Starting phenix.real_space_refine on Mon Mar 11 03:05:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3m_32284/03_2024/7w3m_32284_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3m_32284/03_2024/7w3m_32284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3m_32284/03_2024/7w3m_32284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3m_32284/03_2024/7w3m_32284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3m_32284/03_2024/7w3m_32284_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3m_32284/03_2024/7w3m_32284_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 11 5.49 5 S 630 5.16 5 C 68932 2.51 5 N 18717 2.21 5 O 20729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "c PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 109020 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3091 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 371} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 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: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2979 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 362} 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: {'PTRANS': 17, '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: 6459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6459 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 31, 'TRANS': 795} Chain breaks: 2 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: "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: "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: {'PCIS': 1, 'PTRANS': 33, '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: "x" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3144 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 376} 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: "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: "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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" 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: 40.48, per 1000 atoms: 0.37 Number of scatterers: 109020 At special positions: 0 Unit cell: (330.855, 215.775, 208.24, 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 630 16.00 P 11 15.00 O 20729 8.00 N 18717 7.00 C 68932 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=2.03 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: 31.19 Conformation dependent library (CDL) restraints added in 14.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25944 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: 497 helices and 86 sheets defined 54.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 49.83 Creating SS restraints... Processing helix chain 'A' and resid 41 through 64 removed outlier: 3.740A pdb=" N ILE A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 85 through 92 removed outlier: 4.988A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 159 through 165 removed outlier: 4.844A pdb=" N MET A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 165' Processing helix chain 'A' and resid 179 through 198 removed outlier: 4.615A pdb=" N GLN A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 222 through 231 removed outlier: 5.169A pdb=" N ALA A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.643A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.597A pdb=" N ARG A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 309 removed outlier: 4.133A pdb=" N ASP A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 347 through 363 removed outlier: 5.586A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.465A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 4.583A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.070A pdb=" N LYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 85 removed outlier: 5.151A pdb=" N GLU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 removed outlier: 4.645A pdb=" N GLN B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 175 removed outlier: 4.277A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 removed outlier: 3.770A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix removed outlier: 3.582A pdb=" N HIS B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 232 through 242 removed outlier: 4.576A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 7.222A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.564A pdb=" N HIS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 4.785A pdb=" N GLU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.093A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.542A pdb=" N MET B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.414A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.981A pdb=" N ARG B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.706A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 16 removed outlier: 4.044A pdb=" N LYS C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 16' Processing helix chain 'C' and resid 19 through 68 removed outlier: 5.181A pdb=" N TYR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 140 removed outlier: 4.328A pdb=" N MET C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N MET C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 140' Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.285A 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 removed outlier: 4.550A pdb=" N ALA C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 242 removed outlier: 4.215A pdb=" N GLY C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 282 removed outlier: 3.640A pdb=" N GLN C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 4.443A pdb=" N LEU C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 4.382A pdb=" N LYS C 335 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET C 336 " --> pdb=" O HIS C 332 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 5.065A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 374 removed outlier: 6.341A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.611A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 6.857A pdb=" N LYS C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 85 removed outlier: 3.939A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.401A pdb=" N LYS D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 4.456A 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 Processing helix chain 'D' and resid 211 through 223 removed outlier: 5.590A pdb=" N LEU D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.938A pdb=" N PHE D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 236' Processing helix chain 'D' and resid 241 through 257 removed outlier: 4.767A pdb=" N ARG D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 296 Processing helix chain 'D' and resid 318 through 323 removed outlier: 4.005A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 323' Processing helix chain 'D' and resid 338 through 353 removed outlier: 6.604A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 366 removed outlier: 3.526A pdb=" N VAL D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 360 through 366' Processing helix chain 'D' and resid 371 through 390 removed outlier: 3.730A pdb=" N GLU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 408 removed outlier: 5.438A pdb=" N GLU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 52 removed outlier: 4.055A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.996A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.810A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 4.023A 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 Processing helix chain 'E' and resid 180 through 192 removed outlier: 5.300A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 6.738A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 5.723A 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 207 through 226 removed outlier: 4.097A pdb=" N SER E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.287A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 removed outlier: 4.209A pdb=" N ARG E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 292 Proline residue: E 292 - end of helix Processing helix chain 'E' and resid 305 through 318 removed outlier: 6.499A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.917A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 382 removed outlier: 4.724A pdb=" N SER E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 33 removed outlier: 3.638A pdb=" N ILE F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 84 removed outlier: 4.207A pdb=" N ARG F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 4.971A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.915A pdb=" N LYS F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.987A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.159A 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: 4.385A 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 Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.332A pdb=" N ARG F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR F 244 " --> pdb=" O CYS F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 258 removed outlier: 4.116A pdb=" N LEU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 258' Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 288 through 293 removed outlier: 3.872A pdb=" N GLY F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 288 through 293' Processing helix chain 'F' and resid 303 through 319 removed outlier: 4.992A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 5.189A pdb=" N LEU F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 358 through 372 removed outlier: 3.803A pdb=" N ARG F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.762A pdb=" N GLN F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.933A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.125A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.086A 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: 3.636A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.759A pdb=" N LYS G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.792A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.480A pdb=" N ILE G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 5.669A 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: 3.708A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 12 removed outlier: 6.142A pdb=" N ASP G 10 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG G 11 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 4.472A 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 3 through 8 removed outlier: 3.725A pdb=" N SER H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE H 8 " --> pdb=" O ARG H 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 8' Processing helix chain 'H' and resid 19 through 33 removed outlier: 4.708A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 63 removed outlier: 4.750A pdb=" N VAL H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 5.548A 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: 3.616A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 removed outlier: 4.100A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 removed outlier: 3.739A pdb=" N GLY H 170 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.297A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 removed outlier: 3.675A pdb=" N ALA H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.785A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.610A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.455A 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: 3.717A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 removed outlier: 3.973A pdb=" N TYR h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN h 123 " --> pdb=" O GLN h 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER h 124 " --> pdb=" O GLU h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 removed outlier: 4.097A pdb=" N GLY h 170 " --> pdb=" O ASN h 166 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.874A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 234 removed outlier: 3.992A pdb=" N ILE h 233 " --> pdb=" O TYR h 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 32 removed outlier: 5.407A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.518A pdb=" N LEU I 110 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.850A pdb=" N GLN I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 202 removed outlier: 5.474A pdb=" N ASP I 202 " --> pdb=" O ASN I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 4.014A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.251A 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: 4.035A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.505A pdb=" N GLU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.545A pdb=" N ILE J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.670A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 removed outlier: 4.067A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 177 through 183' Processing helix chain 'J' and resid 184 through 199 removed outlier: 4.001A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 removed outlier: 3.551A pdb=" N ILE J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 30 removed outlier: 3.636A pdb=" N LYS j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.181A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.525A 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 99 Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.593A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 3.853A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN j 175 " --> pdb=" O PHE j 171 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 183 removed outlier: 4.727A pdb=" N THR j 183 " --> pdb=" O GLU j 179 " (cutoff:3.500A) Processing helix chain 'j' and resid 184 through 199 removed outlier: 4.160A pdb=" N GLU j 197 " --> pdb=" O LYS j 193 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL j 199 " --> pdb=" O LEU j 195 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 21 through 35 removed outlier: 3.590A pdb=" N GLU K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SER K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 103 removed outlier: 4.102A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 122 removed outlier: 4.127A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.909A pdb=" N GLN K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.965A 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 211 through 216 removed outlier: 4.453A pdb=" N ILE K 215 " --> pdb=" O ASN K 211 " (cutoff:3.500A) removed outlier: 6.970A 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: 4.733A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 8 removed outlier: 3.630A pdb=" N ASP L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 3 through 8' Processing helix chain 'L' and resid 19 through 33 removed outlier: 3.800A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER L 33 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 122 removed outlier: 3.997A 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 164 through 180 removed outlier: 4.483A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.964A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 225 through 237 removed outlier: 3.663A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 4.038A pdb=" N GLU L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.974A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.651A 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: 4.058A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.345A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 185 removed outlier: 4.096A pdb=" N MET M 184 " --> pdb=" O GLN M 180 " (cutoff:3.500A) removed outlier: 6.450A 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 202 removed outlier: 5.974A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 removed outlier: 3.683A 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: 3.537A pdb=" N ALA N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.530A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.793A 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: 3.560A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.951A 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: 3.544A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG o 89 " --> pdb=" O GLN o 85 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.683A 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: 3.535A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.072A 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 removed outlier: 3.602A pdb=" N LEU P 73 " --> pdb=" O PHE P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.284A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 153 removed outlier: 4.209A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 4.089A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 4.868A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.129A 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: 4.074A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 153 removed outlier: 3.954A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.354A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 72 removed outlier: 3.742A pdb=" N THR Q 53 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 93 removed outlier: 3.892A pdb=" N CYS Q 91 " --> pdb=" O ASN Q 87 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU Q 92 " --> pdb=" O LEU Q 88 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.824A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 170 removed outlier: 3.631A pdb=" N VAL Q 157 " --> pdb=" O ARG Q 153 " (cutoff:3.500A) Processing helix chain 'q' and resid 49 through 72 removed outlier: 3.813A pdb=" N THR q 53 " --> pdb=" O GLU q 49 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 93 removed outlier: 4.268A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.793A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 170 Processing helix chain 'R' and resid 48 through 71 Processing helix chain 'R' and resid 75 through 89 removed outlier: 4.225A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.822A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG R 141 " --> pdb=" O GLY R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 201 Processing helix chain 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 89 removed outlier: 3.973A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.993A pdb=" N GLY r 137 " --> pdb=" O VAL r 133 " (cutoff:3.500A) removed outlier: 3.968A 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: 3.521A pdb=" N GLY r 201 " --> pdb=" O GLU r 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 80 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.786A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.226A 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: 3.880A pdb=" N GLU S 184 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 4.106A 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: 3.812A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.193A 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: 3.913A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.632A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 158 removed outlier: 4.106A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.981A 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 210 through 215 removed outlier: 4.444A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 210 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 4.052A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.884A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 158 removed outlier: 4.267A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.203A 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 210 through 215 removed outlier: 4.257A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 210 through 215' Processing helix chain 'U' and resid 7 through 15 removed outlier: 3.832A pdb=" N GLU U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP U 15 " --> pdb=" O LEU U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 31 removed outlier: 4.046A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 52 removed outlier: 5.486A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER U 39 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 3.619A pdb=" N ALA U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.538A pdb=" N GLY U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 92 removed outlier: 3.719A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP U 92 " --> pdb=" O PHE U 88 " (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 removed outlier: 3.642A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 Processing helix chain 'U' and resid 159 through 169 Processing helix chain 'U' and resid 175 through 186 removed outlier: 3.909A pdb=" N TYR U 179 " --> pdb=" O GLY U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 208 removed outlier: 4.361A pdb=" N ASN U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE U 204 " --> pdb=" O VAL U 200 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN U 207 " --> pdb=" O LYS U 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU U 208 " --> pdb=" O ILE U 204 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 224 removed outlier: 3.993A pdb=" N ASP U 224 " --> pdb=" O LEU U 220 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 4.058A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER U 230 " --> pdb=" O PRO U 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 256 Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.530A pdb=" N LEU U 261 " --> pdb=" O SER U 257 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.100A 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: 4.506A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 3.758A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 365 through 378 Processing helix chain 'U' and resid 383 through 388 removed outlier: 5.174A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) Processing helix chain 'U' and resid 389 through 395 Processing helix chain 'U' and resid 399 through 413 removed outlier: 3.666A pdb=" N LYS U 413 " --> pdb=" O GLY U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 415 through 427 removed outlier: 6.143A pdb=" N ALA U 419 " --> pdb=" O HIS U 415 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU U 420 " --> pdb=" O GLU U 416 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN U 421 " --> pdb=" O LYS U 417 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU U 427 " --> pdb=" O MET U 423 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 451 removed outlier: 3.869A pdb=" N HIS U 450 " --> pdb=" O LEU U 446 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA U 451 " --> pdb=" O GLY U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 Processing helix chain 'U' and resid 470 through 486 Processing helix chain 'U' and resid 490 through 504 removed outlier: 4.208A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 508 through 521 removed outlier: 3.636A pdb=" N LEU U 521 " --> pdb=" O GLY U 517 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 4.409A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 556 removed outlier: 3.860A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU U 548 " --> pdb=" O ILE U 544 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 574 removed outlier: 5.976A pdb=" N LYS U 574 " --> pdb=" O LEU U 570 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 4.576A 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: 3.950A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 632 through 642 removed outlier: 3.753A pdb=" N VAL U 636 " --> pdb=" O GLN U 632 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 3.542A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS U 660 " --> pdb=" O LEU U 656 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 676 removed outlier: 6.348A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN U 670 " --> pdb=" O LYS U 666 " (cutoff:3.500A) Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.621A pdb=" N ARG U 684 " --> pdb=" O VAL U 680 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 removed outlier: 3.717A pdb=" N CYS U 703 " --> pdb=" O THR U 699 " (cutoff:3.500A) Proline residue: U 704 - end of helix No H-bonds generated for 'chain 'U' and resid 699 through 704' Processing helix chain 'U' and resid 705 through 720 removed outlier: 6.224A pdb=" N LYS U 720 " --> pdb=" O VAL U 716 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 739 removed outlier: 3.817A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA U 739 " --> pdb=" O GLY U 735 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 773 removed outlier: 3.642A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TRP U 770 " --> pdb=" O PHE U 766 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE U 771 " --> pdb=" O THR U 767 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP U 772 " --> pdb=" O GLN U 768 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE U 773 " --> pdb=" O PHE U 769 " (cutoff:3.500A) Processing helix chain 'U' and resid 774 through 784 removed outlier: 5.054A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 774 through 784' Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.713A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 90 through 105 removed outlier: 4.582A pdb=" N VAL V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) 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: 3.523A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 4.928A 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: 3.937A pdb=" N ALA V 184 " --> pdb=" O ARG V 180 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 204 through 222 removed outlier: 3.671A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.434A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.776A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER V 262 " --> pdb=" O TYR V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 Processing helix chain 'V' and resid 281 through 300 Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 344 through 350 removed outlier: 4.509A pdb=" N PHE V 348 " --> pdb=" O ASP V 344 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN V 350 " --> pdb=" O LEU V 346 " (cutoff:3.500A) 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: 3.626A 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 415 removed outlier: 4.361A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN V 401 " --> pdb=" O ARG V 397 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL V 402 " --> pdb=" O LEU V 398 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) removed outlier: 5.286A 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 removed outlier: 3.835A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU V 435 " --> pdb=" O PRO V 431 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 495 removed outlier: 5.091A pdb=" N THR V 469 " --> pdb=" O ASP V 465 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU V 471 " --> pdb=" O TYR V 467 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 4.034A pdb=" N ALA V 475 " --> pdb=" O GLU V 471 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET V 494 " --> pdb=" O SER V 490 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG V 495 " --> pdb=" O VAL V 491 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 38 Proline residue: W 29 - end of helix removed outlier: 3.692A pdb=" N GLY W 38 " --> pdb=" O LEU W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 58 Processing helix chain 'W' and resid 59 through 78 removed outlier: 3.951A pdb=" N THR W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 94 removed outlier: 4.648A pdb=" N LEU W 83 " --> pdb=" O GLU W 79 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG W 94 " --> pdb=" O LEU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 116 removed outlier: 3.665A pdb=" N GLU W 114 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE W 115 " --> pdb=" O TYR W 111 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR W 116 " --> pdb=" O VAL W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 133 removed outlier: 4.498A pdb=" N ARG W 123 " --> pdb=" O PRO W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 156 removed outlier: 4.690A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 175 removed outlier: 4.255A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU W 169 " --> pdb=" O ILE W 165 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 181 through 197 removed outlier: 3.510A pdb=" N PHE W 185 " --> pdb=" O GLU W 181 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 209 removed outlier: 3.550A pdb=" N THR W 202 " --> pdb=" O ASP W 198 " (cutoff:3.500A) Processing helix chain 'W' and resid 222 through 238 removed outlier: 4.485A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 257 removed outlier: 5.614A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N CYS W 244 " --> pdb=" O TYR W 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 6.064A 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 277 removed outlier: 6.205A pdb=" N TRP W 263 " --> pdb=" O GLU W 259 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN W 264 " --> pdb=" O SER W 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 292 removed outlier: 5.200A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 295 through 300 removed outlier: 4.561A 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 295 through 300' Processing helix chain 'W' and resid 301 through 307 Processing helix chain 'W' and resid 316 through 330 removed outlier: 4.291A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR W 324 " --> pdb=" O LEU W 320 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 4.236A pdb=" N GLU W 348 " --> pdb=" O THR W 344 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 removed outlier: 4.013A pdb=" N MET W 378 " --> pdb=" O THR W 374 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP W 383 " --> pdb=" O ALA W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 400 removed outlier: 3.562A pdb=" N ASN W 399 " --> pdb=" O ASN W 395 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 456 removed outlier: 3.655A pdb=" N LEU W 455 " --> pdb=" O MET W 451 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 61 removed outlier: 4.187A pdb=" N GLU X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 77 removed outlier: 4.356A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Proline residue: X 75 - end of helix Processing helix chain 'X' and resid 81 through 99 removed outlier: 3.598A pdb=" N ASP X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 Processing helix chain 'X' and resid 122 through 141 removed outlier: 3.555A pdb=" N LYS X 141 " --> pdb=" O TYR X 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 160 removed outlier: 4.771A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 181 removed outlier: 4.125A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 201 removed outlier: 4.571A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE X 200 " --> pdb=" O THR X 196 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 222 removed outlier: 5.384A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.411A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP X 240 " --> pdb=" O PHE X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 3.768A pdb=" N LEU X 261 " --> pdb=" O CYS X 257 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 273 removed outlier: 3.675A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER X 272 " --> pdb=" O GLN X 268 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY X 273 " --> pdb=" O ALA X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.580A pdb=" N GLU X 285 " --> pdb=" O GLY X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.831A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 340 removed outlier: 5.669A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.525A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 removed outlier: 4.913A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 421 removed outlier: 3.714A pdb=" N GLU X 402 " --> pdb=" O GLU X 398 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS X 417 " --> pdb=" O SER X 413 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 28 removed outlier: 5.218A pdb=" N ILE Y 19 " --> pdb=" O PRO Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 46 removed outlier: 6.011A pdb=" N ALA Y 36 " --> pdb=" O ARG Y 32 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL Y 37 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 60 removed outlier: 5.620A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Y 60 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 90 Processing helix chain 'Y' and resid 98 through 114 removed outlier: 3.594A pdb=" N ASP Y 102 " --> pdb=" O SER Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 131 removed outlier: 3.662A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 Processing helix chain 'Y' and resid 153 through 167 removed outlier: 3.992A pdb=" N GLU Y 162 " --> pdb=" O THR Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 191 removed outlier: 4.448A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE Y 191 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 203 removed outlier: 4.565A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU Y 202 " --> pdb=" O ALA Y 198 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP Y 203 " --> pdb=" O GLU Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 232 removed outlier: 4.000A pdb=" N MET Y 228 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA Y 230 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU Y 232 " --> pdb=" O MET Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 241 removed outlier: 4.140A pdb=" N LYS Y 239 " --> pdb=" O ASP Y 235 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 254 Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.642A pdb=" N CYS Y 266 " --> pdb=" O SER Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 285 removed outlier: 3.791A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 309 Processing helix chain 'Y' and resid 315 through 323 removed outlier: 3.751A pdb=" N MET Y 319 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 5.622A pdb=" N ILE Y 330 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY Y 341 " --> pdb=" O PHE Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 388 removed outlier: 6.594A pdb=" N TRP Y 364 " --> pdb=" O ASP Y 360 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN Y 365 " --> pdb=" O SER Y 361 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 27 removed outlier: 3.832A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL Z 20 " --> pdb=" O LEU Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 104 through 116 removed outlier: 4.214A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 177 removed outlier: 3.902A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 218 removed outlier: 4.316A pdb=" N ILE Z 191 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 237 removed outlier: 4.549A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE Z 234 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN Z 235 " --> pdb=" O GLN Z 231 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU Z 236 " --> pdb=" O ASP Z 232 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU Z 237 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 289 removed outlier: 3.698A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU Z 265 " --> pdb=" O TYR Z 261 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER Z 268 " --> pdb=" O SER Z 264 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 removed outlier: 3.752A pdb=" N GLN a 12 " --> pdb=" O LEU a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 32 removed outlier: 4.313A pdb=" N VAL a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS a 32 " --> pdb=" O LEU a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 4.739A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN a 46 " --> pdb=" O LEU a 42 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP a 47 " --> pdb=" O ASP a 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 removed outlier: 4.396A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 88 removed outlier: 3.894A pdb=" N THR a 88 " --> pdb=" O VAL a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 105 removed outlier: 4.060A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 124 removed outlier: 4.622A pdb=" N ILE a 112 " --> pdb=" O ASP a 108 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR a 116 " --> pdb=" O ILE a 112 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 143 removed outlier: 4.452A pdb=" N VAL a 130 " --> pdb=" O GLY a 126 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR a 131 " --> pdb=" O ASP a 127 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS a 132 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLU a 133 " --> pdb=" O GLN a 129 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 165 removed outlier: 6.312A pdb=" N HIS a 152 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 4.133A pdb=" N TYR a 173 " --> pdb=" O HIS a 169 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 5.200A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY a 207 " --> pdb=" O ALA a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 215 through 220 removed outlier: 3.910A pdb=" N HIS a 219 " --> pdb=" O GLU a 215 " (cutoff:3.500A) Proline residue: a 220 - end of helix No H-bonds generated for 'chain 'a' and resid 215 through 220' Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.277A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 4.508A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 285 removed outlier: 4.546A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.775A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 318 removed outlier: 3.605A pdb=" N VAL a 307 " --> pdb=" O THR a 303 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 372 Processing helix chain 'a' and resid 221 through 226 removed outlier: 4.258A pdb=" N ARG a 226 " --> pdb=" O VAL a 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 221 through 226' Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 67 through 78 removed outlier: 4.956A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 3.984A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 4.801A 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: 4.136A pdb=" N GLY b 162 " --> pdb=" O ASN b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 191 removed outlier: 4.291A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix removed outlier: 3.767A pdb=" N GLY b 191 " --> pdb=" O PRO b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 19 removed outlier: 3.784A pdb=" N MET b 16 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY b 19 " --> pdb=" O MET b 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 13 through 19' Processing helix chain 'c' and resid 34 through 49 removed outlier: 4.022A pdb=" N LEU c 38 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU c 39 " --> pdb=" O SER c 35 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY c 48 " --> pdb=" O HIS c 44 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 101 removed outlier: 3.576A pdb=" N LYS c 100 " --> pdb=" O LEU c 96 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 146 through 151 removed outlier: 3.750A pdb=" N SER c 150 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL c 151 " --> pdb=" O PRO c 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 146 through 151' Processing helix chain 'c' and resid 180 through 185 removed outlier: 5.032A pdb=" N LEU c 184 " --> pdb=" O ASN c 180 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN c 185 " --> pdb=" O LEU c 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 185' Processing helix chain 'c' and resid 188 through 195 removed outlier: 3.822A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 223 removed outlier: 6.624A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS c 223 " --> pdb=" O ASN c 219 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 removed outlier: 4.334A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 234 through 262 removed outlier: 4.653A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 274 removed outlier: 5.159A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) Processing helix chain 'c' and resid 283 through 310 removed outlier: 4.008A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE c 309 " --> pdb=" O ASP c 305 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 33 removed outlier: 4.570A pdb=" N GLY d 20 " --> pdb=" O LEU d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 Processing helix chain 'd' and resid 67 through 84 removed outlier: 4.251A pdb=" N ASP d 84 " --> pdb=" O CYS d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 110 removed outlier: 4.645A pdb=" N GLN d 97 " --> pdb=" O ALA d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 121 removed outlier: 3.515A pdb=" N LEU d 119 " --> pdb=" O PHE d 115 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 124 through 129 removed outlier: 3.802A pdb=" N GLN d 128 " --> pdb=" O ALA d 124 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR d 129 " --> pdb=" O LYS d 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 124 through 129' Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.993A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 183 removed outlier: 4.283A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU d 183 " --> pdb=" O ALA d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 198 removed outlier: 3.751A pdb=" N ALA d 194 " --> pdb=" O LEU d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 212 removed outlier: 3.915A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 240 through 255 removed outlier: 3.592A pdb=" N GLU d 254 " --> pdb=" O ALA d 250 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET d 255 " --> pdb=" O ARG d 251 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 16 removed outlier: 3.526A pdb=" N GLN f 15 " --> pdb=" O VAL f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 24 Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 27 through 49 removed outlier: 4.646A pdb=" N GLU f 48 " --> pdb=" O GLU f 44 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP f 49 " --> pdb=" O LEU f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 76 removed outlier: 3.863A pdb=" N LEU f 63 " --> pdb=" O LEU f 59 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS f 66 " --> pdb=" O ARG f 62 " (cutoff:3.500A) Proline residue: f 73 - end of helix Processing helix chain 'f' and resid 79 through 92 removed outlier: 3.881A pdb=" N ARG f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL f 92 " --> pdb=" O SER f 88 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 4.298A pdb=" N PHE f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 107 removed outlier: 4.269A pdb=" N LEU f 106 " --> pdb=" O HIS f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 126 removed outlier: 4.112A pdb=" N ASP f 124 " --> pdb=" O ARG f 120 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE f 125 " --> pdb=" O PHE f 121 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE f 126 " --> pdb=" O ALA f 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 138 removed outlier: 5.068A pdb=" N THR f 132 " --> pdb=" O VAL f 128 " (cutoff:3.500A) Processing helix chain 'f' and resid 140 through 148 Processing helix chain 'f' and resid 153 through 174 removed outlier: 3.784A pdb=" N GLU f 157 " --> pdb=" O SER f 153 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP f 174 " --> pdb=" O TRP f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 178 through 190 removed outlier: 4.279A pdb=" N GLU f 182 " --> pdb=" O LYS f 178 " (cutoff:3.500A) Proline residue: f 183 - end of helix removed outlier: 4.108A pdb=" N LYS f 189 " --> pdb=" O LEU f 185 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 192 through 210 removed outlier: 4.105A pdb=" N MET f 196 " --> pdb=" O VAL f 192 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN f 199 " --> pdb=" O ASN f 195 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP f 206 " --> pdb=" O HIS f 202 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU f 208 " --> pdb=" O ALA f 204 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N MET f 209 " --> pdb=" O CYS f 205 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU f 210 " --> pdb=" O ASP f 206 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 224 removed outlier: 4.005A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) Processing helix chain 'f' and resid 233 through 247 removed outlier: 4.305A pdb=" N VAL f 237 " --> pdb=" O LEU f 233 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL f 240 " --> pdb=" O CYS f 236 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.927A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) Processing helix chain 'f' and resid 253 through 260 removed outlier: 4.361A pdb=" N ARG f 257 " --> pdb=" O LEU f 253 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS f 258 " --> pdb=" O GLY f 254 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 276 removed outlier: 5.099A pdb=" N ASP f 274 " --> pdb=" O LEU f 270 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET f 275 " --> pdb=" O MET f 271 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU f 276 " --> pdb=" O LEU f 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 270 through 276' Processing helix chain 'f' and resid 285 through 297 removed outlier: 4.390A pdb=" N VAL f 289 " --> pdb=" O CYS f 285 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA f 295 " --> pdb=" O GLN f 291 " (cutoff:3.500A) Processing helix chain 'f' and resid 298 through 307 removed outlier: 4.879A pdb=" N GLY f 302 " --> pdb=" O LEU f 298 " (cutoff:3.500A) Processing helix chain 'f' and resid 313 through 321 removed outlier: 4.295A pdb=" N LEU f 317 " --> pdb=" O GLU f 313 " (cutoff:3.500A) Processing helix chain 'f' and resid 323 through 336 removed outlier: 3.761A pdb=" N ASN f 327 " --> pdb=" O ASN f 323 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER f 328 " --> pdb=" O VAL f 324 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN f 329 " --> pdb=" O GLN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 353 through 358 removed outlier: 4.253A pdb=" N ARG f 357 " --> pdb=" O LEU f 353 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE f 358 " --> pdb=" O GLU f 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 353 through 358' Processing helix chain 'f' and resid 369 through 383 Processing helix chain 'f' and resid 396 through 401 removed outlier: 4.674A pdb=" N TYR f 400 " --> pdb=" O ASN f 396 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS f 401 " --> pdb=" O LYS f 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 396 through 401' Processing helix chain 'f' and resid 406 through 419 removed outlier: 4.414A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 422 through 434 removed outlier: 5.486A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 3.576A 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: 4.014A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 4.011A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 471 removed outlier: 4.766A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 4.456A pdb=" N LEU f 479 " --> pdb=" O ASN f 475 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY f 480 " --> pdb=" O THR f 476 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER f 481 " --> pdb=" O MET f 477 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE f 482 " --> pdb=" O ARG f 478 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE f 483 " --> pdb=" O LEU f 479 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR f 489 " --> pdb=" O LEU f 485 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 508 removed outlier: 4.362A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix removed outlier: 4.247A pdb=" N ASP f 507 " --> pdb=" O PRO f 503 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER f 508 " --> pdb=" O VAL f 504 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.555A pdb=" N ALA f 515 " --> pdb=" O SER f 511 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA f 526 " --> pdb=" O CYS f 522 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 3.835A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET f 543 " --> pdb=" O LEU f 539 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 551 removed outlier: 4.367A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (cutoff:3.500A) removed outlier: 3.848A 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 Processing helix chain 'f' and resid 574 through 582 removed outlier: 4.350A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 585 through 600 removed outlier: 4.008A pdb=" N SER f 589 " --> pdb=" O GLU f 585 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) Processing helix chain 'f' and resid 608 through 614 removed outlier: 4.720A pdb=" N LEU f 612 " --> pdb=" O LYS f 608 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU f 613 " --> pdb=" O VAL f 609 " (cutoff:3.500A) Processing helix chain 'f' and resid 648 through 659 Processing helix chain 'f' and resid 671 through 677 removed outlier: 4.399A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) Processing helix chain 'f' and resid 686 through 695 removed outlier: 6.003A pdb=" N VAL f 690 " --> pdb=" O LEU f 686 " (cutoff:3.500A) Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 701 through 717 removed outlier: 3.812A pdb=" N ASN f 705 " --> pdb=" O ASN f 701 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER f 714 " --> pdb=" O LEU f 710 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP f 716 " --> pdb=" O LYS f 712 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA f 717 " --> pdb=" O PHE f 713 " (cutoff:3.500A) Processing helix chain 'f' and resid 723 through 731 removed outlier: 4.398A pdb=" N PHE f 727 " --> pdb=" O TYR f 723 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 754 removed outlier: 3.583A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG f 746 " --> pdb=" O ALA f 742 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS f 754 " --> pdb=" O GLN f 750 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 786 removed outlier: 4.248A pdb=" N THR f 775 " --> pdb=" O LEU f 771 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N CYS f 779 " --> pdb=" O THR f 775 " (cutoff:3.500A) Proline residue: f 780 - end of helix removed outlier: 4.239A pdb=" N SER f 783 " --> pdb=" O CYS f 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP f 784 " --> pdb=" O PRO f 780 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG f 785 " --> pdb=" O TYR f 781 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) Processing helix chain 'f' and resid 788 through 793 removed outlier: 6.787A pdb=" N ALA f 792 " --> pdb=" O MET f 788 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL f 793 " --> pdb=" O SER f 789 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 788 through 793' Processing helix chain 'f' and resid 798 through 805 removed outlier: 4.594A pdb=" N SER f 802 " --> pdb=" O THR f 798 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP f 805 " --> pdb=" O VAL f 801 " (cutoff:3.500A) Processing helix chain 'f' and resid 618 through 623 removed outlier: 4.037A pdb=" N ASP f 621 " --> pdb=" O GLU f 618 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER f 622 " --> pdb=" O HIS f 619 " (cutoff:3.500A) Processing helix chain 'f' and resid 626 through 631 removed outlier: 5.540A pdb=" N LYS f 629 " --> pdb=" O GLU f 626 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP f 630 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS f 631 " --> pdb=" O ASP f 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 626 through 631' Processing helix chain 'g' and resid 22 through 36 removed outlier: 3.718A pdb=" N PHE g 29 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.601A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.425A 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: 3.574A pdb=" N ASN g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 3.549A pdb=" N SER g 175 " --> pdb=" O LYS g 171 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.717A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 211 through 216 removed outlier: 4.221A pdb=" N ILE g 215 " --> pdb=" O LYS g 211 " (cutoff:3.500A) removed outlier: 5.855A 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: 3.558A pdb=" N ARG g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 7 removed outlier: 3.646A pdb=" N ASP i 6 " --> pdb=" O SER i 2 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER i 7 " --> pdb=" O ARG i 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 2 through 7' Processing helix chain 'i' and resid 18 through 32 removed outlier: 3.940A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.666A pdb=" N ALA i 83 " --> pdb=" O ILE i 79 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN i 84 " --> pdb=" O THR i 80 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.553A pdb=" N LEU i 110 " --> pdb=" O PRO i 106 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 Processing helix chain 'i' and resid 185 through 202 removed outlier: 5.157A pdb=" N ASP i 202 " --> pdb=" O ASN i 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 229 through 251 removed outlier: 3.960A pdb=" N LYS i 251 " --> pdb=" O ALA i 247 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 3.510A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.706A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 3.660A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.676A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU k 183 " --> pdb=" O SER k 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL k 184 " --> pdb=" O SER k 180 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR k 185 " --> pdb=" O LEU k 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 207 removed outlier: 3.655A pdb=" N MET k 206 " --> pdb=" O LEU k 202 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU k 207 " --> pdb=" O LYS k 203 " (cutoff:3.500A) Processing helix chain 'k' and resid 211 through 216 removed outlier: 4.305A pdb=" N ILE k 215 " --> pdb=" O ASN k 211 " (cutoff:3.500A) removed outlier: 7.178A 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: 5.353A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 65 removed outlier: 3.539A pdb=" N SER k 63 " --> pdb=" O GLU k 60 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE k 64 " --> pdb=" O PRO k 61 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU k 65 " --> pdb=" O SER k 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 60 through 65' Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.593A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 removed outlier: 3.924A pdb=" N LEU l 83 " --> pdb=" O ALA l 79 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 123 removed outlier: 4.042A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 3.813A pdb=" N ARG l 122 " --> pdb=" O ILE l 118 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR l 123 " --> pdb=" O PRO l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 180 removed outlier: 5.957A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 3.955A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU l 199 " --> pdb=" O LEU l 195 " (cutoff:3.500A) Proline residue: l 200 - end of helix Processing helix chain 'l' and resid 225 through 234 removed outlier: 3.754A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 4.506A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 5.457A pdb=" N ASP l 7 " --> pdb=" O ASN l 4 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN l 8 " --> pdb=" O GLN l 5 " (cutoff:3.500A) removed outlier: 4.512A 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: 3.778A 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: 4.572A 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: 3.998A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TYR m 125 " --> pdb=" O ALA m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 3.934A pdb=" N GLU m 177 " --> pdb=" O LYS m 173 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 180 through 185 removed outlier: 3.885A pdb=" N MET m 184 " --> pdb=" O GLN m 180 " (cutoff:3.500A) removed outlier: 6.091A 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: 3.757A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS m 201 " --> pdb=" O ILE m 197 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 5 through 10 removed outlier: 5.812A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 5.459A 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: 3.728A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.766A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 removed outlier: 3.689A pdb=" N ARG n 166 " --> pdb=" O LEU n 162 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 127 removed outlier: 3.616A pdb=" N ASN x 117 " --> pdb=" O THR x 113 " (cutoff:3.500A) Proline residue: x 127 - end of helix Processing helix chain 'x' and resid 128 through 137 removed outlier: 5.553A pdb=" N ALA x 137 " --> pdb=" O LEU x 133 " (cutoff:3.500A) Processing helix chain 'x' and resid 147 through 167 removed outlier: 3.998A pdb=" N TYR x 151 " --> pdb=" O ALA x 147 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR x 166 " --> pdb=" O SER x 162 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER x 167 " --> pdb=" O MET x 163 " (cutoff:3.500A) Processing helix chain 'x' and resid 172 through 183 removed outlier: 4.412A pdb=" N LEU x 176 " --> pdb=" O PRO x 172 " (cutoff:3.500A) Processing helix chain 'x' and resid 199 through 215 Processing helix chain 'x' and resid 285 through 296 removed outlier: 3.688A pdb=" N GLY x 289 " --> pdb=" O TYR x 285 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU x 296 " --> pdb=" O LEU x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 366 through 383 removed outlier: 4.776A pdb=" N PHE x 370 " --> pdb=" O LYS x 366 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS x 373 " --> pdb=" O SER x 369 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL x 382 " --> pdb=" O GLU x 378 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN x 383 " --> pdb=" O ASP x 379 " (cutoff:3.500A) Processing helix chain 'x' and resid 459 through 467 removed outlier: 4.541A pdb=" N SER x 467 " --> pdb=" O ILE x 463 " (cutoff:3.500A) Processing helix chain 'x' and resid 242 through 247 Processing helix chain 'y' and resid 22 through 34 Processing helix chain 'y' and resid 55 through 60 Processing helix chain 'e' and resid 42 through 48 removed outlier: 4.140A pdb=" N ASP e 46 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN e 47 " --> pdb=" O TRP e 43 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL e 48 " --> pdb=" O ASP e 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 42 through 48' Processing helix chain 'e' and resid 51 through 64 removed outlier: 3.751A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 109 through 115 removed outlier: 5.850A pdb=" N LEU A 125 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 141 through 144 removed outlier: 4.279A pdb=" N GLY A 141 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN A 148 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 236 through 240 removed outlier: 4.264A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 272 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A 274 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 320 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS A 210 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG A 339 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 107 through 112 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.549A pdb=" N HIS B 131 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 281 through 285 removed outlier: 3.797A pdb=" N VAL B 327 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 222 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 224 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 349 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 225 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 71 through 77 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'C' and resid 84 through 88 Processing sheet with id= 9, first strand: chain 'C' and resid 209 through 215 removed outlier: 3.883A pdb=" N THR C 210 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 186 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET C 293 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 188 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.990A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA D 128 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 259 through 265 removed outlier: 3.649A pdb=" N LYS D 306 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 310 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET D 309 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET D 204 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR D 311 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 55 through 61 removed outlier: 4.418A pdb=" N THR E 96 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 68 through 72 Processing sheet with id= 14, first strand: chain 'E' and resid 194 through 198 removed outlier: 3.576A pdb=" N ASP E 233 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR E 279 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E 299 " --> pdb=" O LEU E 171 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 130 through 135 removed outlier: 4.312A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE F 94 " --> pdb=" O VAL F 123 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 223 through 227 Processing sheet with id= 17, first strand: chain 'F' and resid 280 through 286 removed outlier: 4.709A pdb=" N SER F 281 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE F 285 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 69 through 72 removed outlier: 6.514A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 165 through 169 removed outlier: 4.841A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.503A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY H 138 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 160 through 164 removed outlier: 5.990A pdb=" N ASN H 207 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN H 214 " --> pdb=" O GLY H 217 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.481A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER h 133 " --> pdb=" O SER h 77 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP h 158 " --> pdb=" O LEU h 146 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'h' and resid 160 through 164 removed outlier: 3.629A pdb=" N GLU h 49 " --> pdb=" O PRO h 34 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN h 207 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN h 214 " --> pdb=" O GLY h 217 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.538A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU I 134 " --> pdb=" O SER I 150 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 161 through 165 removed outlier: 4.857A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 37 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.371A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 158 through 162 removed outlier: 4.827A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'j' and resid 62 through 65 removed outlier: 6.547A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA j 131 " --> pdb=" O THR j 147 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.493A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 67 through 70 removed outlier: 6.470A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 167 through 171 removed outlier: 5.767A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.428A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'L' and resid 158 through 162 removed outlier: 4.794A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'M' and resid 65 through 69 removed outlier: 6.931A pdb=" N ARG M 65 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL M 69 " --> pdb=" O VAL M 73 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER M 141 " --> pdb=" O GLY M 145 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.624A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.568A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA N 101 " --> pdb=" O PHE N 42 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.536A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER N 18 " --> pdb=" O VAL N 173 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.442A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.521A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP O 17 " --> pdb=" O THR O 2 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.429A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.446A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP o 17 " --> pdb=" O THR o 2 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA o 16 " --> pdb=" O ASP o 174 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 42 through 45 removed outlier: 6.018A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'P' and resid 136 through 140 removed outlier: 5.936A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.910A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.035A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP p 25 " --> pdb=" O ALA p 10 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.762A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Q' and resid 129 through 132 removed outlier: 3.771A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.465A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'q' and resid 129 through 132 removed outlier: 3.776A pdb=" N LEU q 4 " --> pdb=" O HIS q 132 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 34 through 37 removed outlier: 3.740A pdb=" N ILE R 37 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS R 102 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR R 44 " --> pdb=" O MET R 100 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY R 103 " --> pdb=" O GLY R 110 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.596A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER R 18 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'r' and resid 34 through 37 removed outlier: 3.580A pdb=" N ILE r 37 " --> pdb=" O LEU r 41 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR r 44 " --> pdb=" O MET r 100 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA r 46 " --> pdb=" O GLY r 98 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY r 98 " --> pdb=" O ALA r 46 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.392A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL r 12 " --> pdb=" O VAL r 179 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.711A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.919A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP S 26 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 's' and resid 43 through 46 removed outlier: 6.662A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 's' and resid 135 through 139 removed outlier: 5.612A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.645A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.197A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY T 19 " --> pdb=" O PHE T 16 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 't' and resid 42 through 45 removed outlier: 6.657A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 't' and resid 136 through 139 removed outlier: 4.188A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 801 through 805 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'W' and resid 404 through 408 Processing sheet with id= 64, first strand: chain 'X' and resid 375 through 380 removed outlier: 4.968A pdb=" N HIS X 375 " --> pdb=" O PHE X 388 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Y' and resid 345 through 349 removed outlier: 3.509A pdb=" N GLU Y 355 " --> pdb=" O LYS Y 346 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE Y 353 " --> pdb=" O ASP Y 348 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Z' and resid 47 through 50 Processing sheet with id= 67, first strand: chain 'Z' and resid 52 through 55 removed outlier: 4.402A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR Z 97 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL Z 120 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE Z 124 " --> pdb=" O HIS Z 96 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 320 through 326 removed outlier: 4.952A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'b' and resid 49 through 53 removed outlier: 4.719A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N MET b 7 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE b 110 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL b 171 " --> pdb=" O ILE b 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL b 173 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'c' and resid 65 through 69 removed outlier: 3.778A pdb=" N GLN c 30 " --> pdb=" O TYR c 65 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLU c 29 " --> pdb=" O SER c 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N HIS c 199 " --> pdb=" O ILE c 163 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'c' and resid 71 through 74 removed outlier: 4.834A pdb=" N VAL c 53 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.227A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL g 151 " --> pdb=" O PHE g 163 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS g 153 " --> pdb=" O CYS g 161 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS g 161 " --> pdb=" O LYS g 153 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP g 155 " --> pdb=" O TYR g 159 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR g 159 " --> pdb=" O ASP g 155 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'g' and resid 165 through 169 removed outlier: 4.975A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'i' and resid 65 through 68 removed outlier: 6.496A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY i 157 " --> pdb=" O GLN i 149 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN i 155 " --> pdb=" O ASP i 151 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'i' and resid 161 through 165 removed outlier: 4.836A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS i 210 " --> pdb=" O ARG i 49 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'k' and resid 67 through 70 removed outlier: 6.328A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'k' and resid 167 through 171 Processing sheet with id= 78, first strand: chain 'l' and resid 63 through 66 removed outlier: 3.585A pdb=" N ILE l 72 " --> pdb=" O LEU l 64 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'l' and resid 158 through 162 removed outlier: 4.881A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'm' and resid 65 through 69 removed outlier: 6.875A pdb=" N ARG m 65 " --> pdb=" O VAL m 77 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY m 138 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA m 76 " --> pdb=" O MET m 136 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER m 141 " --> pdb=" O GLY m 145 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'm' and resid 162 through 166 removed outlier: 5.071A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU m 50 " --> pdb=" O THR m 35 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.517A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP n 104 " --> pdb=" O GLY n 108 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.556A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER n 18 " --> pdb=" O VAL n 173 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'x' and resid 274 through 277 removed outlier: 4.487A pdb=" N CYS x 277 " --> pdb=" O GLN x 327 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'x' and resid 446 through 451 removed outlier: 6.472A pdb=" N GLU x 446 " --> pdb=" O ARG x 442 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER x 438 " --> pdb=" O PHE x 450 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS x 435 " --> pdb=" O GLN x 427 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN x 427 " --> pdb=" O HIS x 435 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL x 437 " --> pdb=" O THR x 425 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU x 424 " --> pdb=" O TYR x 476 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'y' and resid 12 through 16 removed outlier: 4.359A pdb=" N SER y 65 " --> pdb=" O GLN y 2 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU y 67 " --> pdb=" O PHE y 4 " (cutoff:3.500A) 5569 hydrogen bonds defined for protein. 16638 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: 43.21 Time building geometry restraints manager: 34.24 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: 36057 1.34 - 1.46: 23706 1.46 - 1.59: 50076 1.59 - 1.71: 14 1.71 - 1.83: 1052 Bond restraints: 110905 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.36e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C5 ATP C 501 " pdb=" N7 ATP C 501 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.07e+01 bond pdb=" C8 ATP C 501 " pdb=" N7 ATP C 501 " ideal model delta sigma weight residual 1.310 1.351 -0.041 1.00e-02 1.00e+04 1.66e+01 bond pdb=" C ILE d 68 " pdb=" N PRO d 69 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.23e-02 6.61e+03 1.48e+01 ... (remaining 110900 not shown) Histogram of bond angle deviations from ideal: 95.86 - 104.72: 1678 104.72 - 113.58: 61637 113.58 - 122.44: 71889 122.44 - 131.29: 14466 131.29 - 140.15: 156 Bond angle restraints: 149826 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 123.49 16.38 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 121.82 15.01 1.00e+00 1.00e+00 2.25e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 117.75 9.05 1.00e+00 1.00e+00 8.20e+01 angle pdb=" N3 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N9 ATP C 501 " ideal model delta sigma weight residual 127.04 136.03 -8.99 1.15e+00 7.59e-01 6.13e+01 angle pdb=" C GLU g 223 " pdb=" N ASN g 224 " pdb=" CA ASN g 224 " ideal model delta sigma weight residual 122.26 129.67 -7.41 1.10e+00 8.26e-01 4.54e+01 ... (remaining 149821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.19: 65725 31.19 - 62.39: 1909 62.39 - 93.58: 129 93.58 - 124.77: 0 124.77 - 155.96: 1 Dihedral angle restraints: 67764 sinusoidal: 27452 harmonic: 40312 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 144.04 155.96 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" CA PRO Z 150 " pdb=" C PRO Z 150 " pdb=" N THR Z 151 " pdb=" CA THR Z 151 " ideal model delta harmonic sigma weight residual 180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LYS c 281 " pdb=" C LYS c 281 " pdb=" N ARG c 282 " pdb=" CA ARG c 282 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 67761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 14286 0.065 - 0.130: 2437 0.130 - 0.195: 211 0.195 - 0.260: 20 0.260 - 0.325: 5 Chirality restraints: 16959 Sorted by residual: chirality pdb=" CB VAL X 410 " pdb=" CA VAL X 410 " pdb=" CG1 VAL X 410 " pdb=" CG2 VAL X 410 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE Y 65 " pdb=" CA ILE Y 65 " pdb=" CG1 ILE Y 65 " pdb=" CG2 ILE Y 65 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB THR Q 96 " pdb=" CA THR Q 96 " pdb=" OG1 THR Q 96 " pdb=" CG2 THR Q 96 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 16956 not shown) Planarity restraints: 19324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 255 " 0.030 2.00e-02 2.50e+03 3.10e-02 2.41e+01 pdb=" CG TRP a 255 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP a 255 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP a 255 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP a 255 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 255 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 255 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 255 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 255 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP a 255 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS f 631 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C LYS f 631 " -0.057 2.00e-02 2.50e+03 pdb=" O LYS f 631 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS f 632 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 38 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 39 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 39 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 39 " 0.044 5.00e-02 4.00e+02 ... (remaining 19321 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 671 2.54 - 3.13: 78874 3.13 - 3.72: 172711 3.72 - 4.31: 228089 4.31 - 4.90: 383604 Nonbonded interactions: 863949 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.953 2.230 nonbonded pdb=" OG SER f 367 " pdb=" O LYS f 403 " model vdw 2.201 2.440 nonbonded pdb=" O PHE D 345 " pdb=" OG1 THR D 349 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR H 222 " pdb=" OE1 GLU H 225 " model vdw 2.221 2.440 nonbonded pdb=" OE1 GLU A 262 " pdb=" OG1 THR x 288 " model vdw 2.233 2.440 ... (remaining 863944 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 52.320 Check model and map are aligned: 1.170 Set scattering table: 0.760 Process input model: 265.560 Find NCS groups from input model: 6.670 Set up NCS constraints: 0.550 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: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 338.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 0.086 110905 Z= 0.210 Angle : 0.775 16.383 149826 Z= 0.405 Chirality : 0.048 0.325 16959 Planarity : 0.005 0.080 19324 Dihedral : 14.172 155.965 41814 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.12 % Favored : 93.77 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -1.11 (0.07), residues: 13777 helix: 0.14 (0.06), residues: 6153 sheet: 0.17 (0.12), residues: 1910 loop : -2.04 (0.07), residues: 5714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP a 255 HIS 0.009 0.001 HIS d 96 PHE 0.026 0.001 PHE Z 249 TYR 0.025 0.001 TYR Z 228 ARG 0.016 0.000 ARG U 883 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 464 time to evaluate : 9.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8098 (ppp) cc_final: 0.7873 (ppp) REVERT: B 329 MET cc_start: 0.8937 (mmm) cc_final: 0.8574 (ppp) REVERT: C 273 MET cc_start: 0.8536 (pmm) cc_final: 0.8308 (pmm) REVERT: D 246 MET cc_start: 0.8980 (mpp) cc_final: 0.8659 (mpp) REVERT: U 423 MET cc_start: 0.7802 (mmp) cc_final: 0.7016 (tpt) REVERT: V 176 MET cc_start: 0.7703 (tpt) cc_final: 0.7176 (ttt) REVERT: V 192 MET cc_start: 0.8775 (mmt) cc_final: 0.8532 (mmm) REVERT: W 177 MET cc_start: 0.6186 (tpt) cc_final: 0.5875 (mmm) REVERT: X 254 MET cc_start: 0.8388 (tpp) cc_final: 0.8171 (mmp) REVERT: Y 50 MET cc_start: 0.6138 (mmp) cc_final: 0.5926 (mmm) REVERT: Y 105 MET cc_start: 0.7351 (mmt) cc_final: 0.7149 (mmm) REVERT: a 218 MET cc_start: 0.8242 (mtm) cc_final: 0.7605 (ptm) REVERT: a 278 MET cc_start: 0.8612 (ptm) cc_final: 0.8137 (ptm) REVERT: b 107 MET cc_start: 0.5876 (ppp) cc_final: 0.5665 (ppp) REVERT: c 265 MET cc_start: 0.7913 (pmm) cc_final: 0.7688 (tmm) REVERT: d 1 MET cc_start: 0.5386 (mmt) cc_final: 0.5028 (tpp) REVERT: d 53 ASP cc_start: 0.8628 (m-30) cc_final: 0.8415 (m-30) REVERT: d 75 MET cc_start: 0.8688 (mmp) cc_final: 0.8405 (mmm) REVERT: f 1 MET cc_start: 0.5822 (ptp) cc_final: 0.5574 (ptp) REVERT: f 27 LYS cc_start: 0.7330 (tttp) cc_final: 0.7086 (pttt) REVERT: f 209 MET cc_start: 0.1696 (mtp) cc_final: 0.1034 (pmm) REVERT: f 543 MET cc_start: 0.5132 (tmm) cc_final: 0.4097 (pmm) REVERT: f 635 LYS cc_start: 0.1792 (OUTLIER) cc_final: 0.1528 (ttpt) REVERT: f 811 LEU cc_start: 0.3074 (OUTLIER) cc_final: 0.2713 (tp) REVERT: n 4 MET cc_start: 0.8426 (ttt) cc_final: 0.8146 (ttt) REVERT: x 181 MET cc_start: 0.4113 (ptt) cc_final: 0.3835 (ptm) REVERT: x 255 MET cc_start: 0.4487 (tmm) cc_final: 0.4041 (tmm) REVERT: x 367 MET cc_start: 0.0104 (mtm) cc_final: -0.0576 (mtt) REVERT: y 14 THR cc_start: 0.2327 (m) cc_final: 0.2056 (p) REVERT: y 36 ILE cc_start: 0.3635 (mt) cc_final: 0.3411 (tt) REVERT: y 56 LEU cc_start: 0.1758 (mt) cc_final: 0.1526 (tp) REVERT: y 63 LYS cc_start: 0.6104 (mmpt) cc_final: 0.4572 (tptp) outliers start: 16 outliers final: 4 residues processed: 479 average time/residue: 0.8808 time to fit residues: 756.6834 Evaluate side-chains 446 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 440 time to evaluate : 9.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain f residue 632 LYS Chi-restraints excluded: chain f residue 635 LYS Chi-restraints excluded: chain f residue 811 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1155 optimal weight: 20.0000 chunk 1036 optimal weight: 7.9990 chunk 575 optimal weight: 40.0000 chunk 354 optimal weight: 20.0000 chunk 699 optimal weight: 8.9990 chunk 553 optimal weight: 5.9990 chunk 1072 optimal weight: 30.0000 chunk 414 optimal weight: 9.9990 chunk 651 optimal weight: 30.0000 chunk 798 optimal weight: 4.9990 chunk 1242 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN E 32 GLN F 83 ASN G 147 GLN ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 165 ASN U 115 ASN U 464 GLN U 665 ASN ** U 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 HIS ** Z 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 ASN ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN c 44 HIS c 190 GLN f 291 GLN ** f 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 205 ASN x 197 GLN x 414 ASN e 47 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 110905 Z= 0.229 Angle : 0.570 11.853 149826 Z= 0.298 Chirality : 0.041 0.194 16959 Planarity : 0.004 0.066 19324 Dihedral : 5.365 148.061 15256 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.06 % Favored : 93.86 % Rotamer: Outliers : 0.27 % Allowed : 5.43 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.07), residues: 13777 helix: 1.22 (0.07), residues: 6269 sheet: 0.16 (0.12), residues: 1895 loop : -1.82 (0.08), residues: 5613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP a 255 HIS 0.005 0.001 HIS l 190 PHE 0.018 0.001 PHE h 199 TYR 0.025 0.001 TYR E 12 ARG 0.005 0.000 ARG c 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 441 time to evaluate : 8.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8171 (ppp) cc_final: 0.7761 (ppp) REVERT: A 319 MET cc_start: 0.7123 (tmm) cc_final: 0.6882 (tpt) REVERT: B 107 MET cc_start: 0.7401 (tpp) cc_final: 0.7192 (tpp) REVERT: B 329 MET cc_start: 0.8973 (mmm) cc_final: 0.8654 (mmm) REVERT: C 139 MET cc_start: 0.6374 (mmt) cc_final: 0.6156 (mmt) REVERT: C 368 MET cc_start: 0.8518 (mpp) cc_final: 0.7858 (mpp) REVERT: D 163 MET cc_start: 0.7266 (tpt) cc_final: 0.6996 (tpp) REVERT: D 352 MET cc_start: 0.7495 (pmm) cc_final: 0.7222 (pmm) REVERT: E 277 MET cc_start: 0.8855 (mmp) cc_final: 0.8608 (mmp) REVERT: E 368 MET cc_start: 0.8799 (mmm) cc_final: 0.8589 (ptp) REVERT: M 136 MET cc_start: 0.8498 (mtm) cc_final: 0.8247 (mtt) REVERT: U 423 MET cc_start: 0.7897 (mmp) cc_final: 0.7144 (tpt) REVERT: U 695 MET cc_start: 0.8713 (mmp) cc_final: 0.7897 (mmp) REVERT: V 175 MET cc_start: 0.7251 (tpp) cc_final: 0.6858 (ttm) REVERT: V 176 MET cc_start: 0.7647 (tpt) cc_final: 0.7260 (ttt) REVERT: V 192 MET cc_start: 0.8836 (mmt) cc_final: 0.8534 (mmm) REVERT: W 177 MET cc_start: 0.6172 (tpt) cc_final: 0.5872 (mmm) REVERT: Y 105 MET cc_start: 0.7608 (mmt) cc_final: 0.7227 (mmm) REVERT: Y 228 MET cc_start: 0.8227 (ptp) cc_final: 0.7948 (pmm) REVERT: a 218 MET cc_start: 0.8168 (mtm) cc_final: 0.7561 (ptm) REVERT: a 278 MET cc_start: 0.8612 (ptm) cc_final: 0.8255 (ptm) REVERT: c 95 MET cc_start: 0.8022 (tmm) cc_final: 0.7771 (tmm) REVERT: d 1 MET cc_start: 0.5304 (mmt) cc_final: 0.4977 (tpp) REVERT: d 75 MET cc_start: 0.8618 (mmp) cc_final: 0.8297 (mmm) REVERT: d 95 MET cc_start: 0.8000 (tmm) cc_final: 0.7564 (ptp) REVERT: f 27 LYS cc_start: 0.7378 (tttp) cc_final: 0.7152 (ptpt) REVERT: f 209 MET cc_start: 0.1488 (mtp) cc_final: 0.0521 (pmm) REVERT: f 543 MET cc_start: 0.5178 (tmm) cc_final: 0.4152 (pmm) REVERT: f 761 MET cc_start: -0.1265 (ptp) cc_final: -0.1590 (ttp) REVERT: j 71 MET cc_start: 0.8946 (ppp) cc_final: 0.8622 (ptm) REVERT: p 45 MET cc_start: 0.8469 (mmp) cc_final: 0.8265 (mmt) REVERT: x 255 MET cc_start: 0.4493 (tmm) cc_final: 0.4024 (tmm) REVERT: x 328 MET cc_start: 0.1125 (mpp) cc_final: 0.0778 (mpp) REVERT: x 367 MET cc_start: 0.0064 (mtm) cc_final: -0.0664 (mtt) REVERT: y 63 LYS cc_start: 0.5464 (mmpt) cc_final: 0.4326 (tptp) outliers start: 32 outliers final: 13 residues processed: 457 average time/residue: 0.8730 time to fit residues: 714.4360 Evaluate side-chains 446 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 433 time to evaluate : 9.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain V residue 130 PHE Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 609 VAL Chi-restraints excluded: chain f residue 632 LYS Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 690 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 1033 optimal weight: 0.8980 chunk 845 optimal weight: 40.0000 chunk 342 optimal weight: 20.0000 chunk 1244 optimal weight: 6.9990 chunk 1344 optimal weight: 30.0000 chunk 1108 optimal weight: 5.9990 chunk 1234 optimal weight: 8.9990 chunk 424 optimal weight: 9.9990 chunk 998 optimal weight: 30.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN C 69 GLN C 288 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 GLN X 148 HIS ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 30 GLN d 47 GLN f 291 GLN f 323 ASN f 356 ASN ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 611 GLN f 747 GLN ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 166 ASN q 32 HIS x 150 GLN x 274 GLN ** x 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 68 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 110905 Z= 0.196 Angle : 0.533 10.931 149826 Z= 0.277 Chirality : 0.040 0.209 16959 Planarity : 0.004 0.062 19324 Dihedral : 5.180 145.233 15250 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 0.41 % Allowed : 8.93 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.14 (0.07), residues: 13777 helix: 1.58 (0.07), residues: 6296 sheet: 0.12 (0.12), residues: 1915 loop : -1.72 (0.08), residues: 5566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP m 215 HIS 0.006 0.001 HIS j 154 PHE 0.016 0.001 PHE p 69 TYR 0.019 0.001 TYR Z 228 ARG 0.003 0.000 ARG U 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 433 time to evaluate : 9.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8151 (ppp) cc_final: 0.7669 (ppp) REVERT: A 319 MET cc_start: 0.7301 (tmm) cc_final: 0.6896 (tpt) REVERT: B 107 MET cc_start: 0.7360 (tpp) cc_final: 0.7152 (tpp) REVERT: B 329 MET cc_start: 0.8978 (mmm) cc_final: 0.8687 (mmm) REVERT: C 138 MET cc_start: 0.6987 (pmm) cc_final: 0.6686 (pmm) REVERT: C 139 MET cc_start: 0.6365 (mmt) cc_final: 0.6078 (mmt) REVERT: C 368 MET cc_start: 0.8521 (mpp) cc_final: 0.8007 (mpp) REVERT: D 352 MET cc_start: 0.7881 (pmm) cc_final: 0.7423 (pmm) REVERT: E 277 MET cc_start: 0.8939 (mmp) cc_final: 0.8559 (mmp) REVERT: F 310 MET cc_start: 0.8413 (ppp) cc_final: 0.8021 (ppp) REVERT: M 136 MET cc_start: 0.8530 (mtm) cc_final: 0.8102 (mtt) REVERT: U 206 MET cc_start: 0.7707 (ttm) cc_final: 0.7358 (tpp) REVERT: U 583 MET cc_start: 0.8921 (mmm) cc_final: 0.8561 (mmm) REVERT: U 797 MET cc_start: 0.6217 (tpp) cc_final: 0.5863 (tpp) REVERT: V 100 MET cc_start: 0.8655 (mtm) cc_final: 0.8377 (ptt) REVERT: V 175 MET cc_start: 0.7350 (tpp) cc_final: 0.6916 (ttm) REVERT: V 176 MET cc_start: 0.7628 (tpt) cc_final: 0.7224 (ttt) REVERT: V 192 MET cc_start: 0.8824 (mmt) cc_final: 0.8481 (mmm) REVERT: W 177 MET cc_start: 0.6246 (tpt) cc_final: 0.5958 (mmm) REVERT: X 254 MET cc_start: 0.8315 (mmm) cc_final: 0.8023 (mmm) REVERT: Y 105 MET cc_start: 0.7664 (mmt) cc_final: 0.7304 (mmm) REVERT: Y 228 MET cc_start: 0.8268 (ptp) cc_final: 0.8002 (pmm) REVERT: a 218 MET cc_start: 0.8166 (mtm) cc_final: 0.7572 (ptm) REVERT: a 278 MET cc_start: 0.8559 (ptm) cc_final: 0.8163 (ptm) REVERT: d 1 MET cc_start: 0.5393 (mmt) cc_final: 0.5061 (tpp) REVERT: d 75 MET cc_start: 0.8654 (mmp) cc_final: 0.8405 (mmm) REVERT: f 1 MET cc_start: 0.4043 (ptp) cc_final: 0.3711 (ptp) REVERT: f 27 LYS cc_start: 0.7411 (tttp) cc_final: 0.7187 (ptpt) REVERT: f 209 MET cc_start: 0.1384 (mtp) cc_final: 0.0334 (pmm) REVERT: f 761 MET cc_start: -0.1405 (ptp) cc_final: -0.1684 (ttp) REVERT: p 45 MET cc_start: 0.8462 (mmp) cc_final: 0.8248 (mmt) REVERT: x 255 MET cc_start: 0.4552 (tmm) cc_final: 0.3991 (tmm) REVERT: x 328 MET cc_start: 0.1124 (mpp) cc_final: 0.0768 (mpp) REVERT: x 367 MET cc_start: 0.0039 (mtm) cc_final: -0.0719 (mtt) REVERT: x 488 MET cc_start: -0.0372 (ttt) cc_final: -0.1778 (ptt) REVERT: y 63 LYS cc_start: 0.5431 (mmpt) cc_final: 0.4290 (tmtt) outliers start: 48 outliers final: 17 residues processed: 469 average time/residue: 0.8738 time to fit residues: 738.7769 Evaluate side-chains 449 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 432 time to evaluate : 9.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain V residue 130 PHE Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 611 GLN Chi-restraints excluded: chain f residue 632 LYS Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain r residue 45 MET Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1229 optimal weight: 30.0000 chunk 935 optimal weight: 0.0000 chunk 645 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 593 optimal weight: 30.0000 chunk 835 optimal weight: 8.9990 chunk 1248 optimal weight: 5.9990 chunk 1322 optimal weight: 50.0000 chunk 652 optimal weight: 4.9990 chunk 1183 optimal weight: 20.0000 chunk 356 optimal weight: 5.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN C 288 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 GLN ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 611 GLN ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 150 GLN ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 110905 Z= 0.159 Angle : 0.513 9.405 149826 Z= 0.266 Chirality : 0.040 0.393 16959 Planarity : 0.003 0.059 19324 Dihedral : 5.055 142.646 15250 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.03 % Favored : 93.90 % Rotamer: Outliers : 0.59 % Allowed : 10.60 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.29 (0.07), residues: 13777 helix: 1.75 (0.07), residues: 6290 sheet: 0.16 (0.12), residues: 1913 loop : -1.68 (0.08), residues: 5574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP m 215 HIS 0.011 0.001 HIS t 81 PHE 0.015 0.001 PHE p 69 TYR 0.018 0.001 TYR Z 228 ARG 0.006 0.000 ARG W 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 433 time to evaluate : 9.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8189 (ppp) cc_final: 0.7674 (ppp) REVERT: A 319 MET cc_start: 0.7370 (tmm) cc_final: 0.6965 (tpt) REVERT: B 107 MET cc_start: 0.7262 (tpp) cc_final: 0.7040 (tpp) REVERT: B 329 MET cc_start: 0.8986 (mmm) cc_final: 0.8699 (mmm) REVERT: B 372 MET cc_start: 0.7058 (pmm) cc_final: 0.6263 (pmm) REVERT: C 138 MET cc_start: 0.7068 (pmm) cc_final: 0.6839 (pmm) REVERT: C 139 MET cc_start: 0.6382 (mmt) cc_final: 0.6105 (mmt) REVERT: C 368 MET cc_start: 0.8535 (mpp) cc_final: 0.8027 (mpp) REVERT: D 352 MET cc_start: 0.7970 (pmm) cc_final: 0.7510 (pmm) REVERT: E 277 MET cc_start: 0.8907 (mmp) cc_final: 0.8513 (mmp) REVERT: U 206 MET cc_start: 0.7727 (ttm) cc_final: 0.7398 (tpp) REVERT: U 583 MET cc_start: 0.8956 (mmm) cc_final: 0.8657 (mmm) REVERT: U 797 MET cc_start: 0.6237 (tpp) cc_final: 0.5933 (tpp) REVERT: V 100 MET cc_start: 0.8669 (mtm) cc_final: 0.8429 (ptp) REVERT: V 175 MET cc_start: 0.7373 (tpp) cc_final: 0.6981 (ttm) REVERT: V 176 MET cc_start: 0.7580 (tpt) cc_final: 0.7169 (ttt) REVERT: V 192 MET cc_start: 0.8831 (mmt) cc_final: 0.8510 (mmm) REVERT: W 375 MET cc_start: 0.8643 (mmp) cc_final: 0.8357 (mmm) REVERT: W 378 MET cc_start: 0.7994 (pmm) cc_final: 0.7782 (pmm) REVERT: Y 105 MET cc_start: 0.7685 (mmt) cc_final: 0.7296 (mmm) REVERT: Y 228 MET cc_start: 0.8299 (ptp) cc_final: 0.8025 (pmm) REVERT: a 218 MET cc_start: 0.8151 (mtm) cc_final: 0.7535 (ptm) REVERT: a 278 MET cc_start: 0.8625 (ptm) cc_final: 0.8240 (ptm) REVERT: a 280 MET cc_start: 0.7918 (pmm) cc_final: 0.7592 (pmm) REVERT: b 16 MET cc_start: 0.4831 (tpt) cc_final: 0.4223 (mmm) REVERT: d 1 MET cc_start: 0.5306 (mmt) cc_final: 0.4994 (tpp) REVERT: d 75 MET cc_start: 0.8614 (mmp) cc_final: 0.8339 (mmm) REVERT: d 95 MET cc_start: 0.7983 (tmm) cc_final: 0.7525 (ptp) REVERT: f 1 MET cc_start: 0.3997 (ptp) cc_final: 0.3589 (ptp) REVERT: f 27 LYS cc_start: 0.7400 (tttp) cc_final: 0.7109 (ptpp) REVERT: f 209 MET cc_start: 0.1653 (mtp) cc_final: 0.0687 (pmm) REVERT: f 761 MET cc_start: -0.1420 (ptp) cc_final: -0.1621 (ttp) REVERT: p 45 MET cc_start: 0.8459 (mmp) cc_final: 0.8235 (mmt) REVERT: x 255 MET cc_start: 0.4519 (tmm) cc_final: 0.3850 (tmm) REVERT: x 328 MET cc_start: 0.0965 (mpp) cc_final: 0.0645 (mpp) REVERT: x 367 MET cc_start: -0.0036 (mtm) cc_final: -0.0764 (mtt) REVERT: x 488 MET cc_start: -0.0475 (ttt) cc_final: -0.1827 (ptt) REVERT: y 63 LYS cc_start: 0.5332 (mmpt) cc_final: 0.4136 (tmtt) outliers start: 69 outliers final: 32 residues processed: 489 average time/residue: 0.8353 time to fit residues: 739.7603 Evaluate side-chains 464 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 432 time to evaluate : 9.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain V residue 130 PHE Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain X residue 407 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 611 GLN Chi-restraints excluded: chain f residue 872 VAL Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain j residue 237 GLU Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain r residue 45 MET Chi-restraints excluded: chain x residue 453 ASP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1101 optimal weight: 40.0000 chunk 750 optimal weight: 40.0000 chunk 19 optimal weight: 5.9990 chunk 984 optimal weight: 30.0000 chunk 545 optimal weight: 5.9990 chunk 1128 optimal weight: 10.0000 chunk 914 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 675 optimal weight: 30.0000 chunk 1186 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 595 ASN ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 611 GLN ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 150 GLN ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 110905 Z= 0.174 Angle : 0.517 11.653 149826 Z= 0.268 Chirality : 0.040 0.272 16959 Planarity : 0.003 0.060 19324 Dihedral : 4.969 138.375 15245 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 0.84 % Allowed : 11.81 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.37 (0.07), residues: 13777 helix: 1.83 (0.07), residues: 6292 sheet: 0.19 (0.12), residues: 1908 loop : -1.66 (0.08), residues: 5577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP m 215 HIS 0.005 0.001 HIS E 19 PHE 0.016 0.001 PHE p 69 TYR 0.017 0.001 TYR Z 228 ARG 0.006 0.000 ARG V 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 435 time to evaluate : 9.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8198 (ppp) cc_final: 0.7640 (ppp) REVERT: A 319 MET cc_start: 0.7572 (tmm) cc_final: 0.7127 (tpt) REVERT: B 107 MET cc_start: 0.7275 (tpp) cc_final: 0.7031 (tpp) REVERT: B 329 MET cc_start: 0.9014 (mmm) cc_final: 0.8724 (mmm) REVERT: B 372 MET cc_start: 0.7010 (pmm) cc_final: 0.6194 (pmm) REVERT: C 368 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8045 (mpp) REVERT: D 163 MET cc_start: 0.7313 (tpt) cc_final: 0.6970 (tpp) REVERT: D 389 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5741 (mp0) REVERT: E 277 MET cc_start: 0.8926 (mmp) cc_final: 0.8514 (mmp) REVERT: U 153 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8942 (mm) REVERT: U 206 MET cc_start: 0.7719 (ttm) cc_final: 0.7435 (tpp) REVERT: U 583 MET cc_start: 0.9030 (mmm) cc_final: 0.8799 (mmm) REVERT: U 797 MET cc_start: 0.6206 (tpp) cc_final: 0.6003 (tpp) REVERT: V 139 MET cc_start: 0.3332 (mpp) cc_final: 0.3119 (mmp) REVERT: V 175 MET cc_start: 0.7441 (tpp) cc_final: 0.7228 (tpt) REVERT: V 176 MET cc_start: 0.7573 (tpt) cc_final: 0.7141 (ttt) REVERT: V 192 MET cc_start: 0.8835 (mmt) cc_final: 0.8503 (mmm) REVERT: W 375 MET cc_start: 0.8672 (mmp) cc_final: 0.8010 (mmm) REVERT: W 378 MET cc_start: 0.8040 (pmm) cc_final: 0.7740 (mpp) REVERT: W 451 MET cc_start: 0.5696 (tpt) cc_final: 0.5436 (tpt) REVERT: Y 105 MET cc_start: 0.7708 (mmt) cc_final: 0.7305 (mmm) REVERT: Y 228 MET cc_start: 0.8320 (ptp) cc_final: 0.8031 (pmm) REVERT: a 218 MET cc_start: 0.8151 (mtm) cc_final: 0.7505 (ptm) REVERT: a 278 MET cc_start: 0.8603 (ptm) cc_final: 0.8179 (ptm) REVERT: b 16 MET cc_start: 0.4788 (tpt) cc_final: 0.4213 (mmm) REVERT: d 75 MET cc_start: 0.8605 (mmp) cc_final: 0.8334 (mmm) REVERT: f 27 LYS cc_start: 0.7413 (tttp) cc_final: 0.7127 (ptpp) REVERT: f 209 MET cc_start: 0.2121 (mtp) cc_final: 0.1642 (mtm) REVERT: f 761 MET cc_start: -0.1399 (ptp) cc_final: -0.2821 (mpp) REVERT: p 45 MET cc_start: 0.8446 (mmp) cc_final: 0.8226 (mmt) REVERT: x 180 HIS cc_start: 0.3117 (OUTLIER) cc_final: 0.2842 (t-90) REVERT: x 255 MET cc_start: 0.4750 (tmm) cc_final: 0.4054 (ttp) REVERT: x 328 MET cc_start: 0.0839 (mpp) cc_final: 0.0506 (mpp) REVERT: x 367 MET cc_start: 0.0060 (mtm) cc_final: -0.0683 (mtt) REVERT: x 488 MET cc_start: -0.0538 (ttt) cc_final: -0.1901 (ptt) REVERT: y 63 LYS cc_start: 0.5203 (mmpt) cc_final: 0.4069 (tmtt) outliers start: 99 outliers final: 46 residues processed: 515 average time/residue: 0.8542 time to fit residues: 798.6063 Evaluate side-chains 483 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 433 time to evaluate : 9.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain X residue 407 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain b residue 12 ASN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain j residue 237 GLU Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 45 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 169 ASP Chi-restraints excluded: chain x residue 180 HIS Chi-restraints excluded: chain x residue 453 ASP Chi-restraints excluded: chain e residue 61 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 444 optimal weight: 9.9990 chunk 1190 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 776 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 chunk 1323 optimal weight: 0.0970 chunk 1098 optimal weight: 30.0000 chunk 612 optimal weight: 6.9990 chunk 110 optimal weight: 30.0000 chunk 437 optimal weight: 20.0000 chunk 694 optimal weight: 10.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 380 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 ASN a 91 ASN ** a 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 352 HIS ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 GLN x 150 GLN ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 110905 Z= 0.182 Angle : 0.522 10.446 149826 Z= 0.270 Chirality : 0.040 0.356 16959 Planarity : 0.003 0.061 19324 Dihedral : 4.948 133.317 15245 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.73 % Rotamer: Outliers : 0.83 % Allowed : 12.70 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.41 (0.07), residues: 13777 helix: 1.86 (0.07), residues: 6304 sheet: 0.18 (0.12), residues: 1924 loop : -1.64 (0.08), residues: 5549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP m 215 HIS 0.006 0.001 HIS j 154 PHE 0.017 0.001 PHE p 69 TYR 0.017 0.001 TYR Z 228 ARG 0.009 0.000 ARG W 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 435 time to evaluate : 9.500 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 138 MET cc_start: 0.8144 (ppp) cc_final: 0.7560 (ppp) REVERT: A 319 MET cc_start: 0.7620 (tmm) cc_final: 0.7137 (tpt) REVERT: A 362 MET cc_start: 0.0809 (pmm) cc_final: -0.0091 (pmm) REVERT: B 107 MET cc_start: 0.7317 (tpp) cc_final: 0.7084 (tpp) REVERT: B 329 MET cc_start: 0.9008 (mmm) cc_final: 0.8730 (mmm) REVERT: B 372 MET cc_start: 0.6997 (pmm) cc_final: 0.6161 (pmm) REVERT: C 220 VAL cc_start: 0.7209 (OUTLIER) cc_final: 0.6975 (t) REVERT: C 368 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8009 (mpp) REVERT: D 163 MET cc_start: 0.7326 (tpt) cc_final: 0.7049 (tpp) REVERT: D 352 MET cc_start: 0.8009 (pmm) cc_final: 0.7203 (pmm) REVERT: D 389 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5697 (mp0) REVERT: E 277 MET cc_start: 0.8903 (mmp) cc_final: 0.8473 (mmp) REVERT: R 100 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7513 (mtm) REVERT: U 153 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8958 (mm) REVERT: U 206 MET cc_start: 0.7722 (ttm) cc_final: 0.7458 (tpp) REVERT: U 797 MET cc_start: 0.6289 (tpp) cc_final: 0.6080 (tpp) REVERT: V 192 MET cc_start: 0.8834 (mmt) cc_final: 0.8481 (mmm) REVERT: W 375 MET cc_start: 0.8738 (mmp) cc_final: 0.8246 (mmp) REVERT: W 378 MET cc_start: 0.8087 (pmm) cc_final: 0.7865 (mpp) REVERT: W 451 MET cc_start: 0.5789 (tpt) cc_final: 0.5483 (tpt) REVERT: Y 105 MET cc_start: 0.7733 (mmt) cc_final: 0.7301 (mmm) REVERT: Y 228 MET cc_start: 0.8329 (ptp) cc_final: 0.8089 (pmm) REVERT: a 218 MET cc_start: 0.8062 (mtm) cc_final: 0.7457 (ptm) REVERT: a 278 MET cc_start: 0.8653 (ptm) cc_final: 0.8182 (ptm) REVERT: b 16 MET cc_start: 0.4769 (tpt) cc_final: 0.4381 (mmm) REVERT: d 75 MET cc_start: 0.8609 (mmp) cc_final: 0.8331 (mmm) REVERT: d 95 MET cc_start: 0.7959 (tmm) cc_final: 0.7480 (ptp) REVERT: f 27 LYS cc_start: 0.7417 (tttp) cc_final: 0.7125 (ptpp) REVERT: f 209 MET cc_start: 0.2115 (mtp) cc_final: 0.0890 (pmm) REVERT: f 659 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.3709 (tp) REVERT: f 761 MET cc_start: -0.1452 (ptp) cc_final: -0.2771 (mpp) REVERT: p 45 MET cc_start: 0.8457 (mmp) cc_final: 0.8199 (mmt) REVERT: x 180 HIS cc_start: 0.3114 (OUTLIER) cc_final: 0.2833 (t-90) REVERT: x 255 MET cc_start: 0.4810 (tmm) cc_final: 0.4052 (ttp) REVERT: x 328 MET cc_start: 0.0926 (mpp) cc_final: 0.0609 (mpp) REVERT: x 367 MET cc_start: 0.0040 (mtm) cc_final: -0.0707 (mtt) REVERT: x 488 MET cc_start: -0.0567 (ttt) cc_final: -0.1970 (ptt) outliers start: 98 outliers final: 61 residues processed: 513 average time/residue: 0.8281 time to fit residues: 772.1459 Evaluate side-chains 500 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 432 time to evaluate : 9.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain X residue 407 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Z residue 82 PHE Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain b residue 12 ASN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 611 GLN Chi-restraints excluded: chain f residue 659 LEU Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain j residue 237 GLU Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 14 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 45 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 169 ASP Chi-restraints excluded: chain t residue 108 ASN Chi-restraints excluded: chain x residue 180 HIS Chi-restraints excluded: chain x residue 453 ASP Chi-restraints excluded: chain e residue 61 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1276 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 chunk 754 optimal weight: 7.9990 chunk 966 optimal weight: 0.8980 chunk 748 optimal weight: 5.9990 chunk 1114 optimal weight: 5.9990 chunk 739 optimal weight: 5.9990 chunk 1318 optimal weight: 6.9990 chunk 825 optimal weight: 20.0000 chunk 803 optimal weight: 30.0000 chunk 608 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 57 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 380 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 ASN ** a 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 150 GLN ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 110905 Z= 0.171 Angle : 0.526 12.125 149826 Z= 0.269 Chirality : 0.040 0.277 16959 Planarity : 0.003 0.061 19324 Dihedral : 4.913 128.184 15245 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.27 % Favored : 93.67 % Rotamer: Outliers : 0.93 % Allowed : 13.19 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.45 (0.07), residues: 13777 helix: 1.89 (0.07), residues: 6312 sheet: 0.21 (0.12), residues: 1936 loop : -1.64 (0.08), residues: 5529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP m 215 HIS 0.004 0.001 HIS E 19 PHE 0.037 0.001 PHE V 130 TYR 0.016 0.001 TYR Z 228 ARG 0.006 0.000 ARG W 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 434 time to evaluate : 9.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8086 (ppp) cc_final: 0.7492 (ppp) REVERT: A 319 MET cc_start: 0.7660 (tmm) cc_final: 0.7171 (tpt) REVERT: A 362 MET cc_start: 0.0940 (pmm) cc_final: 0.0139 (pmm) REVERT: B 107 MET cc_start: 0.7214 (tpp) cc_final: 0.6950 (tpp) REVERT: B 329 MET cc_start: 0.9001 (mmm) cc_final: 0.8715 (mmm) REVERT: B 372 MET cc_start: 0.6967 (pmm) cc_final: 0.6313 (pmm) REVERT: C 368 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8000 (mpp) REVERT: D 163 MET cc_start: 0.7312 (tpt) cc_final: 0.7040 (tpp) REVERT: D 352 MET cc_start: 0.8088 (pmm) cc_final: 0.7326 (pmm) REVERT: D 389 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5722 (mp0) REVERT: E 277 MET cc_start: 0.8882 (mmp) cc_final: 0.8501 (mmp) REVERT: E 368 MET cc_start: 0.9169 (ptt) cc_final: 0.8934 (mmt) REVERT: F 215 LEU cc_start: 0.3042 (OUTLIER) cc_final: 0.2617 (tp) REVERT: R 100 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7453 (mtm) REVERT: U 153 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8965 (mm) REVERT: V 192 MET cc_start: 0.8841 (mmt) cc_final: 0.8490 (mmm) REVERT: W 366 MET cc_start: 0.9067 (ptp) cc_final: 0.8210 (ppp) REVERT: W 375 MET cc_start: 0.8747 (mmp) cc_final: 0.8370 (mmp) REVERT: W 451 MET cc_start: 0.5796 (tpt) cc_final: 0.5460 (tpt) REVERT: Y 105 MET cc_start: 0.7742 (mmt) cc_final: 0.7287 (mmm) REVERT: Y 228 MET cc_start: 0.8344 (ptp) cc_final: 0.8107 (pmm) REVERT: a 218 MET cc_start: 0.8056 (mtm) cc_final: 0.7476 (ptm) REVERT: a 278 MET cc_start: 0.8655 (ptm) cc_final: 0.8406 (ptm) REVERT: d 75 MET cc_start: 0.8610 (mmp) cc_final: 0.8320 (mmm) REVERT: d 95 MET cc_start: 0.7947 (tmm) cc_final: 0.7469 (ptp) REVERT: f 27 LYS cc_start: 0.7406 (tttp) cc_final: 0.7111 (ptpp) REVERT: f 209 MET cc_start: 0.2151 (mtp) cc_final: 0.0939 (pmm) REVERT: f 659 LEU cc_start: 0.4201 (OUTLIER) cc_final: 0.3721 (tp) REVERT: f 761 MET cc_start: -0.1471 (ptp) cc_final: -0.2785 (mpp) REVERT: p 45 MET cc_start: 0.8449 (mmp) cc_final: 0.8188 (mmt) REVERT: x 180 HIS cc_start: 0.3093 (OUTLIER) cc_final: 0.2824 (t-90) REVERT: x 255 MET cc_start: 0.4849 (tmm) cc_final: 0.4038 (ttp) REVERT: x 328 MET cc_start: 0.0943 (mpp) cc_final: 0.0648 (mpp) REVERT: x 367 MET cc_start: 0.0050 (mtm) cc_final: -0.0669 (mtt) REVERT: x 488 MET cc_start: -0.0645 (ttt) cc_final: -0.2033 (ptt) REVERT: y 56 LEU cc_start: 0.1813 (mt) cc_final: 0.1561 (tp) outliers start: 110 outliers final: 67 residues processed: 521 average time/residue: 0.8820 time to fit residues: 831.9201 Evaluate side-chains 507 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 433 time to evaluate : 9.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain X residue 407 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Z residue 82 PHE Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 288 HIS Chi-restraints excluded: chain b residue 12 ASN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 659 LEU Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain j residue 237 GLU Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 14 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 169 ASP Chi-restraints excluded: chain t residue 108 ASN Chi-restraints excluded: chain x residue 180 HIS Chi-restraints excluded: chain x residue 453 ASP Chi-restraints excluded: chain e residue 61 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 815 optimal weight: 8.9990 chunk 526 optimal weight: 7.9990 chunk 787 optimal weight: 20.0000 chunk 397 optimal weight: 8.9990 chunk 259 optimal weight: 4.9990 chunk 255 optimal weight: 30.0000 chunk 838 optimal weight: 30.0000 chunk 898 optimal weight: 30.0000 chunk 651 optimal weight: 8.9990 chunk 122 optimal weight: 40.0000 chunk 1036 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 GLN ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 380 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 150 GLN ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 110905 Z= 0.235 Angle : 0.570 15.698 149826 Z= 0.293 Chirality : 0.041 0.385 16959 Planarity : 0.004 0.061 19324 Dihedral : 5.013 119.707 15245 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 0.88 % Allowed : 13.77 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.38 (0.07), residues: 13777 helix: 1.81 (0.07), residues: 6304 sheet: 0.19 (0.12), residues: 1897 loop : -1.64 (0.08), residues: 5576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP W 80 HIS 0.006 0.001 HIS V 400 PHE 0.023 0.001 PHE V 130 TYR 0.017 0.001 TYR x 115 ARG 0.006 0.000 ARG W 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 434 time to evaluate : 9.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8067 (ppp) cc_final: 0.7452 (ppp) REVERT: A 332 MET cc_start: 0.7492 (mmt) cc_final: 0.7177 (mpp) REVERT: A 362 MET cc_start: 0.0787 (pmm) cc_final: 0.0531 (pmm) REVERT: B 107 MET cc_start: 0.7241 (tpp) cc_final: 0.6955 (tpp) REVERT: B 329 MET cc_start: 0.9010 (mmm) cc_final: 0.8747 (mmm) REVERT: C 368 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8086 (mpp) REVERT: C 399 MET cc_start: 0.8700 (tpp) cc_final: 0.8477 (tpp) REVERT: D 352 MET cc_start: 0.8071 (pmm) cc_final: 0.7320 (pmm) REVERT: D 389 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5729 (mp0) REVERT: E 277 MET cc_start: 0.8931 (mmp) cc_final: 0.8574 (mmp) REVERT: E 368 MET cc_start: 0.9178 (ptt) cc_final: 0.8927 (mmt) REVERT: F 215 LEU cc_start: 0.3169 (OUTLIER) cc_final: 0.2737 (tp) REVERT: I 201 MET cc_start: 0.7964 (mtm) cc_final: 0.7145 (mtm) REVERT: M 75 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.6934 (tpt) REVERT: R 100 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: U 153 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8985 (mm) REVERT: U 583 MET cc_start: 0.9138 (mmm) cc_final: 0.8704 (mmm) REVERT: V 176 MET cc_start: 0.6483 (tpt) cc_final: 0.6100 (tpt) REVERT: V 192 MET cc_start: 0.8833 (mmt) cc_final: 0.8421 (mmm) REVERT: W 16 MET cc_start: -0.2290 (mmt) cc_final: -0.2995 (tpt) REVERT: W 366 MET cc_start: 0.9063 (ptp) cc_final: 0.8500 (ppp) REVERT: W 451 MET cc_start: 0.5734 (tpt) cc_final: 0.5355 (tpt) REVERT: Y 105 MET cc_start: 0.7799 (mmt) cc_final: 0.7333 (mmm) REVERT: Y 228 MET cc_start: 0.8345 (ptp) cc_final: 0.8081 (pmm) REVERT: a 218 MET cc_start: 0.8053 (mtm) cc_final: 0.7505 (ptm) REVERT: a 278 MET cc_start: 0.8648 (ptm) cc_final: 0.8394 (ptm) REVERT: d 75 MET cc_start: 0.8590 (mmp) cc_final: 0.8296 (mmm) REVERT: f 27 LYS cc_start: 0.7442 (tttp) cc_final: 0.7146 (ptpp) REVERT: f 209 MET cc_start: 0.2165 (mtp) cc_final: 0.0894 (pmm) REVERT: f 659 LEU cc_start: 0.4187 (OUTLIER) cc_final: 0.3696 (tp) REVERT: f 761 MET cc_start: -0.1497 (ptp) cc_final: -0.2807 (mpp) REVERT: p 45 MET cc_start: 0.8454 (mmp) cc_final: 0.8168 (mmt) REVERT: x 180 HIS cc_start: 0.2982 (OUTLIER) cc_final: 0.2720 (t-90) REVERT: x 255 MET cc_start: 0.4849 (tmm) cc_final: 0.4418 (tmm) REVERT: x 328 MET cc_start: 0.1010 (mpp) cc_final: 0.0738 (mpp) REVERT: x 367 MET cc_start: 0.0082 (mtm) cc_final: -0.0655 (mtt) outliers start: 104 outliers final: 72 residues processed: 514 average time/residue: 0.8272 time to fit residues: 772.4177 Evaluate side-chains 514 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 434 time to evaluate : 8.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain X residue 407 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Z residue 82 PHE Chi-restraints excluded: chain a residue 156 TYR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 288 HIS Chi-restraints excluded: chain a residue 373 ASP Chi-restraints excluded: chain b residue 12 ASN Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 659 LEU Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain j residue 237 GLU Chi-restraints excluded: chain k residue 182 GLN Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain n residue 184 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 14 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 45 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain t residue 108 ASN Chi-restraints excluded: chain x residue 180 HIS Chi-restraints excluded: chain x residue 453 ASP Chi-restraints excluded: chain e residue 61 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1199 optimal weight: 6.9990 chunk 1263 optimal weight: 9.9990 chunk 1152 optimal weight: 20.0000 chunk 1228 optimal weight: 20.0000 chunk 1262 optimal weight: 8.9990 chunk 739 optimal weight: 7.9990 chunk 535 optimal weight: 20.0000 chunk 964 optimal weight: 20.0000 chunk 377 optimal weight: 8.9990 chunk 1110 optimal weight: 8.9990 chunk 1162 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 611 ASN ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 146 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 363 ASN ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 110905 Z= 0.238 Angle : 0.576 14.116 149826 Z= 0.295 Chirality : 0.041 0.281 16959 Planarity : 0.004 0.060 19324 Dihedral : 5.052 110.484 15245 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.63 % Favored : 93.32 % Rotamer: Outliers : 0.84 % Allowed : 14.18 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.33 (0.07), residues: 13777 helix: 1.76 (0.07), residues: 6320 sheet: 0.14 (0.12), residues: 1910 loop : -1.65 (0.08), residues: 5547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP m 215 HIS 0.006 0.001 HIS X 178 PHE 0.019 0.001 PHE V 130 TYR 0.016 0.001 TYR Z 228 ARG 0.005 0.000 ARG b 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 432 time to evaluate : 9.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8022 (ppp) cc_final: 0.7402 (ppp) REVERT: A 332 MET cc_start: 0.7556 (mmt) cc_final: 0.7247 (mpp) REVERT: A 362 MET cc_start: 0.0563 (pmm) cc_final: 0.0266 (pmm) REVERT: B 107 MET cc_start: 0.7212 (tpp) cc_final: 0.6953 (tpp) REVERT: B 329 MET cc_start: 0.9010 (mmm) cc_final: 0.8735 (mmm) REVERT: C 368 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8093 (mpp) REVERT: C 399 MET cc_start: 0.8731 (tpp) cc_final: 0.8507 (tpp) REVERT: D 352 MET cc_start: 0.8073 (pmm) cc_final: 0.7365 (pmm) REVERT: D 389 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5707 (mp0) REVERT: E 277 MET cc_start: 0.8935 (mmp) cc_final: 0.8570 (mmp) REVERT: E 368 MET cc_start: 0.9171 (ptt) cc_final: 0.8899 (mmt) REVERT: F 215 LEU cc_start: 0.3147 (OUTLIER) cc_final: 0.2703 (tp) REVERT: I 201 MET cc_start: 0.7929 (mtm) cc_final: 0.7106 (mtm) REVERT: J 224 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: M 75 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.6943 (tpt) REVERT: R 100 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7452 (mtm) REVERT: U 153 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9008 (mm) REVERT: U 583 MET cc_start: 0.9135 (mmm) cc_final: 0.8691 (mmm) REVERT: U 725 MET cc_start: 0.8061 (ppp) cc_final: 0.7722 (ppp) REVERT: V 192 MET cc_start: 0.8842 (mmt) cc_final: 0.8415 (mmm) REVERT: W 16 MET cc_start: -0.2304 (mmt) cc_final: -0.3015 (tpt) REVERT: W 366 MET cc_start: 0.8935 (ptp) cc_final: 0.8551 (ppp) REVERT: W 451 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.5046 (tpt) REVERT: Y 105 MET cc_start: 0.7838 (mmt) cc_final: 0.7379 (mmm) REVERT: Y 228 MET cc_start: 0.8387 (ptp) cc_final: 0.8094 (pmm) REVERT: a 218 MET cc_start: 0.8065 (mtm) cc_final: 0.7502 (ptm) REVERT: a 278 MET cc_start: 0.8643 (ptm) cc_final: 0.8389 (ptm) REVERT: a 365 MET cc_start: 0.8401 (ppp) cc_final: 0.8113 (tmm) REVERT: b 16 MET cc_start: 0.4760 (tpt) cc_final: 0.4454 (mmm) REVERT: d 75 MET cc_start: 0.8594 (mmp) cc_final: 0.8294 (mmm) REVERT: d 95 MET cc_start: 0.7967 (tmm) cc_final: 0.7481 (ptp) REVERT: f 27 LYS cc_start: 0.7442 (tttp) cc_final: 0.7144 (ptpp) REVERT: f 659 LEU cc_start: 0.4224 (OUTLIER) cc_final: 0.3744 (tp) REVERT: f 761 MET cc_start: -0.1628 (ptp) cc_final: -0.2879 (mpp) REVERT: f 771 LEU cc_start: -0.3857 (OUTLIER) cc_final: -0.4554 (mt) REVERT: p 45 MET cc_start: 0.8451 (mmp) cc_final: 0.8169 (mmt) REVERT: x 116 MET cc_start: 0.6022 (tmm) cc_final: 0.5448 (ptp) REVERT: x 180 HIS cc_start: 0.2913 (OUTLIER) cc_final: 0.2647 (t-90) REVERT: x 255 MET cc_start: 0.4741 (tmm) cc_final: 0.4276 (tmm) REVERT: x 328 MET cc_start: 0.1010 (mpp) cc_final: 0.0759 (mpp) REVERT: x 367 MET cc_start: -0.0148 (mtm) cc_final: -0.0760 (mtt) REVERT: y 56 LEU cc_start: 0.1857 (mt) cc_final: 0.1645 (tp) outliers start: 99 outliers final: 73 residues processed: 510 average time/residue: 0.8560 time to fit residues: 789.7100 Evaluate side-chains 515 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 431 time to evaluate : 9.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 229 VAL Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain X residue 407 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Z residue 82 PHE Chi-restraints excluded: chain a residue 156 TYR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 288 HIS Chi-restraints excluded: chain b residue 12 ASN Chi-restraints excluded: chain b residue 148 VAL Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 659 LEU Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain j residue 237 GLU Chi-restraints excluded: chain k residue 182 GLN Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 14 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 45 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 169 ASP Chi-restraints excluded: chain t residue 108 ASN Chi-restraints excluded: chain x residue 180 HIS Chi-restraints excluded: chain x residue 453 ASP Chi-restraints excluded: chain e residue 61 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1224 optimal weight: 3.9990 chunk 806 optimal weight: 30.0000 chunk 1299 optimal weight: 20.0000 chunk 793 optimal weight: 20.0000 chunk 616 optimal weight: 6.9990 chunk 903 optimal weight: 8.9990 chunk 1362 optimal weight: 0.9980 chunk 1254 optimal weight: 8.9990 chunk 1085 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 838 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 273 GLN ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 GLN ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 110905 Z= 0.189 Angle : 0.559 13.529 149826 Z= 0.284 Chirality : 0.041 0.354 16959 Planarity : 0.003 0.060 19324 Dihedral : 4.979 103.418 15245 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 0.76 % Allowed : 14.35 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.37 (0.07), residues: 13777 helix: 1.81 (0.07), residues: 6310 sheet: 0.17 (0.12), residues: 1918 loop : -1.65 (0.08), residues: 5549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP m 215 HIS 0.005 0.001 HIS X 178 PHE 0.019 0.001 PHE V 130 TYR 0.016 0.001 TYR Z 228 ARG 0.005 0.000 ARG W 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27554 Ramachandran restraints generated. 13777 Oldfield, 0 Emsley, 13777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 431 time to evaluate : 9.578 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 138 MET cc_start: 0.7997 (ppp) cc_final: 0.7376 (ppp) REVERT: A 362 MET cc_start: 0.0607 (pmm) cc_final: 0.0311 (pmm) REVERT: B 107 MET cc_start: 0.7148 (tpp) cc_final: 0.6848 (tpp) REVERT: B 329 MET cc_start: 0.9008 (mmm) cc_final: 0.8739 (mmm) REVERT: C 139 MET cc_start: 0.6209 (mmt) cc_final: 0.5924 (mpp) REVERT: C 368 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8037 (mpp) REVERT: D 352 MET cc_start: 0.8030 (pmm) cc_final: 0.7344 (pmm) REVERT: D 389 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5809 (mp0) REVERT: E 277 MET cc_start: 0.8938 (mmp) cc_final: 0.8581 (mmp) REVERT: E 368 MET cc_start: 0.9181 (ptt) cc_final: 0.8913 (mmt) REVERT: F 215 LEU cc_start: 0.3101 (OUTLIER) cc_final: 0.2664 (tp) REVERT: M 75 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6994 (tpt) REVERT: N 95 MET cc_start: 0.7928 (tpp) cc_final: 0.7489 (mmm) REVERT: R 100 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7417 (mtm) REVERT: U 153 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8995 (mm) REVERT: U 583 MET cc_start: 0.9122 (mmm) cc_final: 0.8659 (mmm) REVERT: U 725 MET cc_start: 0.8056 (ppp) cc_final: 0.7733 (ppp) REVERT: V 192 MET cc_start: 0.8848 (mmt) cc_final: 0.8412 (mmm) REVERT: W 16 MET cc_start: -0.2342 (mmt) cc_final: -0.3051 (tpt) REVERT: W 366 MET cc_start: 0.8952 (ptp) cc_final: 0.8538 (ppp) REVERT: W 451 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.5044 (tpt) REVERT: Y 105 MET cc_start: 0.7805 (mmt) cc_final: 0.7335 (mmm) REVERT: Y 228 MET cc_start: 0.8360 (ptp) cc_final: 0.8070 (pmm) REVERT: a 218 MET cc_start: 0.8054 (mtm) cc_final: 0.7305 (ptp) REVERT: a 278 MET cc_start: 0.8640 (ptm) cc_final: 0.8383 (ptm) REVERT: a 365 MET cc_start: 0.8447 (ppp) cc_final: 0.8174 (tmm) REVERT: b 16 MET cc_start: 0.4822 (tpt) cc_final: 0.4472 (mmm) REVERT: d 75 MET cc_start: 0.8601 (mmp) cc_final: 0.8305 (mmm) REVERT: d 95 MET cc_start: 0.7941 (tmm) cc_final: 0.7451 (ptp) REVERT: f 27 LYS cc_start: 0.7479 (tttp) cc_final: 0.7184 (ptpp) REVERT: f 209 MET cc_start: 0.2416 (mtp) cc_final: 0.1422 (pmm) REVERT: f 524 MET cc_start: 0.4467 (ppp) cc_final: 0.4227 (ppp) REVERT: f 659 LEU cc_start: 0.4234 (OUTLIER) cc_final: 0.3746 (tp) REVERT: f 761 MET cc_start: -0.1929 (ptp) cc_final: -0.2988 (mpp) REVERT: f 771 LEU cc_start: -0.3904 (OUTLIER) cc_final: -0.4457 (mt) REVERT: j 217 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6854 (tt) REVERT: p 45 MET cc_start: 0.8448 (mmp) cc_final: 0.8166 (mmt) REVERT: x 116 MET cc_start: 0.6019 (tmm) cc_final: 0.5414 (ptp) REVERT: x 255 MET cc_start: 0.4681 (tmm) cc_final: 0.4224 (tmm) REVERT: x 328 MET cc_start: 0.0986 (OUTLIER) cc_final: 0.0749 (mpp) REVERT: x 367 MET cc_start: -0.0128 (mtm) cc_final: -0.0812 (mtt) REVERT: y 56 LEU cc_start: 0.1734 (mt) cc_final: 0.1507 (tp) outliers start: 90 outliers final: 69 residues processed: 498 average time/residue: 0.8651 time to fit residues: 782.8843 Evaluate side-chains 511 residues out of total 11862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 431 time to evaluate : 9.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 229 VAL Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain X residue 407 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Z residue 82 PHE Chi-restraints excluded: chain a residue 156 TYR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 288 HIS Chi-restraints excluded: chain b residue 12 ASN Chi-restraints excluded: chain c residue 248 MET Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 659 LEU Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 884 THR Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain j residue 237 GLU Chi-restraints excluded: chain k residue 182 GLN Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 14 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 45 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 169 ASP Chi-restraints excluded: chain t residue 108 ASN Chi-restraints excluded: chain x residue 328 MET Chi-restraints excluded: chain x residue 453 ASP Chi-restraints excluded: chain e residue 61 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 665 optimal weight: 0.9990 chunk 862 optimal weight: 10.0000 chunk 1156 optimal weight: 0.8980 chunk 332 optimal weight: 40.0000 chunk 1000 optimal weight: 40.0000 chunk 160 optimal weight: 30.0000 chunk 301 optimal weight: 8.9990 chunk 1086 optimal weight: 40.0000 chunk 454 optimal weight: 6.9990 chunk 1116 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 380 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 888 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 301 GLN ** y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.035201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.028985 restraints weight = 2162807.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.029400 restraints weight = 1158623.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.029614 restraints weight = 734760.554| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 110905 Z= 0.158 Angle : 0.551 20.765 149826 Z= 0.278 Chirality : 0.040 0.233 16959 Planarity : 0.003 0.061 19324 Dihedral : 4.862 92.513 15245 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 0.76 % Allowed : 14.44 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.45 (0.07), residues: 13777 helix: 1.88 (0.07), residues: 6312 sheet: 0.20 (0.12), residues: 1915 loop : -1.61 (0.08), residues: 5550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP m 215 HIS 0.012 0.001 HIS F 417 PHE 0.018 0.001 PHE V 130 TYR 0.016 0.001 TYR Z 228 ARG 0.005 0.000 ARG W 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16673.74 seconds wall clock time: 299 minutes 2.35 seconds (17942.35 seconds total)