.8082 (ttt) cc_final: 0.7751 (ttt) REVERT: n 95 MET cc_start: 0.6321 (tpt) cc_final: 0.5814 (tpt) REVERT: n 120 MET cc_start: 0.8328 (tpp) cc_final: 0.8067 (ttp) REVERT: x 255 MET cc_start: 0.3708 (mpp) cc_final: 0.3423 (mpp) REVERT: x 352 MET cc_start: 0.7278 (tpt) cc_final: 0.6014 (mmm) REVERT: y 1 MET cc_start: 0.6302 (tmm) cc_final: 0.5316 (tpt) REVERT: W 177 MET cc_start: 0.6649 (tpt) cc_final: 0.6076 (mmt) REVERT: W 230 MET cc_start: 0.8507 (pmm) cc_final: 0.8213 (pmm) REVERT: V 139 MET cc_start: 0.7019 (pmm) cc_final: 0.5072 (ptt) outliers start: 32 outliers final: 12 residues processed: 457 average time/residue: 0.8653 time to fit residues: 713.2903 Evaluate side-chains 457 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 443 time to evaluate : 9.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain U residue 244 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 168 MET Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain t residue 9 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 702 optimal weight: 3.9990 chunk 392 optimal weight: 10.0000 chunk 1051 optimal weight: 6.9990 chunk 860 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 1265 optimal weight: 2.9990 chunk 1367 optimal weight: 7.9990 chunk 1127 optimal weight: 5.9990 chunk 1254 optimal weight: 4.9990 chunk 431 optimal weight: 20.0000 chunk 1015 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS E 316 HIS I 123 GLN O 193 ASN Y 49 ASN Y 273 GLN Z 193 ASN ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 109 ASN x 121 GLN W 257 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 112660 Z= 0.179 Angle : 0.517 15.905 152193 Z= 0.267 Chirality : 0.040 0.163 17230 Planarity : 0.003 0.065 19623 Dihedral : 5.439 109.808 15517 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.87 % Favored : 94.09 % Rotamer: Outliers : 0.38 % Allowed : 8.47 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.57 (0.07), residues: 13974 helix: 2.00 (0.07), residues: 6520 sheet: 0.15 (0.11), residues: 2146 loop : -1.67 (0.08), residues: 5308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP m 215 HIS 0.009 0.001 HIS V 78 PHE 0.024 0.001 PHE f 713 TYR 0.014 0.001 TYR U 682 ARG 0.004 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 443 time to evaluate : 9.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8591 (mmm) cc_final: 0.7940 (mmm) REVERT: E 232 MET cc_start: 0.8757 (mpp) cc_final: 0.8547 (mpp) REVERT: E 258 MET cc_start: 0.8726 (ttm) cc_final: 0.8303 (tmm) REVERT: E 264 MET cc_start: 0.8985 (mmm) cc_final: 0.8766 (mtp) REVERT: F 175 MET cc_start: 0.4941 (mmt) cc_final: 0.3897 (mmm) REVERT: F 310 MET cc_start: 0.4933 (mmt) cc_final: 0.3254 (mmm) REVERT: F 356 MET cc_start: 0.7447 (mmm) cc_final: 0.6841 (tpp) REVERT: F 373 MET cc_start: 0.7498 (ptt) cc_final: 0.6019 (tpp) REVERT: F 405 MET cc_start: 0.9346 (tpt) cc_final: 0.9110 (tpp) REVERT: U 188 MET cc_start: 0.8519 (ppp) cc_final: 0.8243 (ppp) REVERT: U 556 MET cc_start: 0.7789 (tpp) cc_final: 0.7509 (mtt) REVERT: U 588 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8087 (tmm) REVERT: Y 152 MET cc_start: 0.8289 (mmm) cc_final: 0.7841 (tpp) REVERT: Z 81 MET cc_start: 0.8714 (tpp) cc_final: 0.8472 (tpp) REVERT: c 41 MET cc_start: 0.9121 (mmt) cc_final: 0.8846 (mmt) REVERT: c 75 MET cc_start: 0.9058 (mmm) cc_final: 0.8579 (mmm) REVERT: d 75 MET cc_start: 0.8809 (mmm) cc_final: 0.8572 (mmm) REVERT: d 205 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8189 (pptt) REVERT: f 271 MET cc_start: 0.7944 (tmm) cc_final: 0.7659 (tmm) REVERT: f 297 MET cc_start: 0.1804 (tpt) cc_final: 0.1403 (tpt) REVERT: f 543 MET cc_start: 0.8093 (ppp) cc_final: 0.7508 (ppp) REVERT: f 729 MET cc_start: 0.9332 (mpp) cc_final: 0.8861 (mpp) REVERT: n 116 MET cc_start: 0.9061 (mtt) cc_final: 0.8860 (mtp) REVERT: n 120 MET cc_start: 0.8327 (tpp) cc_final: 0.8078 (ttp) REVERT: t 214 MET cc_start: 0.7625 (ppp) cc_final: 0.7373 (ppp) REVERT: x 71 MET cc_start: 0.7803 (pmm) cc_final: 0.7218 (pmm) REVERT: x 255 MET cc_start: 0.3568 (mpp) cc_final: 0.3005 (mpp) REVERT: x 352 MET cc_start: 0.7215 (tpt) cc_final: 0.5959 (mmm) REVERT: W 177 MET cc_start: 0.6391 (tpt) cc_final: 0.5522 (mmt) REVERT: W 230 MET cc_start: 0.8409 (pmm) cc_final: 0.8075 (pmm) REVERT: V 139 MET cc_start: 0.7121 (pmm) cc_final: 0.5228 (ptt) REVERT: V 494 MET cc_start: 0.8379 (tpp) cc_final: 0.8172 (tpp) outliers start: 45 outliers final: 18 residues processed: 469 average time/residue: 0.8322 time to fit residues: 706.9208 Evaluate side-chains 461 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 441 time to evaluate : 9.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain x residue 367 MET Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1250 optimal weight: 20.0000 chunk 951 optimal weight: 40.0000 chunk 656 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 603 optimal weight: 5.9990 chunk 849 optimal weight: 20.0000 chunk 1269 optimal weight: 6.9990 chunk 1344 optimal weight: 7.9990 chunk 663 optimal weight: 0.9990 chunk 1203 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 ASN U 89 ASN U 355 ASN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 220 ASN ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 112660 Z= 0.223 Angle : 0.529 14.776 152193 Z= 0.274 Chirality : 0.040 0.157 17230 Planarity : 0.003 0.061 19623 Dihedral : 5.387 113.401 15516 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.38 % Favored : 93.58 % Rotamer: Outliers : 0.67 % Allowed : 10.36 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.72 (0.07), residues: 13974 helix: 2.17 (0.07), residues: 6528 sheet: 0.12 (0.11), residues: 2148 loop : -1.61 (0.09), residues: 5298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP m 215 HIS 0.009 0.001 HIS U 70 PHE 0.025 0.001 PHE f 713 TYR 0.018 0.001 TYR U 682 ARG 0.006 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 441 time to evaluate : 12.080 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: A 164 MET cc_start: -0.4548 (ttt) cc_final: -0.4858 (ttt) REVERT: A 332 MET cc_start: 0.8634 (mmm) cc_final: 0.8276 (mmm) REVERT: D 352 MET cc_start: 0.8417 (mmp) cc_final: 0.8150 (mmp) REVERT: E 232 MET cc_start: 0.8776 (mpp) cc_final: 0.8566 (mpp) REVERT: E 258 MET cc_start: 0.8736 (ttm) cc_final: 0.8316 (tmm) REVERT: E 264 MET cc_start: 0.9008 (mmm) cc_final: 0.8796 (mtp) REVERT: E 277 MET cc_start: 0.8085 (mmm) cc_final: 0.7442 (mmm) REVERT: F 175 MET cc_start: 0.4968 (mmt) cc_final: 0.4550 (tpp) REVERT: F 310 MET cc_start: 0.4965 (mmt) cc_final: 0.3221 (mmm) REVERT: F 356 MET cc_start: 0.7481 (mmm) cc_final: 0.6926 (tpp) REVERT: F 373 MET cc_start: 0.7561 (ptt) cc_final: 0.6087 (tpp) REVERT: F 405 MET cc_start: 0.9350 (tpt) cc_final: 0.9121 (tpp) REVERT: L 26 MET cc_start: 0.7898 (mmt) cc_final: 0.7603 (tpt) REVERT: U 188 MET cc_start: 0.8561 (ppp) cc_final: 0.8304 (ppp) REVERT: U 588 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8150 (tmm) REVERT: Y 152 MET cc_start: 0.8330 (mmm) cc_final: 0.7933 (tpp) REVERT: a 280 MET cc_start: 0.8958 (mpp) cc_final: 0.8737 (mpp) REVERT: c 41 MET cc_start: 0.9108 (mmt) cc_final: 0.8804 (mmt) REVERT: c 54 MET cc_start: 0.8428 (tmm) cc_final: 0.8155 (tmm) REVERT: d 75 MET cc_start: 0.8830 (mmm) cc_final: 0.8628 (mmm) REVERT: d 205 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8255 (pttp) REVERT: f 271 MET cc_start: 0.8060 (tmm) cc_final: 0.7827 (tmm) REVERT: f 297 MET cc_start: 0.2032 (tpt) cc_final: 0.1397 (tpt) REVERT: f 485 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7945 (mm) REVERT: g 138 MET cc_start: 0.8405 (tpp) cc_final: 0.8181 (ttm) REVERT: n 95 MET cc_start: 0.6545 (tpt) cc_final: 0.6275 (mmm) REVERT: n 120 MET cc_start: 0.8390 (tpp) cc_final: 0.8187 (ttt) REVERT: t 214 MET cc_start: 0.7708 (ppp) cc_final: 0.7414 (ppp) REVERT: x 71 MET cc_start: 0.7522 (pmm) cc_final: 0.7065 (pmm) REVERT: x 255 MET cc_start: 0.3328 (mpp) cc_final: 0.2570 (mpp) REVERT: x 352 MET cc_start: 0.7231 (tpt) cc_final: 0.5998 (mmm) REVERT: W 177 MET cc_start: 0.6264 (tpt) cc_final: 0.5439 (mmt) REVERT: W 230 MET cc_start: 0.8320 (pmm) cc_final: 0.8029 (pmm) REVERT: V 139 MET cc_start: 0.7170 (pmm) cc_final: 0.5264 (ptt) outliers start: 80 outliers final: 36 residues processed: 499 average time/residue: 0.8667 time to fit residues: 783.3754 Evaluate side-chains 479 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 440 time to evaluate : 9.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain S residue 144 MET Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 843 GLU Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 168 MET Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain f residue 89 MET Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 474 SER Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain r residue 2 THR Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 290 ILE Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1119 optimal weight: 0.0770 chunk 763 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 1001 optimal weight: 7.9990 chunk 554 optimal weight: 8.9990 chunk 1147 optimal weight: 9.9990 chunk 929 optimal weight: 7.9990 chunk 1 optimal weight: 40.0000 chunk 686 optimal weight: 20.0000 chunk 1206 optimal weight: 1.9990 chunk 339 optimal weight: 9.9990 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 169 GLN s 108 ASN ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 112660 Z= 0.195 Angle : 0.516 13.979 152193 Z= 0.266 Chirality : 0.039 0.157 17230 Planarity : 0.003 0.059 19623 Dihedral : 5.321 116.144 15516 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 0.75 % Allowed : 11.82 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.82 (0.08), residues: 13974 helix: 2.26 (0.07), residues: 6534 sheet: 0.16 (0.11), residues: 2137 loop : -1.57 (0.09), residues: 5303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP m 215 HIS 0.008 0.001 HIS U 70 PHE 0.024 0.001 PHE f 713 TYR 0.015 0.001 TYR U 682 ARG 0.005 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 441 time to evaluate : 9.821 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: A 164 MET cc_start: -0.4846 (OUTLIER) cc_final: -0.5384 (ttt) REVERT: A 263 MET cc_start: 0.6526 (ppp) cc_final: 0.5836 (ppp) REVERT: A 332 MET cc_start: 0.8627 (mmm) cc_final: 0.8285 (mmm) REVERT: B 309 MET cc_start: 0.8708 (ttp) cc_final: 0.8436 (ptt) REVERT: E 258 MET cc_start: 0.8766 (ttm) cc_final: 0.8336 (tmm) REVERT: F 175 MET cc_start: 0.4983 (mmt) cc_final: 0.3929 (mmm) REVERT: F 310 MET cc_start: 0.4976 (mmt) cc_final: 0.3313 (mmm) REVERT: F 356 MET cc_start: 0.7545 (mmm) cc_final: 0.7124 (tpp) REVERT: F 373 MET cc_start: 0.7579 (ptt) cc_final: 0.6131 (tpp) REVERT: F 405 MET cc_start: 0.9353 (tpt) cc_final: 0.9117 (tpp) REVERT: L 26 MET cc_start: 0.7886 (mmt) cc_final: 0.7579 (tpt) REVERT: M 52 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8759 (pp) REVERT: U 588 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8155 (tmm) REVERT: c 41 MET cc_start: 0.9128 (mmt) cc_final: 0.8826 (mmt) REVERT: c 54 MET cc_start: 0.8430 (tmm) cc_final: 0.8139 (tmm) REVERT: c 75 MET cc_start: 0.9045 (mmm) cc_final: 0.8446 (tmm) REVERT: d 205 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8245 (pttp) REVERT: f 297 MET cc_start: 0.2060 (tpt) cc_final: 0.1458 (tpt) REVERT: f 340 MET cc_start: 0.7991 (ppp) cc_final: 0.7701 (ppp) REVERT: j 23 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: l 140 MET cc_start: 0.8882 (mmm) cc_final: 0.8590 (mmt) REVERT: n 95 MET cc_start: 0.6598 (tpt) cc_final: 0.6356 (mmm) REVERT: t 214 MET cc_start: 0.7707 (ppp) cc_final: 0.7402 (ppp) REVERT: x 71 MET cc_start: 0.7479 (pmm) cc_final: 0.7112 (pmm) REVERT: x 352 MET cc_start: 0.7144 (tpt) cc_final: 0.5925 (mmm) REVERT: W 177 MET cc_start: 0.6239 (tpt) cc_final: 0.5565 (mmt) REVERT: V 139 MET cc_start: 0.7172 (pmm) cc_final: 0.5281 (ptt) outliers start: 90 outliers final: 45 residues processed: 512 average time/residue: 0.8636 time to fit residues: 801.8965 Evaluate side-chains 490 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 440 time to evaluate : 9.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 584 TYR Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 843 GLU Chi-restraints excluded: chain Y residue 86 GLU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 168 MET Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain f residue 89 MET Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 474 SER Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain i residue 52 ILE Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 23 GLN Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain t residue 9 THR Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 104 MET Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 429 ASP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 452 optimal weight: 7.9990 chunk 1210 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 789 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 1345 optimal weight: 30.0000 chunk 1117 optimal weight: 20.0000 chunk 623 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 445 optimal weight: 9.9990 chunk 706 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: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 HIS O 193 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 219 ASN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 112660 Z= 0.224 Angle : 0.534 13.069 152193 Z= 0.274 Chirality : 0.040 0.166 17230 Planarity : 0.003 0.059 19623 Dihedral : 5.331 119.308 15516 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.52 % Favored : 93.44 % Rotamer: Outliers : 0.83 % Allowed : 12.80 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.84 (0.08), residues: 13974 helix: 2.28 (0.07), residues: 6539 sheet: 0.14 (0.11), residues: 2152 loop : -1.56 (0.09), residues: 5283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP m 215 HIS 0.008 0.001 HIS U 70 PHE 0.025 0.001 PHE f 713 TYR 0.016 0.001 TYR U 682 ARG 0.005 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 439 time to evaluate : 9.979 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: A 164 MET cc_start: -0.4418 (ttt) cc_final: -0.4948 (ttt) REVERT: A 263 MET cc_start: 0.6303 (ppp) cc_final: 0.5615 (ppp) REVERT: B 385 MET cc_start: 0.6823 (mmm) cc_final: 0.6371 (tpt) REVERT: E 232 MET cc_start: 0.8590 (mpp) cc_final: 0.8352 (mpp) REVERT: E 258 MET cc_start: 0.8748 (ttm) cc_final: 0.8331 (tmm) REVERT: F 175 MET cc_start: 0.4962 (mmt) cc_final: 0.4166 (mmt) REVERT: F 310 MET cc_start: 0.5205 (mmt) cc_final: 0.3659 (mmm) REVERT: F 356 MET cc_start: 0.7658 (mmm) cc_final: 0.7211 (tpp) REVERT: F 373 MET cc_start: 0.7596 (ptt) cc_final: 0.6217 (tpp) REVERT: F 405 MET cc_start: 0.9346 (tpt) cc_final: 0.9110 (tpp) REVERT: L 26 MET cc_start: 0.7840 (mmt) cc_final: 0.7488 (tpt) REVERT: M 52 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8767 (pp) REVERT: U 588 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8183 (tmm) REVERT: U 681 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8474 (p0) REVERT: Z 81 MET cc_start: 0.8655 (tpp) cc_final: 0.8389 (tpp) REVERT: c 41 MET cc_start: 0.9133 (mmt) cc_final: 0.8823 (mmt) REVERT: c 54 MET cc_start: 0.8457 (tmm) cc_final: 0.8122 (tmm) REVERT: d 205 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8196 (pttm) REVERT: f 297 MET cc_start: 0.2222 (tpt) cc_final: 0.1622 (tpt) REVERT: f 340 MET cc_start: 0.8028 (ppp) cc_final: 0.7717 (ppp) REVERT: j 23 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: l 140 MET cc_start: 0.8913 (mmm) cc_final: 0.8641 (mmt) REVERT: n 95 MET cc_start: 0.6646 (tpt) cc_final: 0.6414 (mmm) REVERT: x 71 MET cc_start: 0.7510 (pmm) cc_final: 0.7198 (pmm) REVERT: x 352 MET cc_start: 0.7228 (tpt) cc_final: 0.6076 (mmm) REVERT: W 177 MET cc_start: 0.6279 (tpt) cc_final: 0.5653 (mmt) REVERT: V 139 MET cc_start: 0.7232 (pmm) cc_final: 0.5369 (ptt) outliers start: 99 outliers final: 60 residues processed: 518 average time/residue: 0.8672 time to fit residues: 813.8855 Evaluate side-chains 504 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 439 time to evaluate : 9.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain R residue 190 ASP Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 584 TYR Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 681 ASN Chi-restraints excluded: chain U residue 843 GLU Chi-restraints excluded: chain Y residue 86 GLU Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Y residue 327 VAL Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 168 MET Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain f residue 89 MET Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 288 VAL Chi-restraints excluded: chain f residue 474 SER Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 23 GLN Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain k residue 133 MET Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain x residue 485 VAL Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 429 ASP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1297 optimal weight: 50.0000 chunk 151 optimal weight: 9.9990 chunk 766 optimal weight: 3.9990 chunk 982 optimal weight: 30.0000 chunk 761 optimal weight: 10.0000 chunk 1132 optimal weight: 10.0000 chunk 751 optimal weight: 30.0000 chunk 1340 optimal weight: 6.9990 chunk 839 optimal weight: 30.0000 chunk 817 optimal weight: 8.9990 chunk 618 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 752 HIS ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 GLN ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 112660 Z= 0.269 Angle : 0.564 12.325 152193 Z= 0.290 Chirality : 0.040 0.205 17230 Planarity : 0.004 0.059 19623 Dihedral : 5.428 123.644 15516 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.67 % Favored : 93.29 % Rotamer: Outliers : 0.99 % Allowed : 13.50 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.80 (0.08), residues: 13974 helix: 2.23 (0.07), residues: 6549 sheet: 0.10 (0.11), residues: 2161 loop : -1.57 (0.09), residues: 5264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP m 215 HIS 0.008 0.001 HIS U 70 PHE 0.028 0.001 PHE f 713 TYR 0.018 0.001 TYR I 121 ARG 0.005 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 438 time to evaluate : 13.076 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: A 164 MET cc_start: -0.4196 (OUTLIER) cc_final: -0.4640 (ttt) REVERT: A 263 MET cc_start: 0.6474 (ppp) cc_final: 0.5728 (ppp) REVERT: B 385 MET cc_start: 0.6894 (mmm) cc_final: 0.6622 (tpt) REVERT: D 352 MET cc_start: 0.8359 (mmp) cc_final: 0.8049 (mmp) REVERT: E 258 MET cc_start: 0.8769 (ttm) cc_final: 0.8377 (tmm) REVERT: F 175 MET cc_start: 0.4953 (mmt) cc_final: 0.4176 (mmt) REVERT: F 310 MET cc_start: 0.5299 (mmt) cc_final: 0.3706 (mmm) REVERT: F 356 MET cc_start: 0.7710 (mmm) cc_final: 0.7300 (tpp) REVERT: F 373 MET cc_start: 0.7505 (ptt) cc_final: 0.6233 (tpp) REVERT: F 405 MET cc_start: 0.9345 (tpt) cc_final: 0.9116 (tpp) REVERT: L 26 MET cc_start: 0.7901 (mmt) cc_final: 0.7516 (tpt) REVERT: M 52 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8840 (pp) REVERT: U 588 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8204 (tmm) REVERT: U 681 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8286 (p0) REVERT: Z 81 MET cc_start: 0.8681 (tpp) cc_final: 0.8431 (tpp) REVERT: c 41 MET cc_start: 0.9127 (mmt) cc_final: 0.8794 (mmt) REVERT: c 54 MET cc_start: 0.8475 (tmm) cc_final: 0.8131 (tmm) REVERT: d 75 MET cc_start: 0.8649 (mmp) cc_final: 0.8396 (mmm) REVERT: d 205 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8189 (pttm) REVERT: f 158 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: f 297 MET cc_start: 0.2286 (tpt) cc_final: 0.1677 (tpt) REVERT: f 340 MET cc_start: 0.8072 (ppp) cc_final: 0.7773 (ppp) REVERT: f 543 MET cc_start: 0.8152 (ppp) cc_final: 0.7842 (ppp) REVERT: j 23 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: l 140 MET cc_start: 0.8917 (mmm) cc_final: 0.8659 (mmt) REVERT: n 95 MET cc_start: 0.6814 (tpt) cc_final: 0.6349 (tpt) REVERT: x 71 MET cc_start: 0.7493 (pmm) cc_final: 0.7262 (pmm) REVERT: x 255 MET cc_start: 0.3214 (mpp) cc_final: 0.2270 (mpp) REVERT: x 352 MET cc_start: 0.7221 (tpt) cc_final: 0.6107 (mmm) REVERT: W 177 MET cc_start: 0.6327 (tpt) cc_final: 0.5558 (mmt) REVERT: V 100 MET cc_start: 0.8758 (tmm) cc_final: 0.8437 (ppp) REVERT: V 139 MET cc_start: 0.7337 (pmm) cc_final: 0.5468 (ptt) outliers start: 118 outliers final: 70 residues processed: 533 average time/residue: 0.8553 time to fit residues: 830.1106 Evaluate side-chains 515 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 438 time to evaluate : 9.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 190 ASP Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 584 TYR Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 681 ASN Chi-restraints excluded: chain U residue 843 GLU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain Y residue 86 GLU Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Y residue 327 VAL Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 168 MET Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain d residue 235 THR Chi-restraints excluded: chain f residue 89 MET Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 288 VAL Chi-restraints excluded: chain f residue 474 SER Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 23 GLN Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 9 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 190 ASP Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain x residue 485 VAL Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 429 ASP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 829 optimal weight: 5.9990 chunk 535 optimal weight: 20.0000 chunk 800 optimal weight: 5.9990 chunk 403 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 852 optimal weight: 5.9990 chunk 913 optimal weight: 5.9990 chunk 662 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 1053 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 157 ASN ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 151 ASN t 147 GLN ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 112660 Z= 0.176 Angle : 0.531 13.643 152193 Z= 0.271 Chirality : 0.040 0.205 17230 Planarity : 0.003 0.058 19623 Dihedral : 5.324 123.866 15516 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.46 % Favored : 93.51 % Rotamer: Outliers : 0.83 % Allowed : 13.95 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.90 (0.08), residues: 13974 helix: 2.32 (0.07), residues: 6534 sheet: 0.19 (0.11), residues: 2133 loop : -1.53 (0.09), residues: 5307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP m 215 HIS 0.007 0.001 HIS U 70 PHE 0.022 0.001 PHE f 713 TYR 0.015 0.001 TYR I 121 ARG 0.006 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 440 time to evaluate : 10.100 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: A 164 MET cc_start: -0.4281 (OUTLIER) cc_final: -0.4851 (ttt) REVERT: A 263 MET cc_start: 0.6602 (ppp) cc_final: 0.5900 (ppp) REVERT: B 385 MET cc_start: 0.6846 (mmm) cc_final: 0.6631 (tpt) REVERT: E 258 MET cc_start: 0.8774 (ttm) cc_final: 0.8366 (tmm) REVERT: F 175 MET cc_start: 0.4835 (mmt) cc_final: 0.4096 (mmt) REVERT: F 310 MET cc_start: 0.5294 (mmt) cc_final: 0.3823 (mmm) REVERT: F 356 MET cc_start: 0.7733 (mmm) cc_final: 0.7284 (tpp) REVERT: F 373 MET cc_start: 0.7448 (ptt) cc_final: 0.6275 (tpp) REVERT: F 405 MET cc_start: 0.9353 (tpt) cc_final: 0.9126 (tpp) REVERT: L 26 MET cc_start: 0.7823 (mmt) cc_final: 0.7412 (tpt) REVERT: M 52 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8771 (pp) REVERT: U 588 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8196 (tmm) REVERT: U 681 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8431 (p0) REVERT: X 415 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8016 (t80) REVERT: c 54 MET cc_start: 0.8408 (tmm) cc_final: 0.8126 (tmm) REVERT: d 75 MET cc_start: 0.8656 (mmp) cc_final: 0.8430 (mmm) REVERT: d 205 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8108 (pttm) REVERT: f 158 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: f 196 MET cc_start: 0.7865 (ppp) cc_final: 0.7527 (ppp) REVERT: f 297 MET cc_start: 0.2233 (tpt) cc_final: 0.1707 (tpt) REVERT: f 340 MET cc_start: 0.8035 (ppp) cc_final: 0.7710 (ppp) REVERT: j 23 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: j 211 MET cc_start: 0.7983 (ttt) cc_final: 0.7559 (ttt) REVERT: l 140 MET cc_start: 0.8892 (mmm) cc_final: 0.8639 (mmt) REVERT: x 71 MET cc_start: 0.7473 (pmm) cc_final: 0.7262 (pmm) REVERT: x 352 MET cc_start: 0.7288 (tpt) cc_final: 0.6146 (mmm) REVERT: W 177 MET cc_start: 0.6296 (tpt) cc_final: 0.5531 (mmt) REVERT: V 139 MET cc_start: 0.7365 (pmm) cc_final: 0.5499 (ptt) outliers start: 99 outliers final: 68 residues processed: 519 average time/residue: 0.9072 time to fit residues: 852.8034 Evaluate side-chains 515 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 439 time to evaluate : 10.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 190 ASP Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 584 TYR Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 681 ASN Chi-restraints excluded: chain U residue 843 GLU Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 86 GLU Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Y residue 327 VAL Chi-restraints excluded: chain Z residue 96 HIS Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain d residue 235 THR Chi-restraints excluded: chain f residue 89 MET Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 288 VAL Chi-restraints excluded: chain f residue 303 VAL Chi-restraints excluded: chain f residue 474 SER Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain f residue 630 ASP Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain j residue 23 GLN Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 190 ASP Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain x residue 485 VAL Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 429 ASP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1219 optimal weight: 2.9990 chunk 1284 optimal weight: 10.0000 chunk 1171 optimal weight: 30.0000 chunk 1249 optimal weight: 9.9990 chunk 751 optimal weight: 9.9990 chunk 544 optimal weight: 40.0000 chunk 981 optimal weight: 2.9990 chunk 383 optimal weight: 0.5980 chunk 1128 optimal weight: 0.0270 chunk 1181 optimal weight: 30.0000 chunk 1244 optimal weight: 10.0000 overall best weight: 3.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 GLN D 414 HIS F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 HIS ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 214 ASN ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 112660 Z= 0.152 Angle : 0.525 14.081 152193 Z= 0.266 Chirality : 0.039 0.218 17230 Planarity : 0.003 0.058 19623 Dihedral : 5.223 124.015 15516 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 0.75 % Allowed : 14.11 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.96 (0.08), residues: 13974 helix: 2.37 (0.07), residues: 6539 sheet: 0.23 (0.11), residues: 2130 loop : -1.49 (0.09), residues: 5305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP m 215 HIS 0.008 0.001 HIS U 475 PHE 0.020 0.001 PHE f 713 TYR 0.014 0.001 TYR U 682 ARG 0.005 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 441 time to evaluate : 10.061 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: A 164 MET cc_start: -0.4440 (OUTLIER) cc_final: -0.5084 (ttt) REVERT: A 263 MET cc_start: 0.6668 (ppp) cc_final: 0.5931 (ppp) REVERT: D 352 MET cc_start: 0.8321 (mmp) cc_final: 0.8064 (mmp) REVERT: E 258 MET cc_start: 0.8767 (ttm) cc_final: 0.8359 (tmm) REVERT: E 352 MET cc_start: 0.8145 (mmm) cc_final: 0.7881 (mmm) REVERT: F 69 MET cc_start: 0.7591 (ppp) cc_final: 0.7305 (tmm) REVERT: F 175 MET cc_start: 0.4857 (mmt) cc_final: 0.4114 (mmt) REVERT: F 310 MET cc_start: 0.5314 (mmt) cc_final: 0.3895 (mmm) REVERT: F 356 MET cc_start: 0.7783 (mmm) cc_final: 0.7307 (tpp) REVERT: F 373 MET cc_start: 0.7255 (ptt) cc_final: 0.6219 (tpp) REVERT: F 405 MET cc_start: 0.9357 (tpt) cc_final: 0.9130 (tpp) REVERT: L 26 MET cc_start: 0.7767 (mmt) cc_final: 0.7344 (tpt) REVERT: M 52 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8689 (pp) REVERT: U 588 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8219 (tmm) REVERT: U 681 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8331 (p0) REVERT: a 141 MET cc_start: 0.8749 (pmm) cc_final: 0.8549 (pmm) REVERT: c 41 MET cc_start: 0.9094 (mmt) cc_final: 0.8719 (mmt) REVERT: c 51 MET cc_start: 0.8503 (mmm) cc_final: 0.7589 (tmm) REVERT: c 54 MET cc_start: 0.8404 (tmm) cc_final: 0.8127 (tmm) REVERT: c 303 MET cc_start: 0.8504 (ptp) cc_final: 0.8302 (mtm) REVERT: d 75 MET cc_start: 0.8603 (mmp) cc_final: 0.8388 (mmm) REVERT: d 205 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8104 (pttm) REVERT: f 158 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: f 196 MET cc_start: 0.7853 (ppp) cc_final: 0.7532 (ppp) REVERT: f 297 MET cc_start: 0.2158 (tpt) cc_final: 0.1678 (tpt) REVERT: f 340 MET cc_start: 0.8008 (ppp) cc_final: 0.7729 (ppp) REVERT: j 23 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: j 211 MET cc_start: 0.7950 (ttt) cc_final: 0.7532 (ttt) REVERT: x 71 MET cc_start: 0.7471 (pmm) cc_final: 0.7268 (pmm) REVERT: x 352 MET cc_start: 0.7251 (tpt) cc_final: 0.6097 (mmm) REVERT: W 60 MET cc_start: 0.6398 (tmm) cc_final: 0.5816 (tpp) REVERT: W 177 MET cc_start: 0.6256 (tpt) cc_final: 0.5072 (mtt) REVERT: V 100 MET cc_start: 0.8485 (tmm) cc_final: 0.8264 (ppp) REVERT: V 139 MET cc_start: 0.7421 (pmm) cc_final: 0.5537 (ptt) outliers start: 90 outliers final: 70 residues processed: 512 average time/residue: 0.9040 time to fit residues: 837.5812 Evaluate side-chains 516 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 439 time to evaluate : 10.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 190 ASP Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 681 ASN Chi-restraints excluded: chain U residue 843 GLU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 86 GLU Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Y residue 327 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 96 HIS Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain d residue 205 LYS Chi-restraints excluded: chain d residue 235 THR Chi-restraints excluded: chain f residue 89 MET Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 288 VAL Chi-restraints excluded: chain f residue 303 VAL Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain f residue 630 ASP Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain j residue 23 GLN Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 190 ASP Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain x residue 485 VAL Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 429 ASP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 820 optimal weight: 50.0000 chunk 1321 optimal weight: 7.9990 chunk 806 optimal weight: 7.9990 chunk 626 optimal weight: 20.0000 chunk 918 optimal weight: 30.0000 chunk 1385 optimal weight: 0.1980 chunk 1275 optimal weight: 20.0000 chunk 1103 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 852 optimal weight: 9.9990 chunk 676 optimal weight: 10.0000 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 214 ASN ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 112660 Z= 0.226 Angle : 0.558 14.966 152193 Z= 0.282 Chirality : 0.040 0.188 17230 Planarity : 0.003 0.059 19623 Dihedral : 5.261 125.169 15516 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.33 % Rotamer: Outliers : 0.75 % Allowed : 14.27 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.93 (0.08), residues: 13974 helix: 2.34 (0.07), residues: 6556 sheet: 0.17 (0.11), residues: 2149 loop : -1.50 (0.09), residues: 5269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP m 215 HIS 0.008 0.001 HIS U 475 PHE 0.023 0.001 PHE f 713 TYR 0.015 0.001 TYR U 682 ARG 0.006 0.000 ARG Y 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 440 time to evaluate : 9.724 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: A 164 MET cc_start: -0.4449 (OUTLIER) cc_final: -0.4964 (ttt) REVERT: A 263 MET cc_start: 0.6736 (ppp) cc_final: 0.6004 (ppp) REVERT: D 352 MET cc_start: 0.8372 (mmp) cc_final: 0.8156 (mmp) REVERT: E 258 MET cc_start: 0.8769 (ttm) cc_final: 0.8364 (tmm) REVERT: F 69 MET cc_start: 0.7594 (ppp) cc_final: 0.7281 (tmm) REVERT: F 175 MET cc_start: 0.4861 (mmt) cc_final: 0.4118 (mmt) REVERT: F 310 MET cc_start: 0.5339 (mmt) cc_final: 0.3922 (mmm) REVERT: F 373 MET cc_start: 0.7285 (ptt) cc_final: 0.6263 (tpp) REVERT: F 405 MET cc_start: 0.9356 (tpt) cc_final: 0.9128 (tpp) REVERT: L 26 MET cc_start: 0.7824 (mmt) cc_final: 0.7398 (tpt) REVERT: M 52 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8719 (pp) REVERT: U 185 MET cc_start: 0.8527 (mmp) cc_final: 0.8230 (mmp) REVERT: U 588 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8229 (tmm) REVERT: U 681 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8402 (p0) REVERT: c 41 MET cc_start: 0.9107 (mmt) cc_final: 0.8706 (mmt) REVERT: c 54 MET cc_start: 0.8432 (tmm) cc_final: 0.8140 (tmm) REVERT: d 75 MET cc_start: 0.8626 (mmp) cc_final: 0.8420 (mmm) REVERT: f 158 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: f 196 MET cc_start: 0.7868 (ppp) cc_final: 0.7546 (ppp) REVERT: f 297 MET cc_start: 0.2260 (tpt) cc_final: 0.1724 (tpt) REVERT: f 340 MET cc_start: 0.8071 (ppp) cc_final: 0.7830 (ppp) REVERT: f 524 MET cc_start: 0.8337 (ppp) cc_final: 0.7976 (ppp) REVERT: j 23 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: n 95 MET cc_start: 0.7255 (mmm) cc_final: 0.6877 (mmm) REVERT: x 255 MET cc_start: 0.3266 (mpp) cc_final: 0.2301 (mpp) REVERT: x 352 MET cc_start: 0.7205 (tpt) cc_final: 0.6072 (mmm) REVERT: W 60 MET cc_start: 0.6401 (tmm) cc_final: 0.5836 (tpp) REVERT: W 177 MET cc_start: 0.6299 (tpt) cc_final: 0.5125 (mtt) REVERT: V 100 MET cc_start: 0.8462 (tmm) cc_final: 0.8251 (ppp) REVERT: V 139 MET cc_start: 0.7480 (pmm) cc_final: 0.5647 (ptt) outliers start: 90 outliers final: 74 residues processed: 510 average time/residue: 0.8842 time to fit residues: 816.9796 Evaluate side-chains 518 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 438 time to evaluate : 9.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain M residue 241 GLU Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 190 ASP Chi-restraints excluded: chain T residue 109 THR Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 681 ASN Chi-restraints excluded: chain U residue 843 GLU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 86 GLU Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Y residue 327 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 96 HIS Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain d residue 235 THR Chi-restraints excluded: chain f residue 89 MET Chi-restraints excluded: chain f residue 131 MET Chi-restraints excluded: chain f residue 158 TYR Chi-restraints excluded: chain f residue 288 VAL Chi-restraints excluded: chain f residue 303 VAL Chi-restraints excluded: chain f residue 485 LEU Chi-restraints excluded: chain f residue 630 ASP Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 23 GLN Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain l residue 105 VAL Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 190 ASP Chi-restraints excluded: chain s residue 80 ASN Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain x residue 485 VAL Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 66 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 429 ASP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 876 optimal weight: 30.0000 chunk 1175 optimal weight: 3.9990 chunk 338 optimal weight: 9.9990 chunk 1017 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 1105 optimal weight: 20.0000 chunk 462 optimal weight: 9.9990 chunk 1134 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 203 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 GLN F 315 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 698 GLN ** X 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.055520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.048598 restraints weight = 1359353.733| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 5.06 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 112660 Z= 0.228 Angle : 0.564 15.016 152193 Z= 0.285 Chirality : 0.040 0.192 17230 Planarity : 0.003 0.059 19623 Dihedral : 5.277 125.678 15512 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 0.81 % Allowed : 14.36 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.90 (0.08), residues: 13974 helix: 2.31 (0.07), residues: 6562 sheet: 0.19 (0.11), residues: 2138 loop : -1.52 (0.09), residues: 5274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP m 215 HIS 0.008 0.001 HIS U 475 PHE 0.025 0.001 PHE f 713 TYR 0.016 0.001 TYR U 682 ARG 0.005 0.000 ARG Y 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18880.76 seconds wall clock time: 334 minutes 59.26 seconds (20099.26 seconds total)