Starting phenix.real_space_refine on Mon Mar 11 04:56:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3b_32276/03_2024/7w3b_32276_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3b_32276/03_2024/7w3b_32276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3b_32276/03_2024/7w3b_32276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3b_32276/03_2024/7w3b_32276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3b_32276/03_2024/7w3b_32276_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3b_32276/03_2024/7w3b_32276_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 631 5.16 5 C 69192 2.51 5 N 18795 2.21 5 O 20811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 212": "OE1" <-> "OE2" Residue "Y TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 181": "OE1" <-> "OE2" Residue "s GLU 116": "OE1" <-> "OE2" Residue "s PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 109441 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 389} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3122 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 377} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 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: "v" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 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: 39.95, per 1000 atoms: 0.37 Number of scatterers: 109441 At special positions: 0 Unit cell: (332.225, 222.625, 212.35, 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 631 16.00 P 11 15.00 O 20811 8.00 N 18795 7.00 C 69192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 270 " distance=2.04 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.30 Conformation dependent library (CDL) restraints added in 14.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26066 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: 498 helices and 91 sheets defined 54.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 51.70 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 4.623A pdb=" N TYR A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 78 through 85 removed outlier: 4.422A pdb=" N ASP A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 160 through 166 removed outlier: 4.148A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.740A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 180 through 197 Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 221 through 231 removed outlier: 4.261A pdb=" N CYS A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 5.072A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.634A pdb=" N ARG A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.518A pdb=" N ASP A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 363 removed outlier: 5.439A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.254A 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: 4.199A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'B' and resid 58 through 86 Processing helix chain 'B' and resid 88 through 104 removed outlier: 6.179A pdb=" N GLN B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 removed outlier: 4.254A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 207 removed outlier: 3.716A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 208 through 215 removed outlier: 5.208A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 removed outlier: 4.635A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 6.903A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.243A 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 277 Processing helix chain 'B' and resid 287 through 292 removed outlier: 4.174A pdb=" N GLY B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 287 through 292' Processing helix chain 'B' and resid 299 through 318 removed outlier: 4.493A pdb=" N ARG B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.176A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.406A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 415 through 426 removed outlier: 3.938A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 68 removed outlier: 6.046A pdb=" N ARG C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.520A pdb=" N MET C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 140' Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.381A pdb=" N ILE C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.392A 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 196 through 208 removed outlier: 4.684A pdb=" N ASP C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 242 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.416A pdb=" N ILE C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY C 255 " --> pdb=" O ILE C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 266 through 281 removed outlier: 6.576A pdb=" N GLN C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 4.493A pdb=" N LEU C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 302 through 307' Processing helix chain 'C' and resid 321 through 337 removed outlier: 4.194A pdb=" N LYS C 335 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET C 336 " --> pdb=" O HIS C 332 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASN C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.089A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 5.645A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 4.174A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 85 removed outlier: 4.026A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 removed outlier: 4.357A pdb=" N LYS D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 279 through 297 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.696A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 removed outlier: 6.442A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 365 removed outlier: 5.595A pdb=" N VAL D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 360 through 365' Processing helix chain 'D' and resid 371 through 390 Processing helix chain 'D' and resid 395 through 408 removed outlier: 6.761A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 4.404A pdb=" N ILE D 167 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 removed outlier: 4.395A pdb=" N PHE D 235 " --> pdb=" O GLY D 232 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL D 236 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 52 removed outlier: 4.265A pdb=" N TYR E 12 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS E 14 " --> pdb=" O GLN E 10 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS E 15 " --> pdb=" O ASP E 11 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.168A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 93' Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.707A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 4.377A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 163 removed outlier: 3.722A pdb=" N VAL E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY E 163 " --> pdb=" O PHE E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 removed outlier: 4.790A pdb=" N LEU E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.226A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 removed outlier: 4.327A pdb=" N ARG E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 305 through 319 removed outlier: 5.600A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Proline residue: E 319 - end of helix Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 358 removed outlier: 5.211A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 382 removed outlier: 3.732A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 removed outlier: 5.955A pdb=" N ILE E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP E 205 " --> pdb=" O SER E 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 205' Processing helix chain 'F' and resid 25 through 34 removed outlier: 3.629A pdb=" N GLU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 84 removed outlier: 4.169A pdb=" N ARG F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.864A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 169 through 177 removed outlier: 5.446A pdb=" N VAL F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.328A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.583A 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 202 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 209 through 216 removed outlier: 5.339A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 252 through 258 removed outlier: 5.191A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.785A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 4.412A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 319 removed outlier: 6.621A pdb=" N ARG F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG F 308 " --> pdb=" O ARG F 304 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 removed outlier: 4.397A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET F 373 " --> pdb=" O HIS F 369 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 5.232A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.886A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.255A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.188A 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: 3.798A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.204A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.656A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.090A pdb=" N ILE G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 6.265A 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: 3.697A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 12 removed outlier: 5.779A pdb=" N ASP G 10 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG G 11 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 4.786A 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 9 removed outlier: 4.303A pdb=" N PHE H 8 " --> pdb=" O ARG H 4 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 4.173A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.660A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 86 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.909A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 removed outlier: 3.589A pdb=" N GLY H 170 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.269A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.707A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 102 removed outlier: 3.589A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 removed outlier: 3.780A pdb=" N TYR h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.923A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 209 removed outlier: 4.258A pdb=" N ILE h 208 " --> pdb=" O THR h 204 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU h 209 " --> pdb=" O GLU h 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 204 through 209' Processing helix chain 'h' and resid 222 through 234 Processing helix chain 'I' and resid 18 through 32 removed outlier: 5.472A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY I 29 " --> pdb=" O MET I 25 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.504A 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: 3.761A pdb=" N ILE I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.761A pdb=" N GLN I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 202 removed outlier: 5.379A pdb=" N ASP I 202 " --> pdb=" O ASN I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 4.157A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 251 Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.789A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 4.453A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.732A 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: 3.753A pdb=" N TYR J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.760A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 removed outlier: 3.717A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 5.411A 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 200 removed outlier: 3.644A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN J 200 " --> pdb=" O LEU J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 Processing helix chain 'j' and resid 16 through 29 removed outlier: 3.762A pdb=" N LYS j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.231A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.413A 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 removed outlier: 3.717A pdb=" N ILE j 82 " --> pdb=" O ALA j 78 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.911A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 4.151A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN j 175 " --> pdb=" O PHE j 171 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 182 Processing helix chain 'j' and resid 183 through 199 removed outlier: 4.154A pdb=" N GLU j 197 " --> pdb=" O LYS j 193 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 4 through 9 removed outlier: 4.300A pdb=" N TYR K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 35 removed outlier: 4.369A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.353A pdb=" N ILE K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 65' Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.810A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 122 removed outlier: 4.121A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.676A pdb=" N GLN K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 230 through 241 removed outlier: 4.826A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 8 removed outlier: 4.404A pdb=" N ASN L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 removed outlier: 3.733A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 5.159A 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: 4.209A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 165 through 180 removed outlier: 5.609A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.959A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 3.903A pdb=" N VAL L 210 " --> pdb=" O THR L 206 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER L 211 " --> pdb=" O THR L 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 211' Processing helix chain 'L' and resid 225 through 236 removed outlier: 4.604A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 4.117A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 4.014A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 124 removed outlier: 4.046A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 3.971A pdb=" N THR M 174 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 185 removed outlier: 4.062A pdb=" N MET M 184 " --> pdb=" O GLN M 180 " (cutoff:3.500A) removed outlier: 5.842A 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: 4.271A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 91 removed outlier: 3.627A pdb=" N TYR N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.607A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 4.041A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.626A pdb=" N VAL O 137 " --> pdb=" O ALA O 133 " (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: 3.727A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 Processing helix chain 'o' and resid 147 through 166 Processing helix chain 'P' and resid 2 through 8 removed outlier: 3.825A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.204A 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: 3.675A pdb=" N LEU P 73 " --> pdb=" O PHE P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.207A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 3.895A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 3.655A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 5.034A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 79 removed outlier: 3.554A pdb=" N ARG p 70 " --> pdb=" O ARG p 66 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.233A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 3.796A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 3.869A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 72 removed outlier: 6.480A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 95 removed outlier: 4.215A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG Q 95 " --> pdb=" O CYS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.676A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.616A 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 'q' and resid 50 through 72 removed outlier: 6.624A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 95 removed outlier: 4.316A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG q 95 " --> pdb=" O CYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.766A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 5.029A 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 91 removed outlier: 3.975A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 4.013A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 3.993A 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: 3.688A pdb=" N GLU R 197 " --> pdb=" O ALA R 193 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 91 removed outlier: 4.149A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 4.296A pdb=" N GLY r 137 " --> pdb=" O VAL r 133 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL r 138 " --> pdb=" O TYR r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 201 Processing helix chain 'S' and resid 57 through 80 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.866A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.230A 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: 3.682A pdb=" N PHE S 179 " --> pdb=" O VAL S 175 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE S 180 " --> pdb=" O LYS S 176 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU S 184 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 4.317A 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: 3.877A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.285A 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: 3.882A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.601A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 157 removed outlier: 4.377A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.635A pdb=" N LYS T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 5.009A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 209 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.548A pdb=" N PHE t 60 " --> pdb=" O ASP t 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.783A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 157 removed outlier: 4.482A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 4.782A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'U' and resid 7 through 14 removed outlier: 3.935A pdb=" N ASP U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 31 removed outlier: 3.910A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 52 removed outlier: 4.455A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP U 43 " --> pdb=" O SER U 39 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS U 44 " --> pdb=" O GLU U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 removed outlier: 4.168A pdb=" N SER U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 92 removed outlier: 3.869A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP U 92 " --> pdb=" O PHE U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 119 removed outlier: 3.784A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.767A pdb=" N ASN U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS U 136 " --> pdb=" O GLY U 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 3.637A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 4.175A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 187 Processing helix chain 'U' and resid 190 through 208 removed outlier: 3.564A pdb=" N ARG U 194 " --> pdb=" O ASN U 190 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE U 204 " --> pdb=" O VAL U 200 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN U 207 " --> pdb=" O LYS U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 4.298A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS U 217 " --> pdb=" O PHE U 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP U 224 " --> pdb=" O LEU U 220 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 Processing helix chain 'U' and resid 241 through 256 removed outlier: 4.186A pdb=" N ALA U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR U 246 " --> pdb=" O LEU U 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 270 removed outlier: 6.459A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG U 269 " --> pdb=" O ILE U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 Processing helix chain 'U' and resid 332 through 346 removed outlier: 4.063A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 3.889A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL U 360 " --> pdb=" O THR U 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 5.527A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 389 removed outlier: 5.399A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) Processing helix chain 'U' and resid 390 through 396 removed outlier: 4.522A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 413 removed outlier: 5.553A pdb=" N LYS U 401 " --> pdb=" O THR U 397 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS U 413 " --> pdb=" O GLY U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 416 through 427 removed outlier: 5.918A pdb=" N LEU U 420 " --> pdb=" O GLU U 416 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR U 425 " --> pdb=" O GLN U 421 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR U 426 " --> pdb=" O LEU U 422 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU U 427 " --> pdb=" O MET U 423 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 451 removed outlier: 4.495A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA U 451 " --> pdb=" O GLY U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 3.985A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 486 removed outlier: 3.764A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 4.387A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 521 removed outlier: 4.307A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 4.474A pdb=" N ILE U 529 " --> pdb=" O ASN U 525 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU U 530 " --> pdb=" O ALA U 526 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 4.497A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 574 removed outlier: 5.710A pdb=" N LYS U 574 " --> pdb=" O LEU U 570 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.970A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) removed outlier: 4.396A 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: 3.856A pdb=" N SER U 621 " --> pdb=" O ALA U 617 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 642 removed outlier: 4.586A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 5.109A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 3.760A 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: 4.604A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 676 removed outlier: 6.573A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 696 removed outlier: 4.637A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 removed outlier: 3.925A 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 719 Processing helix chain 'U' and resid 723 through 739 removed outlier: 3.612A pdb=" N GLY U 729 " --> pdb=" O MET U 725 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA U 730 " --> pdb=" O ALA U 726 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 773 removed outlier: 3.864A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TRP U 770 " --> pdb=" O PHE U 766 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE U 771 " --> pdb=" O THR U 767 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TRP U 772 " --> pdb=" O GLN U 768 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE U 773 " --> pdb=" O PHE U 769 " (cutoff:3.500A) Processing helix chain 'U' and resid 774 through 783 removed outlier: 4.940A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 774 through 783' Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.926A 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 91 through 105 Proline residue: V 102 - end of helix Processing helix chain 'V' and resid 109 through 121 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.738A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 5.013A 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: 3.671A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 222 removed outlier: 4.304A pdb=" N ASP V 204 " --> pdb=" O ARG V 200 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.495A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.752A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 removed outlier: 3.748A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.566A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 344 through 350 removed outlier: 4.794A pdb=" N PHE V 348 " --> pdb=" O ASP V 344 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG V 349 " --> pdb=" O ARG V 345 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN V 350 " --> pdb=" O LEU V 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 344 through 350' Processing helix chain 'V' and resid 353 through 370 Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 383 Processing helix chain 'V' and resid 384 through 390 Processing helix chain 'V' and resid 391 through 414 removed outlier: 3.882A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 3.516A pdb=" N GLN V 427 " --> pdb=" O ALA V 423 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 removed outlier: 3.540A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU V 435 " --> pdb=" O PRO V 431 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 494 removed outlier: 4.017A pdb=" N THR V 469 " --> pdb=" O ASP V 465 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU V 471 " --> pdb=" O TYR V 467 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 3.725A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER V 481 " --> pdb=" O HIS V 477 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE V 482 " --> pdb=" O GLN V 478 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET V 494 " --> pdb=" O SER V 490 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 36 Proline residue: W 29 - end of helix removed outlier: 4.097A pdb=" N LYS W 33 " --> pdb=" O PRO W 29 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA W 35 " --> pdb=" O CYS W 31 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS W 36 " --> pdb=" O ALA W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 58 removed outlier: 4.946A pdb=" N VAL W 43 " --> pdb=" O ARG W 39 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR W 56 " --> pdb=" O LYS W 52 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 78 Processing helix chain 'W' and resid 79 through 94 removed outlier: 3.975A pdb=" N ASN W 84 " --> pdb=" O TRP W 80 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ARG W 94 " --> pdb=" O LEU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 115 removed outlier: 3.686A pdb=" N GLU W 114 " --> pdb=" O THR W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 133 removed outlier: 3.886A pdb=" N LYS W 121 " --> pdb=" O ASP W 117 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU W 133 " --> pdb=" O ARG W 129 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 154 removed outlier: 5.374A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU W 149 " --> pdb=" O LEU W 145 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA W 150 " --> pdb=" O THR W 146 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR W 151 " --> pdb=" O LYS W 147 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE W 152 " --> pdb=" O THR W 148 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS W 153 " --> pdb=" O LEU W 149 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU W 154 " --> pdb=" O ALA W 150 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 176 removed outlier: 4.764A pdb=" N LEU W 169 " --> pdb=" O ILE W 165 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 197 removed outlier: 4.752A pdb=" N GLU W 184 " --> pdb=" O LYS W 180 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 210 removed outlier: 4.530A pdb=" N LYS W 208 " --> pdb=" O ILE W 204 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE W 209 " --> pdb=" O ILE W 205 " (cutoff:3.500A) Processing helix chain 'W' and resid 215 through 220 removed outlier: 4.712A pdb=" N THR W 219 " --> pdb=" O GLN W 215 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU W 220 " --> pdb=" O GLU W 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 215 through 220' Processing helix chain 'W' and resid 222 through 238 removed outlier: 4.561A pdb=" N TYR W 226 " --> pdb=" O LEU W 222 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU W 233 " --> pdb=" O LEU W 229 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP W 234 " --> pdb=" O MET W 230 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 240 through 257 removed outlier: 4.825A pdb=" N CYS W 244 " --> pdb=" O TYR W 240 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS W 246 " --> pdb=" O SER W 242 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 259 through 278 removed outlier: 4.235A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 291 Processing helix chain 'W' and resid 294 through 300 removed outlier: 4.600A pdb=" N GLU W 298 " --> pdb=" O LYS W 294 " (cutoff:3.500A) Proline residue: W 300 - end of helix Processing helix chain 'W' and resid 301 through 307 Processing helix chain 'W' and resid 316 through 324 removed outlier: 4.204A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 4.180A pdb=" N MET W 366 " --> pdb=" O ASN W 362 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 Processing helix chain 'W' and resid 385 through 400 Processing helix chain 'W' and resid 420 through 456 removed outlier: 4.089A pdb=" N ALA W 447 " --> pdb=" O THR W 443 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS W 448 " --> pdb=" O HIS W 444 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 61 Processing helix chain 'X' and resid 63 through 77 Proline residue: X 75 - end of helix Processing helix chain 'X' and resid 82 through 99 removed outlier: 3.796A pdb=" N ARG X 87 " --> pdb=" O ALA X 83 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 121 removed outlier: 3.718A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 Processing helix chain 'X' and resid 143 through 161 removed outlier: 3.738A pdb=" N LYS X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 181 removed outlier: 4.199A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 201 removed outlier: 4.052A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 222 removed outlier: 4.448A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.826A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR X 229 " --> pdb=" O TRP X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 3.693A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER X 250 " --> pdb=" O LYS X 246 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 274 removed outlier: 5.348A pdb=" N LYS X 274 " --> pdb=" O LEU X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 275 through 280 removed outlier: 4.143A pdb=" N TYR X 279 " --> pdb=" O LEU X 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA X 280 " --> pdb=" O ALA X 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 275 through 280' Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.988A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 340 removed outlier: 5.010A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE X 336 " --> pdb=" O GLU X 332 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL X 338 " --> pdb=" O ASN X 334 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE X 339 " --> pdb=" O LEU X 335 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.620A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 removed outlier: 4.800A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 395 through 422 removed outlier: 3.552A pdb=" N ALA X 400 " --> pdb=" O THR X 396 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU X 421 " --> pdb=" O LYS X 417 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 28 removed outlier: 4.540A pdb=" N ILE Y 19 " --> pdb=" O PRO Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 47 removed outlier: 3.700A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU Y 41 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 58 removed outlier: 4.895A pdb=" N TYR Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 93 removed outlier: 3.866A pdb=" N GLU Y 86 " --> pdb=" O LYS Y 82 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU Y 92 " --> pdb=" O LEU Y 88 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 114 Processing helix chain 'Y' and resid 116 through 131 removed outlier: 3.872A 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: 4.198A pdb=" N GLU Y 162 " --> pdb=" O THR Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 191 removed outlier: 5.620A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 202 removed outlier: 5.279A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU Y 202 " --> pdb=" O ALA Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 230 removed outlier: 4.127A pdb=" N MET Y 228 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA Y 230 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 Processing helix chain 'Y' and resid 244 through 254 removed outlier: 3.954A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.826A pdb=" N CYS Y 266 " --> pdb=" O SER Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 285 removed outlier: 4.629A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASP Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) Processing helix chain 'Y' and resid 289 through 310 removed outlier: 5.360A pdb=" N ARG Y 293 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR Y 294 " --> pdb=" O PRO Y 290 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 323 removed outlier: 4.027A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 5.391A pdb=" N ILE Y 330 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) Processing helix chain 'Y' and resid 361 through 384 removed outlier: 4.591A pdb=" N GLN Y 365 " --> pdb=" O SER Y 361 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP Y 374 " --> pdb=" O ILE Y 370 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU Y 375 " --> pdb=" O LYS Y 371 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG Y 379 " --> pdb=" O LEU Y 375 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 30 removed outlier: 4.588A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 102 through 116 removed outlier: 4.860A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 177 removed outlier: 3.788A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG Z 177 " --> pdb=" O GLU Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 218 removed outlier: 4.735A pdb=" N ILE Z 191 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 237 removed outlier: 4.952A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE Z 234 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 290 removed outlier: 4.041A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL Z 260 " --> pdb=" O GLN Z 256 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 Processing helix chain 'a' and resid 17 through 32 removed outlier: 3.941A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 4.730A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 removed outlier: 4.256A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 3.960A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 105 removed outlier: 4.125A pdb=" N LEU a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 124 removed outlier: 4.737A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 removed outlier: 5.254A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 164 removed outlier: 4.339A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 184 removed outlier: 5.554A pdb=" N TYR a 172 " --> pdb=" O ASN a 168 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR a 173 " --> pdb=" O HIS a 169 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 5.027A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 215 through 220 removed outlier: 4.468A 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 231 through 243 Processing helix chain 'a' and resid 246 through 258 removed outlier: 4.743A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 285 removed outlier: 4.362A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) Proline residue: a 285 - end of helix Processing helix chain 'a' and resid 292 through 301 Processing helix chain 'a' and resid 303 through 318 removed outlier: 3.643A pdb=" N VAL a 307 " --> pdb=" O THR a 303 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 376 removed outlier: 5.828A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU a 375 " --> pdb=" O ALA a 371 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 68 through 76 removed outlier: 4.405A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 4.167A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.026A 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 Processing helix chain 'b' and resid 179 through 188 removed outlier: 4.244A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'b' and resid 13 through 18 removed outlier: 3.663A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 49 removed outlier: 4.034A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 103 removed outlier: 4.113A pdb=" N GLN c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 146 through 151 removed outlier: 3.800A pdb=" N SER c 150 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 5.031A 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 Processing helix chain 'c' and resid 188 through 195 removed outlier: 5.171A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 222 removed outlier: 6.733A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 234 through 263 removed outlier: 4.352A pdb=" N CYS c 238 " --> pdb=" O TYR c 234 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS c 257 " --> pdb=" O LYS c 253 " (cutoff:3.500A) Processing helix chain 'c' and resid 282 through 310 removed outlier: 4.051A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL c 297 " --> pdb=" O THR c 293 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN c 298 " --> pdb=" O SER c 294 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR c 306 " --> pdb=" O ALA c 302 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL c 307 " --> pdb=" O MET c 303 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 33 removed outlier: 3.906A pdb=" N CYS d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 Processing helix chain 'd' and resid 67 through 84 removed outlier: 4.279A pdb=" N ASP d 84 " --> pdb=" O CYS d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 110 Processing helix chain 'd' and resid 111 through 120 removed outlier: 4.288A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) 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: 3.854A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 184 removed outlier: 4.145A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 198 removed outlier: 3.666A pdb=" N ALA d 194 " --> pdb=" O LEU d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 213 removed outlier: 4.087A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 254 Proline residue: d 238 - end of helix removed outlier: 6.408A pdb=" N GLU d 241 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU d 242 " --> pdb=" O PRO d 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 7 through 24 removed outlier: 5.375A pdb=" N VAL f 11 " --> pdb=" O ASP f 7 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN f 12 " --> pdb=" O LYS f 8 " (cutoff:3.500A) Proline residue: f 13 - end of helix Proline residue: f 17 - end of helix Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 29 through 47 Processing helix chain 'f' and resid 55 through 60 removed outlier: 4.818A pdb=" N LEU f 59 " --> pdb=" O GLU f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 72 removed outlier: 4.065A pdb=" N LYS f 66 " --> pdb=" O ARG f 62 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 92 removed outlier: 4.790A pdb=" N VAL f 92 " --> pdb=" O SER f 88 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 99 removed outlier: 4.733A pdb=" N LEU f 99 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 110 removed outlier: 3.947A pdb=" N ILE f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 126 removed outlier: 4.058A pdb=" N ASP f 124 " --> pdb=" O ARG f 120 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE f 125 " --> pdb=" O PHE f 121 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE f 126 " --> pdb=" O ALA f 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 147 removed outlier: 5.157A pdb=" N THR f 132 " --> pdb=" O VAL f 128 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS f 139 " --> pdb=" O GLY f 135 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU f 140 " --> pdb=" O GLU f 136 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR f 142 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) Processing helix chain 'f' and resid 154 through 173 Processing helix chain 'f' and resid 178 through 189 Proline residue: f 183 - end of helix Processing helix chain 'f' and resid 193 through 210 removed outlier: 4.233A pdb=" N ASN f 199 " --> pdb=" O ASN f 195 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU f 208 " --> pdb=" O ALA f 204 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET f 209 " --> pdb=" O CYS f 205 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU f 210 " --> pdb=" O ASP f 206 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 227 removed outlier: 4.631A pdb=" N ASP f 215 " --> pdb=" O ILE f 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS f 219 " --> pdb=" O ASP f 215 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 249 removed outlier: 4.010A pdb=" N THR f 234 " --> pdb=" O CYS f 230 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYS f 236 " --> pdb=" O TYR f 232 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL f 237 " --> pdb=" O LEU f 233 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.558A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU f 248 " --> pdb=" O GLU f 244 " (cutoff:3.500A) Processing helix chain 'f' and resid 253 through 263 removed outlier: 4.404A pdb=" N ARG f 257 " --> pdb=" O LEU f 253 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS f 258 " --> pdb=" O GLY f 254 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE f 262 " --> pdb=" O LYS f 258 " (cutoff:3.500A) Proline residue: f 263 - end of helix Processing helix chain 'f' and resid 274 through 279 removed outlier: 5.417A pdb=" N VAL f 278 " --> pdb=" O ASP f 274 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU f 279 " --> pdb=" O MET f 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 274 through 279' Processing helix chain 'f' and resid 285 through 294 removed outlier: 3.634A pdb=" N GLN f 291 " --> pdb=" O ASP f 287 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 299 through 308 removed outlier: 4.214A pdb=" N VAL f 303 " --> pdb=" O GLY f 299 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE f 304 " --> pdb=" O ARG f 300 " (cutoff:3.500A) Processing helix chain 'f' and resid 313 through 321 removed outlier: 4.212A pdb=" N LEU f 317 " --> pdb=" O GLU f 313 " (cutoff:3.500A) Processing helix chain 'f' and resid 322 through 336 removed outlier: 5.505A pdb=" N LEU f 326 " --> pdb=" O SER f 322 " (cutoff:3.500A) Processing helix chain 'f' and resid 345 through 350 removed outlier: 3.973A pdb=" N TYR f 349 " --> pdb=" O PRO f 345 " (cutoff:3.500A) Processing helix chain 'f' and resid 353 through 359 removed outlier: 4.122A pdb=" N ARG f 357 " --> pdb=" O LEU f 353 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY f 359 " --> pdb=" O ASN f 355 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 383 Processing helix chain 'f' and resid 390 through 395 removed outlier: 4.665A pdb=" N ASP f 394 " --> pdb=" O LEU f 390 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY f 395 " --> pdb=" O LEU f 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 390 through 395' Processing helix chain 'f' and resid 396 through 402 removed outlier: 4.370A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 419 removed outlier: 4.098A pdb=" N LEU f 408 " --> pdb=" O ASP f 404 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 425 through 435 removed outlier: 4.927A pdb=" N SER f 435 " --> pdb=" O LYS f 431 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 4.000A pdb=" N ASN f 452 " --> pdb=" O CYS f 448 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) Processing helix chain 'f' and resid 462 through 473 removed outlier: 3.598A pdb=" N LEU f 466 " --> pdb=" O ALA f 462 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS f 472 " --> pdb=" O ASP f 468 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN f 473 " --> pdb=" O TYR f 469 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 4.347A pdb=" N LEU f 479 " --> pdb=" O ASN f 475 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY f 480 " --> pdb=" O THR f 476 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER f 481 " --> pdb=" O MET f 477 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE f 482 " --> pdb=" O ARG f 478 " (cutoff:3.500A) Processing helix chain 'f' and resid 495 through 502 Processing helix chain 'f' and resid 503 through 508 removed outlier: 5.081A pdb=" N SER f 508 " --> pdb=" O VAL f 504 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.719A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 5.072A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 550 removed outlier: 3.776A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (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 570 through 582 removed outlier: 4.101A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU f 577 " --> pdb=" O ILE f 573 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 585 through 601 removed outlier: 4.083A pdb=" N SER f 589 " --> pdb=" O GLU f 585 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP f 596 " --> pdb=" O ASN f 592 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 619 removed outlier: 4.894A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER f 617 " --> pdb=" O LEU f 613 " (cutoff:3.500A) Processing helix chain 'f' and resid 627 through 643 removed outlier: 4.703A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS f 637 " --> pdb=" O GLU f 633 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP f 638 " --> pdb=" O LYS f 634 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS f 639 " --> pdb=" O LYS f 635 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS f 640 " --> pdb=" O ASP f 636 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA f 642 " --> pdb=" O ASP f 638 " (cutoff:3.500A) Proline residue: f 643 - end of helix Processing helix chain 'f' and resid 645 through 658 removed outlier: 4.624A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) Processing helix chain 'f' and resid 671 through 680 removed outlier: 5.619A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU f 679 " --> pdb=" O PHE f 675 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG f 680 " --> pdb=" O GLY f 676 " (cutoff:3.500A) Processing helix chain 'f' and resid 688 through 698 removed outlier: 3.900A pdb=" N LEU f 692 " --> pdb=" O ARG f 688 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 717 removed outlier: 3.760A pdb=" N ASN f 705 " --> pdb=" O ASN f 701 " (cutoff:3.500A) Processing helix chain 'f' and resid 724 through 735 removed outlier: 5.054A pdb=" N GLY f 733 " --> pdb=" O MET f 729 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER f 734 " --> pdb=" O GLY f 730 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY f 735 " --> pdb=" O MET f 731 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 752 removed outlier: 4.033A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR f 751 " --> pdb=" O GLN f 747 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N HIS f 752 " --> pdb=" O LEU f 748 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 783 removed outlier: 5.565A pdb=" N THR f 777 " --> pdb=" O LYS f 773 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N CYS f 779 " --> pdb=" O THR f 775 " (cutoff:3.500A) Proline residue: f 780 - end of helix Processing helix chain 'f' and resid 797 through 804 removed outlier: 4.384A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU f 804 " --> pdb=" O LEU f 800 " (cutoff:3.500A) Processing helix chain 'f' and resid 664 through 669 removed outlier: 4.065A pdb=" N GLU f 669 " --> pdb=" O GLU f 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 664 through 669' Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.989A pdb=" N ALA g 28 " --> pdb=" O GLN g 24 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE g 29 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.075A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.236A 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 106 Processing helix chain 'g' and resid 110 through 129 removed outlier: 3.845A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 4.409A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.731A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 245 Processing helix chain 'i' and resid 18 through 31 removed outlier: 4.120A pdb=" N GLY i 29 " --> pdb=" O MET i 25 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.669A pdb=" N ASN i 84 " --> pdb=" O THR i 80 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.746A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 removed outlier: 4.112A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 202 removed outlier: 4.055A pdb=" N ASP i 202 " --> pdb=" O ASN i 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 229 through 251 Processing helix chain 'k' and resid 21 through 34 removed outlier: 3.776A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.733A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 4.121A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.751A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU k 183 " --> pdb=" O SER k 179 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 230 through 241 removed outlier: 3.832A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.746A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA l 28 " --> pdb=" O TYR l 24 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL l 29 " --> pdb=" O ALA l 25 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 Processing helix chain 'l' and resid 104 through 122 removed outlier: 4.311A 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: 4.667A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 4.003A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 3.887A 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 226 through 233 removed outlier: 4.002A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix No H-bonds generated for 'chain 'l' and resid 226 through 233' Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.879A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 103 Processing helix chain 'm' and resid 107 through 125 removed outlier: 3.968A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR m 125 " --> pdb=" O ALA m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 3.804A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 180 through 185 removed outlier: 3.669A pdb=" N MET m 184 " --> pdb=" O GLN m 180 " (cutoff:3.500A) removed outlier: 5.869A 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: 4.017A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 202 through 207 removed outlier: 4.107A pdb=" N ASP m 206 " --> pdb=" O ASP m 202 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS m 207 " --> pdb=" O GLU m 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 202 through 207' Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 5 through 10 removed outlier: 5.908A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 5.023A 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 Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.808A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 removed outlier: 3.702A pdb=" N ARG n 166 " --> pdb=" O LEU n 162 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 127 removed outlier: 3.784A 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 136 Processing helix chain 'x' and resid 145 through 167 removed outlier: 4.195A pdb=" N ALA x 149 " --> pdb=" O GLU x 145 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN x 150 " --> pdb=" O MET x 146 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR x 151 " --> pdb=" O ALA x 147 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR x 166 " --> pdb=" O SER x 162 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER x 167 " --> pdb=" O MET x 163 " (cutoff:3.500A) Processing helix chain 'x' and resid 172 through 183 Processing helix chain 'x' and resid 199 through 215 Processing helix chain 'x' and resid 220 through 226 removed outlier: 4.205A pdb=" N GLU x 225 " --> pdb=" O ASP x 221 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 247 Processing helix chain 'x' and resid 285 through 296 removed outlier: 3.781A pdb=" N GLN x 295 " --> pdb=" O LYS x 291 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLU x 296 " --> pdb=" O LEU x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 362 through 386 removed outlier: 4.191A pdb=" N LYS x 366 " --> pdb=" O GLU x 362 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER x 369 " --> pdb=" O GLU x 365 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE x 370 " --> pdb=" O LYS x 366 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU x 377 " --> pdb=" O LYS x 373 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS x 380 " --> pdb=" O ASP x 376 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASN x 383 " --> pdb=" O ASP x 379 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLN x 384 " --> pdb=" O LYS x 380 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN x 385 " --> pdb=" O LYS x 381 " (cutoff:3.500A) Proline residue: x 386 - end of helix Processing helix chain 'x' and resid 459 through 468 removed outlier: 4.657A pdb=" N GLY x 468 " --> pdb=" O LEU x 464 " (cutoff:3.500A) Processing helix chain 'y' and resid 22 through 34 removed outlier: 3.790A pdb=" N VAL y 26 " --> pdb=" O THR y 22 " (cutoff:3.500A) Processing helix chain 'y' and resid 37 through 42 removed outlier: 5.643A pdb=" N ARG y 42 " --> pdb=" O PRO y 38 " (cutoff:3.500A) Processing helix chain 'y' and resid 55 through 60 Processing helix chain 'e' and resid 51 through 64 removed outlier: 5.516A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.619A pdb=" N VAL A 140 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.600A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 236 through 240 removed outlier: 4.808A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 4.928A 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 removed outlier: 4.709A pdb=" N CYS B 148 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 120 through 125 removed outlier: 3.520A pdb=" N VAL B 123 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 131 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 282 through 285 removed outlier: 3.931A pdb=" N THR B 331 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG B 349 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 71 through 77 Processing sheet with id= 8, first strand: chain 'C' and resid 83 through 88 removed outlier: 8.409A pdb=" N LYS C 83 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 85 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 210 through 215 removed outlier: 3.571A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 186 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 87 through 90 removed outlier: 5.090A pdb=" N SER D 129 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 100 through 104 Processing sheet with id= 12, first strand: chain 'D' and resid 226 through 230 removed outlier: 5.122A pdb=" N ALA D 226 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 265 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 260 " --> pdb=" O ASN D 304 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 55 through 60 removed outlier: 4.249A pdb=" N THR E 96 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 68 through 72 Processing sheet with id= 15, first strand: chain 'E' and resid 194 through 199 removed outlier: 3.613A pdb=" N VAL E 198 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP E 233 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS E 274 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS E 168 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET E 275 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 95 through 98 removed outlier: 6.795A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 93 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU F 150 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU F 164 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 246 through 251 removed outlier: 4.592A pdb=" N THR F 247 " --> pdb=" O PRO F 280 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG F 350 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.985A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 69 through 72 removed outlier: 6.561A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 164 through 169 removed outlier: 6.845A pdb=" N LYS G 164 " --> pdb=" O ARG G 43 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 44 through 48 Processing sheet with id= 22, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.456A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N HIS H 71 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 210 through 214 removed outlier: 5.339A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.484A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N HIS h 71 " --> pdb=" O TRP h 139 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU h 134 " --> pdb=" O SER h 149 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'h' and resid 160 through 164 removed outlier: 5.722A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN h 214 " --> pdb=" O GLY h 217 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 64 through 68 removed outlier: 6.572A pdb=" N LYS I 64 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP I 71 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU I 134 " --> pdb=" O SER I 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 161 through 165 removed outlier: 5.194A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.167A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN J 68 " --> pdb=" O PHE J 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE J 136 " --> pdb=" O ASN J 68 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 158 through 162 removed outlier: 5.393A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU J 208 " --> pdb=" O LEU J 220 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'j' and resid 62 through 65 removed outlier: 6.523A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.172A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 67 through 70 removed outlier: 6.506A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS K 73 " --> pdb=" O VAL K 146 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 167 through 171 removed outlier: 6.752A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ASN K 214 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.560A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 158 through 162 Processing sheet with id= 36, first strand: chain 'M' and resid 66 through 69 removed outlier: 3.579A pdb=" N VAL M 69 " --> pdb=" O VAL M 73 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.868A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.608A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.263A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.482A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP O 104 " --> pdb=" O GLY O 107 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.059A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.383A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.331A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA o 16 " --> pdb=" O ASP o 174 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'P' and resid 42 through 45 removed outlier: 6.038A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.903A 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: 5.871A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.376A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'p' and resid 136 through 140 removed outlier: 5.979A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.333A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 6.226A 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: 4.000A 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= 50, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.429A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'q' and resid 129 through 132 removed outlier: 6.666A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP q 18 " --> pdb=" O TYR q 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL q 13 " --> pdb=" O ILE q 183 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 34 through 37 removed outlier: 6.551A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.058A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY R 11 " --> pdb=" O PHE R 8 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'r' and resid 34 through 37 removed outlier: 3.715A pdb=" N ILE r 37 " --> pdb=" O LEU r 41 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR r 44 " --> pdb=" O MET r 100 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA r 46 " --> pdb=" O GLY r 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY r 98 " --> pdb=" O ALA r 46 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.060A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL r 12 " --> pdb=" O VAL r 179 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.660A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.642A 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: 5.668A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP S 26 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 's' and resid 43 through 46 removed outlier: 6.737A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 's' and resid 135 through 139 removed outlier: 5.605A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.616A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.412A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 't' and resid 42 through 45 removed outlier: 6.784A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 't' and resid 136 through 139 removed outlier: 4.234A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'U' and resid 874 through 878 removed outlier: 5.800A pdb=" N ASN U 874 " --> pdb=" O CYS U 806 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS U 806 " --> pdb=" O ASN U 874 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN U 876 " --> pdb=" O SER U 804 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER U 804 " --> pdb=" O GLN U 876 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 878 " --> pdb=" O TYR U 802 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL U 891 " --> pdb=" O ASN U 805 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'W' and resid 404 through 408 removed outlier: 3.506A pdb=" N LYS W 405 " --> pdb=" O ASN W 414 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'X' and resid 376 through 380 Processing sheet with id= 67, first strand: chain 'Y' and resid 345 through 348 Processing sheet with id= 68, first strand: chain 'Z' and resid 47 through 50 removed outlier: 3.544A pdb=" N VAL Z 9 " --> pdb=" O THR Z 159 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Z' and resid 52 through 56 removed outlier: 4.987A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL Z 120 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE Z 124 " --> pdb=" O HIS Z 96 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 320 through 326 removed outlier: 3.721A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'b' and resid 47 through 53 removed outlier: 3.995A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL b 10 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP b 11 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY b 114 " --> pdb=" O ASP b 11 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'c' and resid 65 through 69 removed outlier: 4.692A pdb=" N GLN c 30 " --> pdb=" O TYR c 65 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL c 67 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLU c 29 " --> pdb=" O SER c 202 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'f' and resid 825 through 829 removed outlier: 3.988A pdb=" N GLN f 826 " --> pdb=" O THR f 863 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR f 863 " --> pdb=" O GLN f 826 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.337A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'g' and resid 165 through 169 removed outlier: 5.945A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.505A pdb=" N LYS i 64 " --> pdb=" O VAL i 76 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'i' and resid 161 through 165 removed outlier: 5.335A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS i 210 " --> pdb=" O ARG i 49 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'k' and resid 67 through 70 removed outlier: 6.451A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS k 73 " --> pdb=" O VAL k 146 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'k' and resid 167 through 171 removed outlier: 6.042A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASN k 214 " --> pdb=" O LYS k 52 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.627A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP l 138 " --> pdb=" O GLY l 141 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'l' and resid 158 through 162 removed outlier: 4.895A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'm' and resid 65 through 69 removed outlier: 6.592A pdb=" N ARG m 65 " --> pdb=" O VAL m 77 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'm' and resid 162 through 166 removed outlier: 5.044A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU m 50 " --> pdb=" O THR m 35 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.538A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL n 121 " --> pdb=" O SER n 113 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.609A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER n 18 " --> pdb=" O VAL n 173 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'x' and resid 265 through 273 removed outlier: 3.973A pdb=" N LYS x 316 " --> pdb=" O GLU x 252 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'x' and resid 274 through 278 removed outlier: 6.843A pdb=" N LEU x 351 " --> pdb=" O LEU x 420 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'x' and resid 331 through 335 removed outlier: 3.739A pdb=" N VAL x 339 " --> pdb=" O LYS x 334 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'x' and resid 454 through 458 removed outlier: 6.682A pdb=" N GLU x 446 " --> pdb=" O ARG x 442 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU x 424 " --> pdb=" O TYR x 476 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'x' and resid 248 through 251 removed outlier: 7.270A pdb=" N GLY x 248 " --> pdb=" O PRO x 321 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'y' and resid 11 through 17 removed outlier: 4.409A pdb=" N LYS y 11 " --> pdb=" O THR y 7 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER y 65 " --> pdb=" O GLN y 2 " (cutoff:3.500A) 5770 hydrogen bonds defined for protein. 17223 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: 45.39 Time building geometry restraints manager: 32.71 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: 36183 1.34 - 1.46: 23310 1.46 - 1.58: 50770 1.58 - 1.71: 15 1.71 - 1.83: 1053 Bond restraints: 111331 Sorted by residual: bond pdb=" C VAL U 173 " pdb=" N PRO U 174 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.11e+00 bond pdb=" C THR Z 149 " pdb=" N PRO Z 150 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.55e+00 bond pdb=" CA ASP d 67 " pdb=" CB ASP d 67 " ideal model delta sigma weight residual 1.527 1.571 -0.044 1.75e-02 3.27e+03 6.25e+00 bond pdb=" CA LEU f 266 " pdb=" C LEU f 266 " ideal model delta sigma weight residual 1.524 1.578 -0.055 2.25e-02 1.98e+03 5.92e+00 bond pdb=" C LEU W 118 " pdb=" N PRO W 119 " ideal model delta sigma weight residual 1.337 1.362 -0.026 1.11e-02 8.12e+03 5.47e+00 ... (remaining 111326 not shown) Histogram of bond angle deviations from ideal: 94.16 - 103.27: 1003 103.27 - 112.37: 56278 112.37 - 121.48: 66618 121.48 - 130.59: 26067 130.59 - 139.70: 442 Bond angle restraints: 150408 Sorted by residual: angle pdb=" N ILE q 25 " pdb=" CA ILE q 25 " pdb=" C ILE q 25 " ideal model delta sigma weight residual 113.71 107.84 5.87 9.50e-01 1.11e+00 3.81e+01 angle pdb=" N LEU j 220 " pdb=" CA LEU j 220 " pdb=" C LEU j 220 " ideal model delta sigma weight residual 110.43 118.17 -7.74 1.31e+00 5.83e-01 3.49e+01 angle pdb=" C GLY s 190 " pdb=" N ASP s 191 " pdb=" CA ASP s 191 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C GLU W 139 " pdb=" N ILE W 140 " pdb=" CA ILE W 140 " ideal model delta sigma weight residual 121.97 130.95 -8.98 1.80e+00 3.09e-01 2.49e+01 angle pdb=" N GLN D 340 " pdb=" CA GLN D 340 " pdb=" C GLN D 340 " ideal model delta sigma weight residual 114.56 108.25 6.31 1.27e+00 6.20e-01 2.47e+01 ... (remaining 150403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 61183 17.85 - 35.70: 5749 35.70 - 53.55: 897 53.55 - 71.40: 123 71.40 - 89.25: 76 Dihedral angle restraints: 68028 sinusoidal: 27530 harmonic: 40498 Sorted by residual: dihedral pdb=" CA VAL g 222 " pdb=" C VAL g 222 " pdb=" N GLU g 223 " pdb=" CA GLU g 223 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA TYR U 813 " pdb=" C TYR U 813 " pdb=" N PRO U 814 " pdb=" CA PRO U 814 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA VAL Z 144 " pdb=" C VAL Z 144 " pdb=" N HIS Z 145 " pdb=" CA HIS Z 145 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 68025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 14595 0.069 - 0.138: 2281 0.138 - 0.207: 135 0.207 - 0.276: 15 0.276 - 0.346: 5 Chirality restraints: 17031 Sorted by residual: 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 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL J 98 " pdb=" CA VAL J 98 " pdb=" CG1 VAL J 98 " pdb=" CG2 VAL J 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.47e+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 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 17028 not shown) Planarity restraints: 19402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP d 61 " 0.031 2.00e-02 2.50e+03 3.45e-02 2.97e+01 pdb=" CG TRP d 61 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP d 61 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP d 61 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP d 61 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP d 61 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP d 61 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 61 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 61 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP d 61 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR x 235 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO x 236 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO x 236 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO x 236 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 215 " 0.020 2.00e-02 2.50e+03 2.07e-02 1.08e+01 pdb=" CG TRP m 215 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP m 215 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP m 215 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP m 215 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP m 215 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 215 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 215 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP m 215 " 0.002 2.00e-02 2.50e+03 ... (remaining 19399 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1844 2.68 - 3.23: 100090 3.23 - 3.79: 171850 3.79 - 4.34: 221312 4.34 - 4.90: 367886 Nonbonded interactions: 862982 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 2.122 2.230 nonbonded pdb=" OH TYR X 397 " pdb=" O LYS Y 362 " model vdw 2.212 2.440 nonbonded pdb=" O MET c 226 " pdb=" OG1 THR c 230 " model vdw 2.224 2.440 nonbonded pdb=" O GLU A 189 " pdb=" OG1 THR A 193 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR H 6 " pdb=" OD2 ASP I 6 " model vdw 2.232 2.440 ... (remaining 862977 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: 10.380 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: 0.100 Extract box with map and model: 51.690 Check model and map are aligned: 1.310 Set scattering table: 0.720 Process input model: 271.330 Find NCS groups from input model: 6.740 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 0.069 111331 Z= 0.221 Angle : 0.785 14.683 150408 Z= 0.409 Chirality : 0.048 0.346 17031 Planarity : 0.005 0.124 19402 Dihedral : 13.945 89.245 41956 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 0.12 % Allowed : 0.59 % Favored : 99.29 % 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: -0.88 (0.07), residues: 13813 helix: 0.31 (0.06), residues: 6416 sheet: 0.23 (0.12), residues: 2049 loop : -2.02 (0.08), residues: 5348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP d 61 HIS 0.015 0.001 HIS M 120 PHE 0.037 0.002 PHE D 235 TYR 0.028 0.001 TYR W 247 ARG 0.012 0.000 ARG Y 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 486 time to evaluate : 9.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 384 MET cc_start: 0.8081 (tmm) cc_final: 0.7650 (tmm) REVERT: E 108 MET cc_start: 0.6565 (pmm) cc_final: 0.6032 (pmm) REVERT: E 122 MET cc_start: 0.8804 (mpp) cc_final: 0.7991 (ppp) REVERT: E 218 MET cc_start: 0.9390 (tpt) cc_final: 0.9187 (mmm) REVERT: E 258 MET cc_start: 0.7921 (ptt) cc_final: 0.7641 (ptp) REVERT: F 366 MET cc_start: 0.9272 (tpp) cc_final: 0.8893 (tpp) REVERT: N 164 MET cc_start: 0.8094 (mtp) cc_final: 0.7833 (mtp) REVERT: U 118 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5774 (pt) REVERT: U 560 MET cc_start: 0.6788 (mpp) cc_final: 0.6389 (ttm) REVERT: U 885 MET cc_start: 0.7869 (tpt) cc_final: 0.7275 (tpt) REVERT: U 894 MET cc_start: 0.7489 (tmm) cc_final: 0.7014 (ppp) REVERT: V 463 MET cc_start: 0.7205 (tpt) cc_final: 0.6683 (ttt) REVERT: W 230 MET cc_start: 0.8093 (ppp) cc_final: 0.7790 (ppp) REVERT: W 451 MET cc_start: 0.7010 (ppp) cc_final: 0.6777 (ppp) REVERT: X 254 MET cc_start: 0.8076 (mmt) cc_final: 0.7526 (mmm) REVERT: X 260 MET cc_start: 0.7890 (ppp) cc_final: 0.7666 (ppp) REVERT: Y 50 MET cc_start: 0.5093 (mpp) cc_final: 0.4004 (mpp) REVERT: Y 104 MET cc_start: 0.6927 (ppp) cc_final: 0.6638 (ppp) REVERT: Y 377 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8595 (pp) REVERT: Z 78 MET cc_start: 0.8462 (mmt) cc_final: 0.8175 (tpp) REVERT: b 107 MET cc_start: 0.5225 (mmt) cc_final: 0.4975 (mmp) REVERT: c 98 MET cc_start: 0.8422 (tpp) cc_final: 0.8100 (mmm) REVERT: c 167 MET cc_start: 0.6937 (mmp) cc_final: 0.6674 (tpp) REVERT: c 168 MET cc_start: 0.7714 (tpp) cc_final: 0.7482 (tmm) REVERT: d 1 MET cc_start: 0.4595 (mpp) cc_final: 0.3595 (tpp) REVERT: d 75 MET cc_start: 0.8456 (mmp) cc_final: 0.8013 (mmm) REVERT: d 95 MET cc_start: 0.8037 (tpp) cc_final: 0.7823 (tpp) REVERT: f 294 MET cc_start: -0.1478 (mmp) cc_final: -0.4049 (ppp) REVERT: f 297 MET cc_start: 0.1783 (ptp) cc_final: 0.1563 (ptt) REVERT: f 321 MET cc_start: -0.3429 (mmm) cc_final: -0.3708 (tpp) REVERT: f 407 MET cc_start: -0.4484 (tpt) cc_final: -0.4705 (tpt) REVERT: p 171 MET cc_start: 0.9090 (mmm) cc_final: 0.8505 (tpt) REVERT: x 116 MET cc_start: 0.7668 (ptt) cc_final: 0.7142 (ptp) REVERT: x 488 MET cc_start: 0.3156 (ttt) cc_final: 0.2331 (ptm) REVERT: y 23 ILE cc_start: 0.0037 (mp) cc_final: -0.0172 (pt) outliers start: 14 outliers final: 2 residues processed: 499 average time/residue: 0.8636 time to fit residues: 778.0560 Evaluate side-chains 446 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 442 time to evaluate : 9.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain Y residue 377 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 1159 optimal weight: 20.0000 chunk 1040 optimal weight: 8.9990 chunk 577 optimal weight: 9.9990 chunk 355 optimal weight: 20.0000 chunk 701 optimal weight: 20.0000 chunk 555 optimal weight: 8.9990 chunk 1076 optimal weight: 7.9990 chunk 416 optimal weight: 30.0000 chunk 654 optimal weight: 30.0000 chunk 800 optimal weight: 8.9990 chunk 1246 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN U 111 GLN U 115 ASN U 734 GLN U 801 GLN ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 236 HIS ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 158 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 GLN ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 826 GLN f 876 HIS j 221 ASN ** m 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 158 ASN x 197 GLN y 40 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 111331 Z= 0.264 Angle : 0.591 9.726 150408 Z= 0.308 Chirality : 0.042 0.193 17031 Planarity : 0.004 0.076 19402 Dihedral : 5.595 88.503 15314 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 0.25 % Allowed : 5.76 % Favored : 94.00 % 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: 13813 helix: 1.18 (0.07), residues: 6440 sheet: 0.18 (0.12), residues: 2023 loop : -1.90 (0.08), residues: 5350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP m 215 HIS 0.008 0.001 HIS c 44 PHE 0.024 0.001 PHE Q 171 TYR 0.022 0.001 TYR x 151 ARG 0.010 0.000 ARG d 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 442 time to evaluate : 11.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.7416 (ttp) cc_final: 0.6877 (ptm) REVERT: A 319 MET cc_start: 0.8555 (tmm) cc_final: 0.8101 (ppp) REVERT: D 384 MET cc_start: 0.8105 (tmm) cc_final: 0.7682 (tmm) REVERT: E 108 MET cc_start: 0.6616 (pmm) cc_final: 0.6110 (pmm) REVERT: E 122 MET cc_start: 0.8866 (mpp) cc_final: 0.8090 (ppp) REVERT: E 258 MET cc_start: 0.8112 (ptt) cc_final: 0.7909 (ptp) REVERT: F 310 MET cc_start: 0.7698 (mmp) cc_final: 0.7324 (mmm) REVERT: F 366 MET cc_start: 0.9269 (tpp) cc_final: 0.8865 (tpp) REVERT: K 156 MET cc_start: 0.8036 (tpp) cc_final: 0.7437 (ttm) REVERT: P 131 MET cc_start: 0.6979 (ttm) cc_final: 0.6442 (ttm) REVERT: U 118 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5627 (pp) REVERT: U 185 MET cc_start: 0.7547 (tpp) cc_final: 0.6928 (tpp) REVERT: U 885 MET cc_start: 0.7885 (tpt) cc_final: 0.7614 (tpp) REVERT: U 894 MET cc_start: 0.7462 (tmm) cc_final: 0.6638 (ppp) REVERT: V 463 MET cc_start: 0.7248 (tpt) cc_final: 0.6677 (ttt) REVERT: W 230 MET cc_start: 0.8343 (ppp) cc_final: 0.8106 (ppp) REVERT: X 254 MET cc_start: 0.8159 (mmt) cc_final: 0.7601 (mmm) REVERT: X 260 MET cc_start: 0.7751 (ppp) cc_final: 0.7511 (ppp) REVERT: Y 104 MET cc_start: 0.6997 (ppp) cc_final: 0.6726 (ppp) REVERT: Y 214 MET cc_start: 0.3450 (mmp) cc_final: 0.2326 (mmm) REVERT: Y 377 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8529 (pp) REVERT: Z 78 MET cc_start: 0.8571 (mmt) cc_final: 0.8158 (tpp) REVERT: b 107 MET cc_start: 0.5721 (mmt) cc_final: 0.5144 (mmt) REVERT: c 167 MET cc_start: 0.6929 (mmp) cc_final: 0.6499 (tpp) REVERT: c 292 MET cc_start: 0.9048 (mmm) cc_final: 0.8810 (mmm) REVERT: d 75 MET cc_start: 0.8628 (mmp) cc_final: 0.7922 (mmm) REVERT: d 95 MET cc_start: 0.8047 (tpp) cc_final: 0.7828 (tpp) REVERT: f 407 MET cc_start: -0.4382 (tpt) cc_final: -0.4582 (tpt) REVERT: f 825 MET cc_start: 0.3980 (mmm) cc_final: 0.3475 (ttp) REVERT: g 131 MET cc_start: 0.8192 (pmm) cc_final: 0.7858 (pmm) REVERT: m 27 MET cc_start: 0.8665 (mtm) cc_final: 0.8386 (mtm) REVERT: p 171 MET cc_start: 0.9180 (mmm) cc_final: 0.8624 (tpt) REVERT: x 116 MET cc_start: 0.7666 (ptt) cc_final: 0.7138 (ptp) REVERT: x 181 MET cc_start: 0.4761 (ppp) cc_final: 0.4476 (mmm) REVERT: x 488 MET cc_start: 0.3200 (ttt) cc_final: 0.2391 (ptm) outliers start: 29 outliers final: 11 residues processed: 452 average time/residue: 0.9016 time to fit residues: 736.0774 Evaluate side-chains 449 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 436 time to evaluate : 9.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain y residue 17 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 692 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 1037 optimal weight: 0.5980 chunk 849 optimal weight: 20.0000 chunk 343 optimal weight: 0.1980 chunk 1249 optimal weight: 20.0000 chunk 1349 optimal weight: 7.9990 chunk 1112 optimal weight: 8.9990 chunk 1238 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 1002 optimal weight: 9.9990 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 238 ASN ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 790 GLN m 221 ASN n 123 GLN x 197 GLN e 63 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 111331 Z= 0.170 Angle : 0.525 10.871 150408 Z= 0.272 Chirality : 0.040 0.154 17031 Planarity : 0.004 0.059 19402 Dihedral : 5.366 89.465 15313 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 0.44 % Allowed : 8.98 % Favored : 90.58 % 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: 0.13 (0.07), residues: 13813 helix: 1.51 (0.07), residues: 6446 sheet: 0.24 (0.12), residues: 2027 loop : -1.80 (0.08), residues: 5340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP c 225 HIS 0.007 0.001 HIS c 44 PHE 0.022 0.001 PHE X 96 TYR 0.021 0.001 TYR x 151 ARG 0.004 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 436 time to evaluate : 9.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.0078 (tmm) cc_final: -0.0803 (ptt) REVERT: A 299 MET cc_start: 0.7412 (ttp) cc_final: 0.6945 (tmm) REVERT: A 319 MET cc_start: 0.8623 (tmm) cc_final: 0.8116 (ppp) REVERT: C 139 MET cc_start: 0.4351 (mmp) cc_final: 0.3296 (mtm) REVERT: C 404 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8224 (pp) REVERT: D 384 MET cc_start: 0.8071 (tmm) cc_final: 0.7643 (tmm) REVERT: E 108 MET cc_start: 0.6570 (pmm) cc_final: 0.6182 (pmm) REVERT: E 122 MET cc_start: 0.8843 (mpp) cc_final: 0.8075 (ppp) REVERT: F 310 MET cc_start: 0.7694 (mmp) cc_final: 0.7296 (mmm) REVERT: F 317 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6861 (mt) REVERT: F 366 MET cc_start: 0.9254 (tpp) cc_final: 0.8848 (tpp) REVERT: K 156 MET cc_start: 0.7913 (tpp) cc_final: 0.7242 (ttm) REVERT: P 131 MET cc_start: 0.6917 (ttm) cc_final: 0.6405 (ttm) REVERT: Q 28 MET cc_start: 0.8427 (mpp) cc_final: 0.8046 (mpp) REVERT: U 118 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5595 (pp) REVERT: U 185 MET cc_start: 0.7541 (tpp) cc_final: 0.6957 (tpp) REVERT: U 556 MET cc_start: 0.8218 (tmm) cc_final: 0.7872 (tmm) REVERT: U 885 MET cc_start: 0.7938 (tpt) cc_final: 0.7666 (tpp) REVERT: U 894 MET cc_start: 0.7519 (tmm) cc_final: 0.6878 (ppp) REVERT: V 463 MET cc_start: 0.7267 (tpt) cc_final: 0.6698 (ttt) REVERT: W 230 MET cc_start: 0.8385 (ppp) cc_final: 0.8159 (ppp) REVERT: W 334 GLU cc_start: 0.3335 (OUTLIER) cc_final: 0.2230 (tt0) REVERT: X 260 MET cc_start: 0.7660 (ppp) cc_final: 0.7330 (ppp) REVERT: Y 104 MET cc_start: 0.6934 (ppp) cc_final: 0.6589 (ppp) REVERT: Y 214 MET cc_start: 0.3388 (mmp) cc_final: 0.2446 (mmm) REVERT: Y 377 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8535 (pp) REVERT: Z 78 MET cc_start: 0.8579 (mmt) cc_final: 0.8166 (tpp) REVERT: b 107 MET cc_start: 0.5996 (mmt) cc_final: 0.5427 (mmt) REVERT: c 167 MET cc_start: 0.7032 (mmp) cc_final: 0.6750 (tpp) REVERT: c 292 MET cc_start: 0.8996 (mmm) cc_final: 0.8768 (mmm) REVERT: d 75 MET cc_start: 0.8661 (mmp) cc_final: 0.7879 (mmm) REVERT: f 407 MET cc_start: -0.4326 (tpt) cc_final: -0.4533 (tpt) REVERT: f 825 MET cc_start: 0.3935 (mmm) cc_final: 0.3525 (ttm) REVERT: g 131 MET cc_start: 0.8010 (pmm) cc_final: 0.7755 (pmm) REVERT: p 171 MET cc_start: 0.9188 (mmm) cc_final: 0.8584 (tpt) REVERT: x 116 MET cc_start: 0.7624 (ptt) cc_final: 0.7086 (ptp) REVERT: x 181 MET cc_start: 0.4798 (ppp) cc_final: 0.4443 (mmm) REVERT: x 488 MET cc_start: 0.3065 (ttt) cc_final: 0.2263 (ptm) outliers start: 52 outliers final: 26 residues processed: 470 average time/residue: 0.8611 time to fit residues: 736.9202 Evaluate side-chains 467 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 436 time to evaluate : 9.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain y residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 1234 optimal weight: 1.9990 chunk 939 optimal weight: 40.0000 chunk 648 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 596 optimal weight: 10.0000 chunk 838 optimal weight: 6.9990 chunk 1253 optimal weight: 7.9990 chunk 1327 optimal weight: 7.9990 chunk 654 optimal weight: 6.9990 chunk 1188 optimal weight: 6.9990 chunk 357 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN U 91 ASN ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 311 ASN ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 178 HIS Y 388 ASN a 152 HIS ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 7 GLN x 197 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 111331 Z= 0.197 Angle : 0.538 14.327 150408 Z= 0.278 Chirality : 0.040 0.263 17031 Planarity : 0.004 0.055 19402 Dihedral : 5.298 88.998 15313 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.39 % Favored : 93.56 % Rotamer: Outliers : 0.74 % Allowed : 11.63 % Favored : 87.64 % 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: 0.23 (0.07), residues: 13813 helix: 1.63 (0.07), residues: 6433 sheet: 0.22 (0.12), residues: 2038 loop : -1.79 (0.08), residues: 5342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 215 HIS 0.008 0.001 HIS c 44 PHE 0.018 0.001 PHE f 713 TYR 0.022 0.001 TYR x 151 ARG 0.004 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 437 time to evaluate : 9.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: -0.0061 (tmm) cc_final: -0.0785 (ptt) REVERT: A 299 MET cc_start: 0.7397 (ttp) cc_final: 0.6937 (tmm) REVERT: A 319 MET cc_start: 0.8657 (tmm) cc_final: 0.8135 (ppp) REVERT: C 399 MET cc_start: 0.7895 (mmt) cc_final: 0.7565 (mmt) REVERT: C 404 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8256 (pp) REVERT: D 163 MET cc_start: 0.8449 (tpp) cc_final: 0.8226 (tpp) REVERT: D 384 MET cc_start: 0.8076 (tmm) cc_final: 0.7674 (tmm) REVERT: E 108 MET cc_start: 0.6508 (pmm) cc_final: 0.6161 (pmm) REVERT: E 122 MET cc_start: 0.8877 (mpp) cc_final: 0.8126 (ppp) REVERT: E 218 MET cc_start: 0.9358 (tpp) cc_final: 0.9130 (mmm) REVERT: F 366 MET cc_start: 0.9223 (tpp) cc_final: 0.8808 (tpp) REVERT: K 156 MET cc_start: 0.7924 (tpp) cc_final: 0.7300 (ttm) REVERT: P 131 MET cc_start: 0.6956 (ttm) cc_final: 0.6420 (ttm) REVERT: Q 28 MET cc_start: 0.8397 (mpp) cc_final: 0.8005 (mpp) REVERT: U 118 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5493 (pp) REVERT: U 137 MET cc_start: 0.8840 (mmm) cc_final: 0.8558 (mmm) REVERT: U 185 MET cc_start: 0.7579 (tpp) cc_final: 0.7014 (tpp) REVERT: U 885 MET cc_start: 0.7967 (tpt) cc_final: 0.7548 (tpt) REVERT: U 894 MET cc_start: 0.7535 (tmm) cc_final: 0.7003 (ppp) REVERT: V 463 MET cc_start: 0.7248 (tpt) cc_final: 0.6722 (ttt) REVERT: W 315 MET cc_start: 0.6163 (tpp) cc_final: 0.5952 (ttp) REVERT: W 436 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7571 (ppp) REVERT: X 260 MET cc_start: 0.7591 (ppp) cc_final: 0.7261 (ppp) REVERT: Y 104 MET cc_start: 0.6967 (ppp) cc_final: 0.6633 (ppp) REVERT: Y 214 MET cc_start: 0.3374 (mmp) cc_final: 0.2667 (mmm) REVERT: Z 78 MET cc_start: 0.8587 (mmt) cc_final: 0.8169 (tpp) REVERT: b 107 MET cc_start: 0.6092 (mmt) cc_final: 0.5574 (mmt) REVERT: c 41 MET cc_start: 0.8734 (tpp) cc_final: 0.8223 (mmm) REVERT: c 82 VAL cc_start: 0.0348 (OUTLIER) cc_final: 0.0043 (m) REVERT: c 167 MET cc_start: 0.7032 (mmp) cc_final: 0.6464 (tmm) REVERT: c 229 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7685 (pp) REVERT: c 292 MET cc_start: 0.8983 (mmm) cc_final: 0.8771 (mmm) REVERT: d 44 THR cc_start: 0.5302 (OUTLIER) cc_final: 0.5044 (p) REVERT: d 75 MET cc_start: 0.8698 (mmp) cc_final: 0.7854 (mmm) REVERT: d 237 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7153 (tp) REVERT: x 116 MET cc_start: 0.7618 (ptt) cc_final: 0.7059 (ptp) REVERT: x 181 MET cc_start: 0.4914 (ppp) cc_final: 0.4545 (mmm) REVERT: x 488 MET cc_start: 0.3265 (ttt) cc_final: 0.2433 (ptm) REVERT: y 58 ASP cc_start: 0.3567 (t70) cc_final: 0.3324 (t0) outliers start: 87 outliers final: 46 residues processed: 503 average time/residue: 0.8511 time to fit residues: 776.3702 Evaluate side-chains 489 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 436 time to evaluate : 9.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 82 VAL Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain k residue 94 VAL Chi-restraints excluded: chain o residue 178 ILE Chi-restraints excluded: chain p residue 165 GLU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain x residue 494 GLN Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 23 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 1105 optimal weight: 0.8980 chunk 753 optimal weight: 0.4980 chunk 19 optimal weight: 40.0000 chunk 988 optimal weight: 8.9990 chunk 547 optimal weight: 50.0000 chunk 1132 optimal weight: 9.9990 chunk 917 optimal weight: 40.0000 chunk 1 optimal weight: 9.9990 chunk 677 optimal weight: 30.0000 chunk 1191 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 overall best weight: 6.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 345 ASN ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 197 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 111331 Z= 0.189 Angle : 0.534 16.740 150408 Z= 0.275 Chirality : 0.040 0.272 17031 Planarity : 0.004 0.053 19402 Dihedral : 5.203 88.689 15311 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 1.21 % Allowed : 12.75 % Favored : 86.04 % 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: 0.28 (0.07), residues: 13813 helix: 1.68 (0.07), residues: 6453 sheet: 0.22 (0.12), residues: 2034 loop : -1.77 (0.08), residues: 5326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 215 HIS 0.008 0.001 HIS c 44 PHE 0.019 0.001 PHE f 713 TYR 0.022 0.001 TYR x 151 ARG 0.004 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 436 time to evaluate : 9.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: -0.0099 (tmm) cc_final: -0.0737 (ptt) REVERT: A 299 MET cc_start: 0.7375 (ttp) cc_final: 0.6922 (tmm) REVERT: A 319 MET cc_start: 0.8671 (tmm) cc_final: 0.8108 (ppp) REVERT: C 139 MET cc_start: 0.4515 (mmp) cc_final: 0.3559 (mtt) REVERT: C 399 MET cc_start: 0.7824 (mmt) cc_final: 0.7529 (mmt) REVERT: C 404 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8254 (pp) REVERT: D 163 MET cc_start: 0.8485 (tpp) cc_final: 0.8277 (tpp) REVERT: D 384 MET cc_start: 0.8074 (tmm) cc_final: 0.7780 (tmm) REVERT: E 108 MET cc_start: 0.6518 (pmm) cc_final: 0.6219 (pmm) REVERT: E 122 MET cc_start: 0.8909 (mpp) cc_final: 0.8123 (ppp) REVERT: F 175 MET cc_start: 0.7049 (ppp) cc_final: 0.6630 (ppp) REVERT: F 310 MET cc_start: 0.7659 (mmp) cc_final: 0.7420 (mmm) REVERT: F 366 MET cc_start: 0.9205 (tpp) cc_final: 0.8732 (tpp) REVERT: K 156 MET cc_start: 0.7951 (tpp) cc_final: 0.7545 (ttm) REVERT: Q 28 MET cc_start: 0.8327 (mpp) cc_final: 0.7887 (mpp) REVERT: U 118 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5454 (pp) REVERT: U 137 MET cc_start: 0.8837 (mmm) cc_final: 0.8589 (mmm) REVERT: U 185 MET cc_start: 0.7573 (tpp) cc_final: 0.7008 (tpp) REVERT: U 532 MET cc_start: 0.8675 (mtt) cc_final: 0.8371 (mtp) REVERT: U 885 MET cc_start: 0.7968 (tpt) cc_final: 0.7433 (tpt) REVERT: U 894 MET cc_start: 0.7579 (tmm) cc_final: 0.6811 (ppp) REVERT: V 463 MET cc_start: 0.7283 (tpt) cc_final: 0.6757 (ttt) REVERT: W 230 MET cc_start: 0.8422 (ppp) cc_final: 0.7841 (ppp) REVERT: W 334 GLU cc_start: 0.3558 (OUTLIER) cc_final: 0.2402 (tt0) REVERT: X 260 MET cc_start: 0.7542 (ppp) cc_final: 0.7225 (ppp) REVERT: Y 104 MET cc_start: 0.6932 (ppp) cc_final: 0.6589 (ppp) REVERT: Y 214 MET cc_start: 0.3256 (mmp) cc_final: 0.2709 (mmm) REVERT: Z 78 MET cc_start: 0.8608 (mmt) cc_final: 0.8174 (tpp) REVERT: b 107 MET cc_start: 0.6155 (mmt) cc_final: 0.5635 (mmt) REVERT: c 41 MET cc_start: 0.8765 (tpp) cc_final: 0.8348 (mmm) REVERT: c 167 MET cc_start: 0.7115 (mmp) cc_final: 0.6545 (tmm) REVERT: c 168 MET cc_start: 0.7661 (mmp) cc_final: 0.7432 (mmp) REVERT: c 226 MET cc_start: 0.8183 (mmp) cc_final: 0.7732 (mmp) REVERT: c 229 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7714 (pp) REVERT: c 292 MET cc_start: 0.8975 (mmm) cc_final: 0.8770 (mmm) REVERT: d 44 THR cc_start: 0.5305 (OUTLIER) cc_final: 0.5027 (p) REVERT: f 407 MET cc_start: -0.3938 (tpt) cc_final: -0.4264 (tpt) REVERT: m 27 MET cc_start: 0.8667 (mtm) cc_final: 0.8438 (mtm) REVERT: p 171 MET cc_start: 0.9181 (mmm) cc_final: 0.8907 (tpt) REVERT: t 50 MET cc_start: 0.8502 (ptt) cc_final: 0.8230 (ptt) REVERT: x 181 MET cc_start: 0.4899 (ppp) cc_final: 0.4539 (mmm) REVERT: x 488 MET cc_start: 0.3251 (ttt) cc_final: 0.2433 (ptm) REVERT: y 60 ASN cc_start: 0.5239 (t0) cc_final: 0.4930 (m110) outliers start: 143 outliers final: 77 residues processed: 553 average time/residue: 0.8674 time to fit residues: 875.0267 Evaluate side-chains 517 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 435 time to evaluate : 9.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain V residue 190 ASP Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 260 ASP Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain k residue 94 VAL Chi-restraints excluded: chain k residue 183 GLU Chi-restraints excluded: chain o residue 178 ILE Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain r residue 111 LEU Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain x residue 494 GLN Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 23 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 446 optimal weight: 6.9990 chunk 1195 optimal weight: 40.0000 chunk 262 optimal weight: 30.0000 chunk 779 optimal weight: 30.0000 chunk 327 optimal weight: 6.9990 chunk 1328 optimal weight: 9.9990 chunk 1102 optimal weight: 9.9990 chunk 615 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 439 optimal weight: 6.9990 chunk 697 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 463 ASN ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN ** c 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 475 ASN g 53 GLN x 197 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 111331 Z= 0.198 Angle : 0.544 16.050 150408 Z= 0.279 Chirality : 0.040 0.214 17031 Planarity : 0.004 0.052 19402 Dihedral : 5.190 88.236 15311 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.51 % Rotamer: Outliers : 1.18 % Allowed : 13.79 % Favored : 85.03 % 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: 0.30 (0.07), residues: 13813 helix: 1.69 (0.07), residues: 6458 sheet: 0.24 (0.12), residues: 2009 loop : -1.76 (0.08), residues: 5346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 215 HIS 0.008 0.001 HIS c 44 PHE 0.020 0.001 PHE O 36 TYR 0.022 0.001 TYR x 151 ARG 0.005 0.000 ARG T 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 437 time to evaluate : 9.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: -0.0127 (tmm) cc_final: -0.0656 (ptt) REVERT: A 319 MET cc_start: 0.8709 (tmm) cc_final: 0.7715 (mmt) REVERT: B 107 MET cc_start: 0.8281 (mmm) cc_final: 0.8062 (mpp) REVERT: C 139 MET cc_start: 0.4604 (mmp) cc_final: 0.3670 (mtt) REVERT: C 404 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8279 (pp) REVERT: D 384 MET cc_start: 0.8060 (tmm) cc_final: 0.7760 (tmm) REVERT: E 108 MET cc_start: 0.6491 (pmm) cc_final: 0.6225 (pmm) REVERT: E 122 MET cc_start: 0.8921 (mpp) cc_final: 0.8173 (ppp) REVERT: E 218 MET cc_start: 0.9182 (tpp) cc_final: 0.8973 (mmm) REVERT: F 310 MET cc_start: 0.7617 (mmp) cc_final: 0.7352 (mmm) REVERT: F 366 MET cc_start: 0.9191 (tpp) cc_final: 0.8725 (tpp) REVERT: G 80 MET cc_start: 0.7346 (mtp) cc_final: 0.7095 (mtp) REVERT: K 156 MET cc_start: 0.7950 (tpp) cc_final: 0.7556 (ttm) REVERT: U 118 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5465 (pp) REVERT: U 137 MET cc_start: 0.8820 (mmm) cc_final: 0.8607 (mmm) REVERT: U 185 MET cc_start: 0.7628 (tpp) cc_final: 0.6999 (tpp) REVERT: U 885 MET cc_start: 0.7964 (tpt) cc_final: 0.7452 (tpt) REVERT: U 894 MET cc_start: 0.7577 (tmm) cc_final: 0.7027 (ppp) REVERT: V 463 MET cc_start: 0.7301 (tpt) cc_final: 0.6775 (ttt) REVERT: W 230 MET cc_start: 0.8537 (ppp) cc_final: 0.8326 (ppp) REVERT: W 334 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2500 (tt0) REVERT: W 451 MET cc_start: 0.7614 (tmm) cc_final: 0.7311 (ppp) REVERT: X 260 MET cc_start: 0.7580 (ppp) cc_final: 0.7258 (ppp) REVERT: Y 104 MET cc_start: 0.6977 (ppp) cc_final: 0.6625 (ppp) REVERT: Y 214 MET cc_start: 0.3292 (mmp) cc_final: 0.2907 (mmm) REVERT: Z 78 MET cc_start: 0.8602 (mmt) cc_final: 0.8161 (tpp) REVERT: b 107 MET cc_start: 0.6208 (mmt) cc_final: 0.5641 (mmt) REVERT: c 41 MET cc_start: 0.8739 (tpp) cc_final: 0.8387 (mmm) REVERT: c 57 MET cc_start: 0.7337 (pmm) cc_final: 0.6754 (pmm) REVERT: c 167 MET cc_start: 0.7109 (mmp) cc_final: 0.6359 (pmm) REVERT: c 229 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7734 (pp) REVERT: d 44 THR cc_start: 0.5308 (OUTLIER) cc_final: 0.5027 (p) REVERT: d 237 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7129 (tp) REVERT: f 407 MET cc_start: -0.4022 (tpt) cc_final: -0.4257 (tpt) REVERT: f 788 MET cc_start: 0.4407 (mtm) cc_final: 0.4017 (mtm) REVERT: n 120 MET cc_start: 0.8358 (tpp) cc_final: 0.7716 (ttp) REVERT: t 50 MET cc_start: 0.8482 (ptt) cc_final: 0.8278 (ptt) REVERT: x 116 MET cc_start: 0.7626 (ptt) cc_final: 0.7123 (ptt) REVERT: x 163 MET cc_start: -0.0801 (ttp) cc_final: -0.1076 (tmm) REVERT: x 488 MET cc_start: 0.3281 (ttt) cc_final: 0.2465 (ptm) REVERT: y 60 ASN cc_start: 0.5121 (t0) cc_final: 0.4875 (m110) outliers start: 139 outliers final: 93 residues processed: 550 average time/residue: 0.8498 time to fit residues: 858.3420 Evaluate side-chains 535 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 436 time to evaluate : 9.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 135 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 182 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 260 ASP Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain d residue 248 GLU Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain k residue 94 VAL Chi-restraints excluded: chain k residue 183 GLU Chi-restraints excluded: chain o residue 178 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain r residue 86 MET Chi-restraints excluded: chain r residue 111 LEU Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain x residue 376 ASP Chi-restraints excluded: chain x residue 462 ASP Chi-restraints excluded: chain x residue 494 GLN Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 23 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 1280 optimal weight: 30.0000 chunk 149 optimal weight: 6.9990 chunk 756 optimal weight: 9.9990 chunk 970 optimal weight: 0.9980 chunk 751 optimal weight: 20.0000 chunk 1118 optimal weight: 0.1980 chunk 741 optimal weight: 0.7980 chunk 1323 optimal weight: 40.0000 chunk 828 optimal weight: 9.9990 chunk 806 optimal weight: 10.0000 chunk 610 optimal weight: 50.0000 overall best weight: 3.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 HIS ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 194 HIS ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 876 HIS k 224 GLN m 63 ASN n 123 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 111331 Z= 0.149 Angle : 0.529 16.746 150408 Z= 0.269 Chirality : 0.040 0.197 17031 Planarity : 0.003 0.055 19402 Dihedral : 5.082 87.982 15311 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 1.06 % Allowed : 14.36 % Favored : 84.58 % 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: 0.37 (0.07), residues: 13813 helix: 1.76 (0.07), residues: 6456 sheet: 0.24 (0.12), residues: 2009 loop : -1.73 (0.08), residues: 5348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 215 HIS 0.007 0.001 HIS c 44 PHE 0.020 0.001 PHE f 713 TYR 0.019 0.001 TYR x 151 ARG 0.004 0.000 ARG T 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 436 time to evaluate : 8.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: -0.0158 (tmm) cc_final: -0.0717 (ptt) REVERT: A 319 MET cc_start: 0.8730 (tmm) cc_final: 0.7736 (mmt) REVERT: B 107 MET cc_start: 0.8295 (mmm) cc_final: 0.8068 (mpp) REVERT: C 139 MET cc_start: 0.4692 (mmp) cc_final: 0.3782 (mtt) REVERT: C 404 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8244 (pp) REVERT: D 384 MET cc_start: 0.8050 (tmm) cc_final: 0.7738 (tmm) REVERT: E 108 MET cc_start: 0.6525 (pmm) cc_final: 0.6258 (pmm) REVERT: E 122 MET cc_start: 0.8913 (mpp) cc_final: 0.8167 (ppp) REVERT: E 218 MET cc_start: 0.9169 (tpp) cc_final: 0.8955 (mmm) REVERT: F 192 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7441 (t0) REVERT: F 310 MET cc_start: 0.7584 (mmp) cc_final: 0.7354 (mmm) REVERT: F 366 MET cc_start: 0.9177 (tpp) cc_final: 0.8698 (tpp) REVERT: K 156 MET cc_start: 0.7891 (tpp) cc_final: 0.7496 (ttm) REVERT: U 137 MET cc_start: 0.8815 (mmm) cc_final: 0.8595 (mmm) REVERT: U 185 MET cc_start: 0.7607 (tpp) cc_final: 0.6910 (tpp) REVERT: U 532 MET cc_start: 0.8719 (mtp) cc_final: 0.8419 (mtp) REVERT: U 885 MET cc_start: 0.7976 (tpt) cc_final: 0.7452 (tpt) REVERT: U 894 MET cc_start: 0.7519 (tmm) cc_final: 0.7018 (ppp) REVERT: V 463 MET cc_start: 0.7317 (tpt) cc_final: 0.6772 (ttt) REVERT: W 88 MET cc_start: 0.7654 (ptm) cc_final: 0.6555 (mmm) REVERT: W 334 GLU cc_start: 0.3508 (OUTLIER) cc_final: 0.2558 (tt0) REVERT: X 260 MET cc_start: 0.7549 (ppp) cc_final: 0.7231 (ppp) REVERT: Y 104 MET cc_start: 0.6919 (ppp) cc_final: 0.6573 (ppp) REVERT: Y 214 MET cc_start: 0.3394 (mmp) cc_final: 0.2848 (mmm) REVERT: Z 78 MET cc_start: 0.8599 (mmt) cc_final: 0.8153 (tpp) REVERT: b 107 MET cc_start: 0.6200 (mmt) cc_final: 0.5638 (mmt) REVERT: c 41 MET cc_start: 0.8735 (tpp) cc_final: 0.8424 (mmm) REVERT: c 51 MET cc_start: 0.7895 (mmm) cc_final: 0.7654 (ppp) REVERT: c 57 MET cc_start: 0.7407 (pmm) cc_final: 0.6922 (pmm) REVERT: c 167 MET cc_start: 0.7110 (mmp) cc_final: 0.6569 (tmm) REVERT: c 168 MET cc_start: 0.7551 (mmp) cc_final: 0.7327 (mmp) REVERT: c 229 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7766 (pp) REVERT: c 248 MET cc_start: 0.9147 (tmm) cc_final: 0.8811 (ppp) REVERT: d 44 THR cc_start: 0.5248 (OUTLIER) cc_final: 0.4970 (p) REVERT: f 407 MET cc_start: -0.4108 (tpt) cc_final: -0.4324 (tpt) REVERT: f 825 MET cc_start: 0.3922 (mmm) cc_final: 0.3641 (ptm) REVERT: m 27 MET cc_start: 0.8600 (mtm) cc_final: 0.8341 (mtm) REVERT: n 120 MET cc_start: 0.8359 (tpp) cc_final: 0.7750 (ttp) REVERT: p 124 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8799 (mp) REVERT: x 163 MET cc_start: -0.0762 (ttp) cc_final: -0.1051 (tmm) REVERT: x 181 MET cc_start: 0.5052 (ppp) cc_final: 0.4729 (mmm) REVERT: x 488 MET cc_start: 0.3222 (ttt) cc_final: 0.2963 (ttt) outliers start: 125 outliers final: 90 residues processed: 538 average time/residue: 0.8478 time to fit residues: 836.8698 Evaluate side-chains 531 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 435 time to evaluate : 9.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 135 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 908 ILE Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 182 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 260 ASP Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain k residue 183 GLU Chi-restraints excluded: chain o residue 178 ILE Chi-restraints excluded: chain p residue 124 LEU Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 92 LEU Chi-restraints excluded: chain r residue 111 LEU Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 23 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 818 optimal weight: 40.0000 chunk 528 optimal weight: 10.0000 chunk 790 optimal weight: 50.0000 chunk 398 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 841 optimal weight: 8.9990 chunk 901 optimal weight: 50.0000 chunk 654 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 chunk 1040 optimal weight: 8.9990 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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 333 GLN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 230 GLN ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 540 GLN f 868 HIS k 224 GLN ** p 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 197 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 111331 Z= 0.239 Angle : 0.585 17.788 150408 Z= 0.298 Chirality : 0.041 0.208 17031 Planarity : 0.004 0.053 19402 Dihedral : 5.207 88.649 15309 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 1.22 % Allowed : 14.78 % Favored : 84.01 % 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: 0.24 (0.07), residues: 13813 helix: 1.63 (0.07), residues: 6473 sheet: 0.24 (0.12), residues: 2002 loop : -1.79 (0.08), residues: 5338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 215 HIS 0.009 0.001 HIS c 44 PHE 0.020 0.001 PHE O 36 TYR 0.024 0.001 TYR x 151 ARG 0.007 0.000 ARG f 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 440 time to evaluate : 9.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8752 (tmm) cc_final: 0.7806 (mmt) REVERT: B 107 MET cc_start: 0.8339 (mmm) cc_final: 0.8099 (mpp) REVERT: B 214 MET cc_start: 0.6967 (tmm) cc_final: 0.6760 (tpp) REVERT: C 139 MET cc_start: 0.4714 (mmp) cc_final: 0.3852 (mtt) REVERT: C 404 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8308 (pp) REVERT: D 204 MET cc_start: 0.5994 (tpt) cc_final: 0.5232 (tpt) REVERT: D 384 MET cc_start: 0.8043 (tmm) cc_final: 0.7766 (tmm) REVERT: E 108 MET cc_start: 0.6583 (pmm) cc_final: 0.6325 (pmm) REVERT: E 122 MET cc_start: 0.8928 (mpp) cc_final: 0.8199 (ppp) REVERT: E 218 MET cc_start: 0.9152 (tpp) cc_final: 0.8930 (mmm) REVERT: F 192 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7373 (t0) REVERT: F 310 MET cc_start: 0.7603 (mmp) cc_final: 0.7346 (mmm) REVERT: F 366 MET cc_start: 0.9159 (tpp) cc_final: 0.8675 (tpp) REVERT: K 156 MET cc_start: 0.7919 (tpp) cc_final: 0.7569 (ttm) REVERT: Q 38 MET cc_start: 0.7939 (mmm) cc_final: 0.7615 (tpp) REVERT: U 137 MET cc_start: 0.8836 (mmm) cc_final: 0.8631 (mmm) REVERT: U 185 MET cc_start: 0.7573 (tpp) cc_final: 0.6887 (tpp) REVERT: U 532 MET cc_start: 0.8818 (mtp) cc_final: 0.8543 (mtp) REVERT: U 885 MET cc_start: 0.7961 (tpt) cc_final: 0.7395 (tpt) REVERT: U 894 MET cc_start: 0.7537 (tmm) cc_final: 0.7161 (ppp) REVERT: V 463 MET cc_start: 0.7284 (tpt) cc_final: 0.6814 (ttt) REVERT: V 494 MET cc_start: 0.6556 (mmm) cc_final: 0.6289 (mmm) REVERT: W 88 MET cc_start: 0.7674 (ptm) cc_final: 0.6572 (mmm) REVERT: W 230 MET cc_start: 0.8225 (ppp) cc_final: 0.7434 (ppp) REVERT: W 334 GLU cc_start: 0.3704 (OUTLIER) cc_final: 0.2973 (tt0) REVERT: W 451 MET cc_start: 0.7292 (ppp) cc_final: 0.7075 (ppp) REVERT: X 260 MET cc_start: 0.7499 (ppp) cc_final: 0.7186 (ppp) REVERT: Y 104 MET cc_start: 0.6986 (ppp) cc_final: 0.6627 (ppp) REVERT: Y 214 MET cc_start: 0.3450 (mmp) cc_final: 0.3058 (mmm) REVERT: Z 78 MET cc_start: 0.8645 (mmt) cc_final: 0.8178 (tpp) REVERT: b 107 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5383 (mmt) REVERT: c 41 MET cc_start: 0.8762 (tpp) cc_final: 0.8475 (mmm) REVERT: c 167 MET cc_start: 0.7145 (mmp) cc_final: 0.6426 (ppp) REVERT: c 226 MET cc_start: 0.8176 (mmp) cc_final: 0.7775 (mmp) REVERT: c 229 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7816 (pp) REVERT: c 248 MET cc_start: 0.9154 (tmm) cc_final: 0.8819 (ppp) REVERT: d 44 THR cc_start: 0.5331 (OUTLIER) cc_final: 0.5045 (p) REVERT: d 237 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7147 (tp) REVERT: d 255 MET cc_start: 0.5990 (mtm) cc_final: 0.5752 (mtm) REVERT: f 407 MET cc_start: -0.4004 (tpt) cc_final: -0.4226 (tpt) REVERT: f 788 MET cc_start: 0.4574 (mtm) cc_final: 0.4307 (mtm) REVERT: f 825 MET cc_start: 0.4061 (mmm) cc_final: 0.3817 (ptm) REVERT: g 131 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7696 (mpp) REVERT: m 27 MET cc_start: 0.8653 (mtm) cc_final: 0.8375 (mtm) REVERT: n 120 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7752 (ttp) REVERT: p 171 MET cc_start: 0.9180 (mmm) cc_final: 0.8875 (tpt) REVERT: x 116 MET cc_start: 0.7613 (ptt) cc_final: 0.7109 (ptt) REVERT: x 163 MET cc_start: -0.0615 (ttp) cc_final: -0.0875 (tmm) REVERT: x 181 MET cc_start: 0.5172 (ppp) cc_final: 0.4829 (mmm) REVERT: x 488 MET cc_start: 0.3437 (ttt) cc_final: 0.2605 (ptm) REVERT: y 34 GLU cc_start: 0.4358 (pt0) cc_final: 0.4120 (pt0) REVERT: y 58 ASP cc_start: 0.3430 (t70) cc_final: 0.3189 (t0) outliers start: 144 outliers final: 109 residues processed: 558 average time/residue: 0.8359 time to fit residues: 851.2406 Evaluate side-chains 556 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 438 time to evaluate : 9.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 135 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 908 ILE Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 259 LEU Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 182 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 118 ASN Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 260 ASP Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 107 MET Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain d residue 248 GLU Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 112 ASN Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 198 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain k residue 94 VAL Chi-restraints excluded: chain k residue 183 GLU Chi-restraints excluded: chain n residue 93 ASP Chi-restraints excluded: chain n residue 120 MET Chi-restraints excluded: chain o residue 178 ILE Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 92 LEU Chi-restraints excluded: chain r residue 111 LEU Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain x residue 462 ASP Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 23 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 1203 optimal weight: 5.9990 chunk 1267 optimal weight: 30.0000 chunk 1156 optimal weight: 5.9990 chunk 1233 optimal weight: 4.9990 chunk 742 optimal weight: 7.9990 chunk 537 optimal weight: 7.9990 chunk 968 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 1114 optimal weight: 7.9990 chunk 1166 optimal weight: 5.9990 chunk 1228 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 749 GLN ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 109 ASN ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 224 GLN n 123 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 111331 Z= 0.194 Angle : 0.562 17.956 150408 Z= 0.286 Chirality : 0.041 0.213 17031 Planarity : 0.004 0.055 19402 Dihedral : 5.149 89.437 15309 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 1.15 % Allowed : 15.09 % Favored : 83.76 % 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: 0.28 (0.07), residues: 13813 helix: 1.68 (0.07), residues: 6453 sheet: 0.20 (0.12), residues: 2005 loop : -1.76 (0.08), residues: 5355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 215 HIS 0.008 0.001 HIS c 44 PHE 0.021 0.001 PHE O 36 TYR 0.022 0.001 TYR x 151 ARG 0.006 0.000 ARG G 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 441 time to evaluate : 9.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8751 (tmm) cc_final: 0.7790 (mmt) REVERT: B 107 MET cc_start: 0.8357 (mmm) cc_final: 0.8110 (mpp) REVERT: C 139 MET cc_start: 0.4568 (mmp) cc_final: 0.3798 (mtt) REVERT: C 150 MET cc_start: 0.7156 (ptt) cc_final: 0.6951 (ptp) REVERT: C 404 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8228 (pp) REVERT: D 384 MET cc_start: 0.8023 (tmm) cc_final: 0.7735 (tmm) REVERT: E 108 MET cc_start: 0.6607 (pmm) cc_final: 0.6353 (pmm) REVERT: E 122 MET cc_start: 0.8899 (mpp) cc_final: 0.8149 (ppp) REVERT: E 218 MET cc_start: 0.9166 (tpp) cc_final: 0.8936 (mmm) REVERT: F 192 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7404 (t0) REVERT: F 366 MET cc_start: 0.9150 (tpp) cc_final: 0.8660 (tpp) REVERT: G 131 MET cc_start: 0.9139 (pmm) cc_final: 0.8879 (pmm) REVERT: K 156 MET cc_start: 0.7922 (tpp) cc_final: 0.7552 (ttm) REVERT: L 159 MET cc_start: 0.8999 (tpp) cc_final: 0.8740 (tpt) REVERT: Q 38 MET cc_start: 0.8033 (mmm) cc_final: 0.7505 (tpp) REVERT: U 137 MET cc_start: 0.8803 (mmm) cc_final: 0.8600 (mmm) REVERT: U 185 MET cc_start: 0.7539 (tpp) cc_final: 0.6864 (tpp) REVERT: U 532 MET cc_start: 0.8835 (mtp) cc_final: 0.8589 (mtp) REVERT: U 885 MET cc_start: 0.7953 (tpt) cc_final: 0.7371 (tpt) REVERT: U 894 MET cc_start: 0.7564 (tmm) cc_final: 0.7245 (ppp) REVERT: V 463 MET cc_start: 0.7308 (tpt) cc_final: 0.6819 (ttt) REVERT: V 494 MET cc_start: 0.6576 (mmm) cc_final: 0.6328 (mmm) REVERT: W 88 MET cc_start: 0.7612 (ptm) cc_final: 0.6553 (mmm) REVERT: W 230 MET cc_start: 0.8309 (ppp) cc_final: 0.7458 (ppp) REVERT: W 334 GLU cc_start: 0.3872 (OUTLIER) cc_final: 0.3173 (tt0) REVERT: W 451 MET cc_start: 0.7500 (ppp) cc_final: 0.7231 (ppp) REVERT: X 260 MET cc_start: 0.7460 (ppp) cc_final: 0.7149 (ppp) REVERT: Y 104 MET cc_start: 0.6993 (ppp) cc_final: 0.6638 (ppp) REVERT: Y 214 MET cc_start: 0.3525 (mmp) cc_final: 0.3185 (mmm) REVERT: Z 78 MET cc_start: 0.8625 (mmt) cc_final: 0.8164 (tpp) REVERT: b 107 MET cc_start: 0.6205 (mmt) cc_final: 0.5400 (mmt) REVERT: c 41 MET cc_start: 0.8748 (tpp) cc_final: 0.8486 (mmm) REVERT: c 57 MET cc_start: 0.7341 (pmm) cc_final: 0.6725 (pmm) REVERT: c 167 MET cc_start: 0.7165 (mmp) cc_final: 0.6485 (ppp) REVERT: c 226 MET cc_start: 0.8212 (mmp) cc_final: 0.7784 (mmp) REVERT: c 229 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7826 (pp) REVERT: c 248 MET cc_start: 0.9155 (tmm) cc_final: 0.8836 (ppp) REVERT: d 44 THR cc_start: 0.5284 (OUTLIER) cc_final: 0.4994 (p) REVERT: d 237 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7152 (tp) REVERT: d 255 MET cc_start: 0.5987 (mtm) cc_final: 0.5758 (mtm) REVERT: f 133 MET cc_start: 0.2307 (mmm) cc_final: 0.2046 (mmm) REVERT: f 788 MET cc_start: 0.4609 (mtm) cc_final: 0.4343 (mtm) REVERT: f 825 MET cc_start: 0.4075 (mmm) cc_final: 0.3853 (ptm) REVERT: m 27 MET cc_start: 0.8653 (mtm) cc_final: 0.8347 (mtm) REVERT: n 120 MET cc_start: 0.8387 (tpp) cc_final: 0.7758 (ttp) REVERT: p 38 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7848 (p0) REVERT: p 131 MET cc_start: 0.7156 (mmp) cc_final: 0.6794 (mmp) REVERT: x 116 MET cc_start: 0.7610 (ptt) cc_final: 0.7103 (ptt) REVERT: x 163 MET cc_start: -0.0534 (ttp) cc_final: -0.0788 (tmm) REVERT: x 181 MET cc_start: 0.5175 (ppp) cc_final: 0.4896 (mmm) REVERT: x 488 MET cc_start: 0.3337 (ttt) cc_final: 0.2495 (ptm) REVERT: y 34 GLU cc_start: 0.4330 (pt0) cc_final: 0.4088 (pt0) REVERT: y 58 ASP cc_start: 0.3530 (t70) cc_final: 0.3296 (t0) outliers start: 136 outliers final: 106 residues processed: 556 average time/residue: 0.8313 time to fit residues: 845.4612 Evaluate side-chains 551 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 438 time to evaluate : 9.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 135 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 214 ILE Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 908 ILE Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 259 LEU Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 182 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 118 ASN Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 260 ASP Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain d residue 248 GLU Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 112 ASN Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain f residue 808 ASN Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain k residue 94 VAL Chi-restraints excluded: chain k residue 183 GLU Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain o residue 178 ILE Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 92 LEU Chi-restraints excluded: chain r residue 111 LEU Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain x residue 376 ASP Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 23 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 809 optimal weight: 7.9990 chunk 1304 optimal weight: 20.0000 chunk 795 optimal weight: 6.9990 chunk 618 optimal weight: 7.9990 chunk 906 optimal weight: 40.0000 chunk 1367 optimal weight: 20.0000 chunk 1258 optimal weight: 10.0000 chunk 1089 optimal weight: 30.0000 chunk 113 optimal weight: 0.0980 chunk 841 optimal weight: 0.8980 chunk 667 optimal weight: 8.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 426 ASN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS n 123 GLN x 197 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 111331 Z= 0.170 Angle : 0.560 18.808 150408 Z= 0.282 Chirality : 0.040 0.360 17031 Planarity : 0.003 0.072 19402 Dihedral : 5.087 89.560 15309 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 1.09 % Allowed : 15.21 % Favored : 83.70 % 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: 0.32 (0.07), residues: 13813 helix: 1.72 (0.07), residues: 6446 sheet: 0.17 (0.12), residues: 2022 loop : -1.73 (0.08), residues: 5345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 215 HIS 0.008 0.001 HIS c 44 PHE 0.021 0.001 PHE O 36 TYR 0.022 0.001 TYR x 151 ARG 0.018 0.000 ARG F 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27626 Ramachandran restraints generated. 13813 Oldfield, 0 Emsley, 13813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 437 time to evaluate : 9.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8767 (tmm) cc_final: 0.7795 (mmt) REVERT: B 107 MET cc_start: 0.8379 (mmm) cc_final: 0.8124 (mpp) REVERT: C 138 MET cc_start: 0.6058 (mpp) cc_final: 0.5831 (mpp) REVERT: C 139 MET cc_start: 0.4540 (mmp) cc_final: 0.3785 (mtt) REVERT: C 404 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8278 (pp) REVERT: D 384 MET cc_start: 0.8021 (tmm) cc_final: 0.7738 (tmm) REVERT: E 108 MET cc_start: 0.6549 (pmm) cc_final: 0.6298 (pmm) REVERT: E 122 MET cc_start: 0.8901 (mpp) cc_final: 0.8152 (ppp) REVERT: E 192 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6652 (t0) REVERT: E 218 MET cc_start: 0.9183 (tpp) cc_final: 0.8958 (mmm) REVERT: F 192 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7439 (t0) REVERT: F 366 MET cc_start: 0.9157 (tpp) cc_final: 0.8656 (tpp) REVERT: K 156 MET cc_start: 0.7929 (tpp) cc_final: 0.7571 (ttm) REVERT: L 159 MET cc_start: 0.8992 (tpp) cc_final: 0.8737 (tpt) REVERT: Q 38 MET cc_start: 0.8042 (mmm) cc_final: 0.7824 (tpp) REVERT: U 137 MET cc_start: 0.8794 (mmm) cc_final: 0.8592 (mmm) REVERT: U 532 MET cc_start: 0.8847 (mtp) cc_final: 0.8644 (mtp) REVERT: U 885 MET cc_start: 0.7949 (tpt) cc_final: 0.7368 (tpt) REVERT: U 894 MET cc_start: 0.7548 (tmm) cc_final: 0.7019 (ppp) REVERT: V 463 MET cc_start: 0.7286 (tpt) cc_final: 0.6786 (ttt) REVERT: W 88 MET cc_start: 0.7591 (ptm) cc_final: 0.6535 (mmm) REVERT: W 230 MET cc_start: 0.8355 (ppp) cc_final: 0.7552 (ppp) REVERT: W 314 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5679 (mm) REVERT: W 334 GLU cc_start: 0.3893 (OUTLIER) cc_final: 0.3224 (tt0) REVERT: W 375 MET cc_start: 0.8425 (mmm) cc_final: 0.7998 (mpp) REVERT: W 451 MET cc_start: 0.7441 (ppp) cc_final: 0.7163 (ppp) REVERT: X 260 MET cc_start: 0.7441 (ppp) cc_final: 0.7131 (ppp) REVERT: Y 104 MET cc_start: 0.6925 (ppp) cc_final: 0.6574 (ppp) REVERT: Y 214 MET cc_start: 0.3424 (mmp) cc_final: 0.3089 (mmm) REVERT: Z 78 MET cc_start: 0.8618 (mmt) cc_final: 0.8164 (tpp) REVERT: c 41 MET cc_start: 0.8748 (tpp) cc_final: 0.8504 (mmm) REVERT: c 57 MET cc_start: 0.7384 (pmm) cc_final: 0.6780 (pmm) REVERT: c 167 MET cc_start: 0.7196 (mmp) cc_final: 0.6380 (ppp) REVERT: c 226 MET cc_start: 0.8290 (mmp) cc_final: 0.7861 (mmp) REVERT: c 229 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7821 (pp) REVERT: c 248 MET cc_start: 0.9149 (tmm) cc_final: 0.8824 (ppp) REVERT: d 44 THR cc_start: 0.5205 (OUTLIER) cc_final: 0.4911 (p) REVERT: d 237 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7108 (tp) REVERT: d 255 MET cc_start: 0.6021 (mtm) cc_final: 0.5800 (mtm) REVERT: f 133 MET cc_start: 0.2408 (mmm) cc_final: 0.2169 (mmm) REVERT: f 788 MET cc_start: 0.4602 (mtm) cc_final: 0.4368 (mtm) REVERT: n 120 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: p 38 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7835 (p0) REVERT: p 131 MET cc_start: 0.7029 (mmp) cc_final: 0.6752 (mmp) REVERT: x 163 MET cc_start: -0.0548 (ttp) cc_final: -0.0823 (tmm) REVERT: x 181 MET cc_start: 0.5150 (ppp) cc_final: 0.4863 (mmm) REVERT: x 488 MET cc_start: 0.3282 (ttt) cc_final: 0.2465 (ptm) REVERT: y 34 GLU cc_start: 0.4408 (pt0) cc_final: 0.4172 (pt0) REVERT: y 58 ASP cc_start: 0.3555 (t70) cc_final: 0.3313 (t0) outliers start: 129 outliers final: 110 residues processed: 547 average time/residue: 0.9405 time to fit residues: 943.4139 Evaluate side-chains 557 residues out of total 11891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 437 time to evaluate : 9.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 184 MET Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain S residue 74 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 214 ILE Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 908 ILE Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 259 LEU Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 314 LEU Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 182 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 118 ASN Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 260 ASP Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain d residue 248 GLU Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 112 ASN Chi-restraints excluded: chain f residue 209 MET Chi-restraints excluded: chain f residue 808 ASN Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 83 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 198 VAL Chi-restraints excluded: chain j residue 219 ILE Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain k residue 94 VAL Chi-restraints excluded: chain k residue 183 GLU Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain n residue 93 ASP Chi-restraints excluded: chain n residue 120 MET Chi-restraints excluded: chain o residue 178 ILE Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 92 LEU Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 111 LEU Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain x residue 376 ASP Chi-restraints excluded: chain x residue 462 ASP Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 23 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1373 random chunks: chunk 865 optimal weight: 6.9990 chunk 1160 optimal weight: 30.0000 chunk 333 optimal weight: 8.9990 chunk 1004 optimal weight: 40.0000 chunk 160 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 1090 optimal weight: 2.9990 chunk 456 optimal weight: 10.0000 chunk 1120 optimal weight: 20.0000 chunk 138 optimal weight: 40.0000 chunk 200 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** Q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 426 ASN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 197 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.034248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.028898 restraints weight = 1957134.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.029314 restraints weight = 1096652.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.029611 restraints weight = 718740.913| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 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 = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 111331 Z= 0.206 Angle : 0.579 18.280 150408 Z= 0.293 Chirality : 0.041 0.271 17031 Planarity : 0.004 0.062 19402 Dihedral : 5.130 90.014 15309 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.50 % Favored : 93.45 % Rotamer: Outliers : 1.12 % Allowed : 15.30 % Favored : 83.58 % 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: 0.27 (0.07), residues: 13813 helix: 1.68 (0.07), residues: 6445 sheet: 0.19 (0.12), residues: 2024 loop : -1.76 (0.08), residues: 5344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 215 HIS 0.009 0.001 HIS c 44 PHE 0.021 0.001 PHE O 36 TYR 0.024 0.001 TYR x 151 ARG 0.011 0.000 ARG F 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17279.62 seconds wall clock time: 309 minutes 2.83 seconds (18542.83 seconds total)