Starting phenix.real_space_refine on Sat Apr 6 12:15:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3g_32279/04_2024/7w3g_32279_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3g_32279/04_2024/7w3g_32279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3g_32279/04_2024/7w3g_32279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3g_32279/04_2024/7w3g_32279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3g_32279/04_2024/7w3g_32279_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3g_32279/04_2024/7w3g_32279_updated.pdb" } resolution = 3.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 S 640 5.16 5 C 70002 2.51 5 N 19009 2.21 5 O 21075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "T TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 25": "OD1" <-> "OD2" Residue "h ASP 181": "OD1" <-> "OD2" Residue "h GLU 183": "OE1" <-> "OE2" Residue "l TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 110741 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 389} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3207 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 389} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3105 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 379} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3097 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 19, 'TRANS': 369} Chain: "F" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Link IDs: {'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: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6828 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 31, 'TRANS': 840} Chain breaks: 1 Chain: "X" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 369} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "f" Number of atoms: 6866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6866 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 34, 'TRANS': 854} Chain: "g" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1879 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "h" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1782 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1861 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "m" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "n" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "p" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "q" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1549 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "s" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "t" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "x" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3929 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "y" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "W" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3635 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 437} Chain: "v" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'UNK:plan-1': 34} Unresolved non-hydrogen planarities: 34 Chain: "V" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3612 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 15, 'TRANS': 428} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 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: 41.90, per 1000 atoms: 0.38 Number of scatterers: 110741 At special positions: 0 Unit cell: (326.745, 219.885, 225.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 640 16.00 P 14 15.00 O 21075 8.00 N 19009 7.00 C 70002 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: 32.51 Conformation dependent library (CDL) restraints added in 15.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26378 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: 513 helices and 94 sheets defined 54.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 55.92 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.666A pdb=" N LEU A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 74 through 82 removed outlier: 4.315A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 5.461A pdb=" N LEU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.908A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.929A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.246A 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 192 Processing helix chain 'A' and resid 193 through 198 Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.262A pdb=" N LEU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.656A pdb=" N THR A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 5.066A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.584A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.373A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.714A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 361 removed outlier: 5.849A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.575A pdb=" N CYS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 4.564A 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 33 through 38 removed outlier: 4.504A pdb=" N LYS B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 38' Processing helix chain 'B' and resid 58 through 86 removed outlier: 4.798A pdb=" N LYS B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 6.377A pdb=" N SER B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.948A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 208 through 215 removed outlier: 5.235A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.593A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 4.060A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 357 through 373 removed outlier: 5.160A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.745A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'C' and resid 21 through 68 removed outlier: 3.882A pdb=" N ARG C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 removed outlier: 4.315A pdb=" N MET C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 139' Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.050A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 195 through 207 removed outlier: 3.712A pdb=" N HIS C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 242 removed outlier: 5.711A pdb=" N MET C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS C 241 " --> pdb=" O MET C 237 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 282 removed outlier: 4.172A pdb=" N GLN C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.901A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ASP C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 302' Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.804A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 7.281A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.653A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 406 removed outlier: 3.966A pdb=" N LYS C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TRP C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 83 removed outlier: 3.966A pdb=" N ILE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.445A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 211 through 223 removed outlier: 3.964A pdb=" N LEU D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 removed outlier: 4.016A pdb=" N PHE D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 236' Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.592A pdb=" N VAL D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 297 removed outlier: 3.755A pdb=" N GLN D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.845A pdb=" N LYS D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 5.147A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 390 Processing helix chain 'D' and resid 395 through 409 removed outlier: 7.009A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 5.046A pdb=" N GLY D 168 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 51 removed outlier: 6.487A pdb=" N ALA E 8 " --> pdb=" O PRO E 4 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.465A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 123 removed outlier: 3.727A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN E 121 " --> pdb=" O PRO E 117 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 154 removed outlier: 3.965A pdb=" N ILE E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 155 through 163 removed outlier: 3.707A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 190 removed outlier: 3.929A pdb=" N LEU E 182 " --> pdb=" O THR E 178 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 3.663A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 267 removed outlier: 5.214A pdb=" N GLY E 266 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE E 267 " --> pdb=" O GLN E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 305 through 318 removed outlier: 5.967A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 358 removed outlier: 5.704A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.621A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 33 Processing helix chain 'F' and resid 37 through 85 removed outlier: 4.134A pdb=" N ILE F 41 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS F 56 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.987A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.510A 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 176 removed outlier: 4.169A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.418A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 removed outlier: 5.111A pdb=" N GLU F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 245 removed outlier: 4.894A pdb=" N LYS F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.492A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 removed outlier: 4.060A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 320 removed outlier: 5.650A pdb=" N ARG F 308 " --> pdb=" O ARG F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 4.363A pdb=" N ASP F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 372 removed outlier: 5.789A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 4.825A 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 'F' and resid 184 through 189 removed outlier: 3.532A pdb=" N ASP F 187 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 188 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLY F 189 " --> pdb=" O SER F 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.581A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.636A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.361A 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: 3.868A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.486A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.998A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 4.474A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.740A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.590A pdb=" N SER H 116 " --> pdb=" O GLN H 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.099A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 removed outlier: 4.181A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 209' Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'H' and resid 4 through 9 removed outlier: 3.742A pdb=" N SER H 7 " --> pdb=" O ARG H 4 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE H 8 " --> pdb=" O GLY H 5 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER H 9 " --> pdb=" O TYR H 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 4 through 9' Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.675A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.585A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N HIS h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 58 through 63' Processing helix chain 'h' and resid 79 through 102 Processing helix chain 'h' and resid 106 through 124 removed outlier: 3.946A pdb=" N TYR h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN h 123 " --> pdb=" O GLN h 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 5.348A pdb=" N ALA h 187 " --> pdb=" O GLU h 183 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 209 removed outlier: 4.220A pdb=" N ILE h 208 " --> pdb=" O THR h 204 " (cutoff:3.500A) removed outlier: 6.207A 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 29 removed outlier: 3.907A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLY I 29 " --> pdb=" O MET I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 4.006A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.798A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 202 removed outlier: 5.704A pdb=" N ASP I 202 " --> pdb=" O ASN I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 4.001A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 251 removed outlier: 3.580A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 28 removed outlier: 3.820A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 4.673A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.541A 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: 3.743A pdb=" N ALA J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.701A pdb=" N TYR J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 177 through 183 removed outlier: 3.853A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 177 through 183' Processing helix chain 'J' and resid 184 through 199 removed outlier: 3.822A pdb=" N GLU J 197 " --> pdb=" O LYS J 193 " (cutoff:3.500A) removed outlier: 4.413A 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 'j' and resid 16 through 30 removed outlier: 3.661A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.945A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.609A 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: 3.638A pdb=" N ILE j 107 " --> pdb=" O THR j 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 3.545A pdb=" N VAL j 168 " --> pdb=" O GLY j 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 184 removed outlier: 4.232A pdb=" N THR j 183 " --> pdb=" O GLU j 179 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP j 184 " --> pdb=" O ALA j 180 " (cutoff:3.500A) Processing helix chain 'j' and resid 185 through 199 removed outlier: 3.805A 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 5 through 10 removed outlier: 3.523A pdb=" N ASP K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 5 through 10' Processing helix chain 'K' and resid 21 through 35 removed outlier: 3.838A pdb=" N GLU K 29 " --> pdb=" O GLU K 25 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA K 30 " --> pdb=" O TYR K 26 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.021A 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: 4.163A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 122 removed outlier: 4.054A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.906A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 211 through 216 removed outlier: 4.261A pdb=" N ILE K 215 " --> pdb=" O ASN K 211 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU K 216 " --> pdb=" O ALA K 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 211 through 216' Processing helix chain 'K' and resid 230 through 241 removed outlier: 3.844A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 8 removed outlier: 3.831A pdb=" N TYR L 6 " --> pdb=" O PHE L 2 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.599A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 4.507A 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: 4.143A 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: 4.702A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.957A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 225 through 236 removed outlier: 4.310A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 4.059A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.693A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 125 removed outlier: 4.000A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.377A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.915A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (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: 3.735A pdb=" N TYR N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.473A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.515A 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: 3.928A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.805A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.531A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG o 89 " --> pdb=" O GLN o 85 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.703A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 Processing helix chain 'P' and resid 3 through 8 removed outlier: 5.266A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 3 through 8' Processing helix chain 'P' and resid 56 through 79 Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.214A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 3.926A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 3.955A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 8 removed outlier: 4.880A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 3 through 8' Processing helix chain 'p' and resid 56 through 79 Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.288A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 3.989A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.082A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 72 removed outlier: 6.699A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 95 removed outlier: 4.200A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG Q 95 " --> pdb=" O CYS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.619A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 171 Processing helix chain 'q' and resid 50 through 72 removed outlier: 6.781A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 95 removed outlier: 4.366A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG q 95 " --> pdb=" O CYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.784A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 171 Processing helix chain 'R' and resid 48 through 71 Processing helix chain 'R' and resid 75 through 91 removed outlier: 4.020A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.980A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 4.026A 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 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 91 removed outlier: 4.015A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 4.001A pdb=" N GLY r 137 " --> pdb=" O VAL r 133 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.925A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.319A 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: 3.941A pdb=" N GLU S 184 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 80 Processing helix chain 's' and resid 84 through 100 removed outlier: 4.008A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.303A 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: 3.946A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.941A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 158 removed outlier: 4.364A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix Proline residue: T 158 - end of helix Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 4.821A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.216A 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: 3.543A pdb=" N PHE t 60 " --> pdb=" O ASP t 56 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.661A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 158 removed outlier: 4.275A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Proline residue: t 158 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 5.044A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'U' and resid 8 through 15 removed outlier: 3.651A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP U 15 " --> pdb=" O LEU U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 35 removed outlier: 3.933A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASN U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 42 removed outlier: 4.309A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 52 removed outlier: 5.282A pdb=" N GLU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 Processing helix chain 'U' and resid 94 through 119 Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 removed outlier: 4.003A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 4.224A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 171 removed outlier: 5.003A pdb=" N SER U 170 " --> pdb=" O THR U 166 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN U 171 " --> pdb=" O ILE U 167 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 187 removed outlier: 4.520A pdb=" N ALA U 178 " --> pdb=" O PRO U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 209 removed outlier: 4.076A pdb=" N ASN U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU U 209 " --> pdb=" O TYR U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 Processing helix chain 'U' and resid 225 through 240 Processing helix chain 'U' and resid 241 through 256 Processing helix chain 'U' and resid 258 through 270 removed outlier: 6.160A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 removed outlier: 3.831A pdb=" N LYS U 324 " --> pdb=" O ASP U 320 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 346 Processing helix chain 'U' and resid 349 through 361 removed outlier: 5.324A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG U 361 " --> pdb=" O LYS U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 3.966A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 390 removed outlier: 4.489A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU U 390 " --> pdb=" O LEU U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 391 through 397 removed outlier: 4.426A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR U 397 " --> pdb=" O LEU U 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 413 removed outlier: 6.437A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR U 403 " --> pdb=" O TRP U 399 " (cutoff:3.500A) Processing helix chain 'U' and resid 418 through 427 Processing helix chain 'U' and resid 435 through 451 removed outlier: 3.775A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS U 450 " --> pdb=" O LEU U 446 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 4.580A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR U 460 " --> pdb=" O ASP U 456 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN U 467 " --> pdb=" O ASN U 463 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 486 removed outlier: 4.660A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 3.828A pdb=" N GLN U 503 " --> pdb=" O THR U 499 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 521 removed outlier: 3.953A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 3.854A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 4.828A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 573 Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.821A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.226A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 643 removed outlier: 4.017A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 4.812A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 4.152A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 677 removed outlier: 6.462A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) Proline residue: U 674 - end of helix removed outlier: 5.053A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.757A pdb=" N ARG U 684 " --> pdb=" O VAL U 680 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 removed outlier: 4.458A pdb=" N CYS U 703 " --> pdb=" O THR U 699 " (cutoff:3.500A) Proline residue: U 704 - end of helix No H-bonds generated for 'chain 'U' and resid 699 through 704' Processing helix chain 'U' and resid 705 through 720 removed outlier: 5.806A pdb=" N LYS U 720 " --> pdb=" O VAL U 716 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 739 removed outlier: 3.608A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 769 removed outlier: 3.707A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) Processing helix chain 'U' and resid 778 through 784 removed outlier: 4.018A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) Processing helix chain 'U' and resid 835 through 850 Processing helix chain 'U' and resid 864 through 871 removed outlier: 4.471A pdb=" N GLU U 870 " --> pdb=" O GLU U 866 " (cutoff:3.500A) Proline residue: U 871 - end of helix Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.774A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'U' and resid 772 through 777 removed outlier: 3.722A pdb=" N HIS U 777 " --> pdb=" O PRO U 774 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 61 Processing helix chain 'X' and resid 62 through 74 removed outlier: 4.547A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 100 Processing helix chain 'X' and resid 105 through 121 Processing helix chain 'X' and resid 122 through 141 Processing helix chain 'X' and resid 143 through 161 removed outlier: 5.100A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 4.598A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 198 removed outlier: 3.904A pdb=" N ASN X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 222 removed outlier: 5.052A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.590A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR X 229 " --> pdb=" O TRP X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 3.975A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 274 removed outlier: 4.760A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY X 273 " --> pdb=" O ALA X 269 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS X 274 " --> pdb=" O LEU X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 275 through 280 removed outlier: 3.957A pdb=" N TYR X 279 " --> pdb=" O LEU X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.985A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 340 removed outlier: 5.030A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE X 339 " --> pdb=" O LEU X 335 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.626A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 Processing helix chain 'X' and resid 394 through 422 removed outlier: 3.805A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 80 removed outlier: 3.728A pdb=" N SER X 79 " --> pdb=" O PHE X 76 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE X 80 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 29 removed outlier: 3.816A pdb=" N LEU Y 28 " --> pdb=" O PHE Y 24 " (cutoff:3.500A) Proline residue: Y 29 - end of helix Processing helix chain 'Y' and resid 34 through 48 removed outlier: 4.619A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN Y 48 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 61 removed outlier: 4.693A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 92 removed outlier: 5.856A pdb=" N LEU Y 69 " --> pdb=" O ILE Y 65 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 114 Processing helix chain 'Y' and resid 116 through 129 removed outlier: 5.004A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 4.429A pdb=" N ILE Y 140 " --> pdb=" O HIS Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 167 Processing helix chain 'Y' and resid 173 through 191 removed outlier: 7.003A pdb=" N ARG Y 177 " --> pdb=" O ASP Y 173 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL Y 182 " --> pdb=" O ASN Y 178 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR Y 183 " --> pdb=" O ARG Y 179 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE Y 191 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 202 removed outlier: 4.024A pdb=" N PHE Y 201 " --> pdb=" O ALA Y 197 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU Y 202 " --> pdb=" O ALA Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 Processing helix chain 'Y' and resid 243 through 254 removed outlier: 3.807A pdb=" N SER Y 252 " --> pdb=" O GLU Y 248 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU Y 253 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.688A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 286 removed outlier: 3.986A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TRP Y 286 " --> pdb=" O MET Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 310 removed outlier: 4.328A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 324 removed outlier: 3.903A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 3.998A pdb=" N GLY Y 341 " --> pdb=" O PHE Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 388 removed outlier: 4.262A pdb=" N LYS Y 371 " --> pdb=" O GLN Y 367 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP Y 374 " --> pdb=" O ILE Y 370 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 237 through 242 Processing helix chain 'Z' and resid 12 through 30 removed outlier: 4.138A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) removed outlier: 5.047A 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 104 through 117 removed outlier: 4.673A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS Z 116 " --> pdb=" O MET Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix Processing helix chain 'Z' and resid 166 through 177 removed outlier: 6.561A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 218 Processing helix chain 'Z' and resid 225 through 238 removed outlier: 5.050A pdb=" N GLN Z 229 " --> pdb=" O GLN Z 225 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE Z 234 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) Proline residue: Z 238 - end of helix Processing helix chain 'Z' and resid 241 through 260 removed outlier: 4.351A pdb=" N PHE Z 245 " --> pdb=" O SER Z 241 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL Z 246 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS Z 247 " --> pdb=" O GLN Z 243 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR Z 250 " --> pdb=" O VAL Z 246 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU Z 251 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS Z 252 " --> pdb=" O ALA Z 248 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR Z 253 " --> pdb=" O PHE Z 249 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 262 through 290 removed outlier: 3.702A pdb=" N GLU Z 289 " --> pdb=" O ALA Z 285 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY Z 290 " --> pdb=" O GLU Z 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 removed outlier: 3.769A pdb=" N GLN a 12 " --> pdb=" O LEU a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 32 removed outlier: 4.500A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR a 29 " --> pdb=" O LEU a 25 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 4.335A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 removed outlier: 4.746A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU a 68 " --> pdb=" O ILE a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 Processing helix chain 'a' and resid 89 through 105 removed outlier: 3.670A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 124 removed outlier: 4.609A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 142 removed outlier: 4.670A pdb=" N GLU a 133 " --> pdb=" O GLN a 129 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 163 removed outlier: 4.084A pdb=" N TYR a 163 " --> pdb=" O SER a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 4.531A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 Processing helix chain 'a' and resid 215 through 220 removed outlier: 3.783A 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 221 through 226 removed outlier: 4.013A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 243 Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.734A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 265 removed outlier: 6.460A pdb=" N ALA a 263 " --> pdb=" O PRO a 259 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 284 removed outlier: 3.664A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 292 through 301 removed outlier: 3.931A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 318 removed outlier: 4.619A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 376 removed outlier: 4.740A pdb=" N LYS a 347 " --> pdb=" O LEU a 343 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY a 348 " --> pdb=" O GLN a 344 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 45 removed outlier: 3.919A pdb=" N ALA b 28 " --> pdb=" O THR b 24 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Proline residue: b 45 - end of helix Processing helix chain 'b' and resid 67 through 77 removed outlier: 4.275A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 4.903A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 removed outlier: 4.424A pdb=" N LEU b 124 " --> pdb=" O ASN b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 162 Processing helix chain 'b' and resid 179 through 190 removed outlier: 4.365A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'c' and resid 34 through 49 Processing helix chain 'c' and resid 88 through 103 removed outlier: 3.973A 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: 3.577A pdb=" N SER c 150 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 5.378A 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 164 through 170 removed outlier: 4.685A pdb=" N MET c 168 " --> pdb=" O ASN c 164 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL c 169 " --> pdb=" O ALA c 165 " (cutoff:3.500A) Processing helix chain 'c' and resid 179 through 184 removed outlier: 4.572A pdb=" N HIS c 183 " --> pdb=" O SER c 179 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU c 184 " --> pdb=" O ASN c 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 179 through 184' Processing helix chain 'c' and resid 188 through 195 removed outlier: 4.001A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 220 removed outlier: 7.013A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 removed outlier: 4.909A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR c 230 " --> pdb=" O MET c 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 224 through 230' Processing helix chain 'c' and resid 234 through 260 removed outlier: 3.817A pdb=" N CYS c 238 " --> pdb=" O TYR c 234 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS c 240 " --> pdb=" O GLU c 236 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 275 Processing helix chain 'c' and resid 284 through 310 removed outlier: 4.245A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE c 309 " --> pdb=" O ASP c 305 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 34 removed outlier: 4.434A pdb=" N LEU d 33 " --> pdb=" O VAL d 29 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN d 34 " --> pdb=" O LEU d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 66 Processing helix chain 'd' and resid 67 through 84 Processing helix chain 'd' and resid 94 through 110 Processing helix chain 'd' and resid 111 through 122 removed outlier: 3.777A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 4.396A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 156 removed outlier: 4.895A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 184 removed outlier: 4.272A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 199 Processing helix chain 'd' and resid 203 through 214 removed outlier: 4.673A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP d 208 " --> pdb=" O LYS d 204 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY d 214 " --> pdb=" O ALA d 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 254 removed outlier: 5.313A pdb=" N SER d 239 " --> pdb=" O THR d 235 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR d 240 " --> pdb=" O THR d 236 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU d 241 " --> pdb=" O ILE d 237 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 23 Proline residue: f 10 - end of helix Proline residue: f 13 - end of helix Proline residue: f 17 - end of helix removed outlier: 3.827A pdb=" N ALA f 20 " --> pdb=" O SER f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 27 through 49 removed outlier: 4.558A pdb=" N GLU f 32 " --> pdb=" O PRO f 28 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA f 36 " --> pdb=" O GLU f 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS f 41 " --> pdb=" O GLY f 37 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASP f 49 " --> pdb=" O LEU f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 62 removed outlier: 4.156A pdb=" N ARG f 62 " --> pdb=" O MET f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 63 through 75 removed outlier: 4.061A pdb=" N SER f 69 " --> pdb=" O GLU f 65 " (cutoff:3.500A) Proline residue: f 73 - end of helix Processing helix chain 'f' and resid 81 through 95 removed outlier: 4.657A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) Proline residue: f 93 - end of helix Processing helix chain 'f' and resid 105 through 114 removed outlier: 4.463A pdb=" N ILE f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR f 110 " --> pdb=" O LEU f 106 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN f 112 " --> pdb=" O GLU f 108 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N MET f 113 " --> pdb=" O ILE f 109 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA f 114 " --> pdb=" O TYR f 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 124 removed outlier: 4.588A pdb=" N ASP f 124 " --> pdb=" O ARG f 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 146 Processing helix chain 'f' and resid 153 through 175 removed outlier: 4.424A pdb=" N GLU f 157 " --> pdb=" O SER f 153 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL f 159 " --> pdb=" O GLY f 155 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG f 160 " --> pdb=" O HIS f 156 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN f 171 " --> pdb=" O ALA f 167 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU f 172 " --> pdb=" O LYS f 168 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP f 174 " --> pdb=" O TRP f 170 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP f 175 " --> pdb=" O GLN f 171 " (cutoff:3.500A) Processing helix chain 'f' and resid 177 through 189 Proline residue: f 183 - end of helix Processing helix chain 'f' and resid 193 through 208 removed outlier: 3.652A pdb=" N ALA f 200 " --> pdb=" O MET f 196 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP f 206 " --> pdb=" O HIS f 202 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 209 through 227 removed outlier: 4.393A pdb=" N GLN f 213 " --> pdb=" O MET f 209 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL f 214 " --> pdb=" O GLU f 210 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP f 215 " --> pdb=" O ILE f 211 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA f 225 " --> pdb=" O ILE f 221 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA f 227 " --> pdb=" O GLU f 223 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 247 removed outlier: 4.335A pdb=" N THR f 234 " --> pdb=" O CYS f 230 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL f 237 " --> pdb=" O LEU f 233 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.751A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) Processing helix chain 'f' and resid 253 through 263 removed outlier: 3.783A 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 270 through 278 removed outlier: 4.956A pdb=" N ASP f 274 " --> pdb=" O LEU f 270 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU f 276 " --> pdb=" O LEU f 272 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU f 277 " --> pdb=" O ASN f 273 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL f 278 " --> pdb=" O ASP f 274 " (cutoff:3.500A) Processing helix chain 'f' and resid 285 through 294 removed outlier: 3.537A pdb=" N VAL f 290 " --> pdb=" O LYS f 286 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN f 291 " --> pdb=" O ASP f 287 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 296 through 303 removed outlier: 3.593A pdb=" N ARG f 300 " --> pdb=" O PHE f 296 " (cutoff:3.500A) Processing helix chain 'f' and resid 313 through 323 removed outlier: 4.288A pdb=" N SER f 322 " --> pdb=" O THR f 318 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN f 323 " --> pdb=" O GLU f 319 " (cutoff:3.500A) Processing helix chain 'f' and resid 324 through 336 removed outlier: 4.043A pdb=" N ARG f 335 " --> pdb=" O LEU f 331 " (cutoff:3.500A) Processing helix chain 'f' and resid 345 through 352 removed outlier: 4.264A pdb=" N TYR f 349 " --> pdb=" O PRO f 345 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS f 352 " --> pdb=" O ILE f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 383 removed outlier: 3.623A pdb=" N ASN f 371 " --> pdb=" O SER f 367 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE f 376 " --> pdb=" O LEU f 372 " (cutoff:3.500A) Processing helix chain 'f' and resid 390 through 395 removed outlier: 4.347A pdb=" N ASP f 394 " --> pdb=" O LEU f 390 " (cutoff:3.500A) removed outlier: 3.717A 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: 4.140A pdb=" N TYR f 400 " --> pdb=" O ASN f 396 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS f 401 " --> pdb=" O LYS f 397 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 396 through 402' Processing helix chain 'f' and resid 403 through 419 removed outlier: 3.666A pdb=" N SER f 409 " --> pdb=" O HIS f 405 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA f 412 " --> pdb=" O LEU f 408 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER f 413 " --> pdb=" O SER f 409 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 422 through 433 removed outlier: 5.339A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 3.527A pdb=" N ASN f 452 " --> pdb=" O CYS f 448 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 471 removed outlier: 4.372A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU f 466 " --> pdb=" O ALA f 462 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TYR f 469 " --> pdb=" O LEU f 465 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 3.507A pdb=" N GLY f 480 " --> pdb=" O THR f 476 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU f 485 " --> pdb=" O SER f 481 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY f 486 " --> pdb=" O ILE f 482 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 507 removed outlier: 4.011A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU f 500 " --> pdb=" O ASP f 496 " (cutoff:3.500A) Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.019A pdb=" N GLY f 516 " --> pdb=" O MET f 512 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA f 526 " --> pdb=" O CYS f 522 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 4.748A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 552 removed outlier: 3.585A pdb=" N LYS f 551 " --> pdb=" O GLU f 547 " (cutoff:3.500A) Processing helix chain 'f' and resid 554 through 567 removed outlier: 4.449A pdb=" N LEU f 558 " --> pdb=" O TYR f 554 " (cutoff:3.500A) Proline residue: f 559 - end of helix removed outlier: 4.206A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN f 565 " --> pdb=" O GLY f 561 " (cutoff:3.500A) Processing helix chain 'f' and resid 570 through 582 removed outlier: 3.847A pdb=" N GLU f 574 " --> pdb=" O GLY f 570 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 585 through 601 removed outlier: 4.250A pdb=" N SER f 589 " --> pdb=" O GLU f 585 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE f 590 " --> pdb=" O PRO f 586 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 624 removed outlier: 5.405A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS f 616 " --> pdb=" O LEU f 612 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER f 617 " --> pdb=" O LEU f 613 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER f 622 " --> pdb=" O GLU f 618 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS f 623 " --> pdb=" O HIS f 619 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU f 624 " --> pdb=" O PHE f 620 " (cutoff:3.500A) Processing helix chain 'f' and resid 625 through 641 removed outlier: 4.606A pdb=" N LYS f 629 " --> pdb=" O LYS f 625 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP f 630 " --> pdb=" O GLU f 626 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS f 637 " --> pdb=" O GLU f 633 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP f 638 " --> pdb=" O LYS f 634 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LYS f 639 " --> pdb=" O LYS f 635 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS f 640 " --> pdb=" O ASP f 636 " (cutoff:3.500A) Processing helix chain 'f' and resid 645 through 658 removed outlier: 4.973A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY f 651 " --> pdb=" O GLY f 647 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL f 652 " --> pdb=" O ALA f 648 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA f 653 " --> pdb=" O HIS f 649 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA f 658 " --> pdb=" O VAL f 654 " (cutoff:3.500A) Processing helix chain 'f' and resid 666 through 679 removed outlier: 3.669A pdb=" N MET f 670 " --> pdb=" O ILE f 666 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA f 671 " --> pdb=" O GLY f 667 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU f 672 " --> pdb=" O ALA f 668 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR f 674 " --> pdb=" O MET f 670 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) Processing helix chain 'f' and resid 691 through 698 removed outlier: 5.176A pdb=" N ALA f 695 " --> pdb=" O PRO f 691 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 717 removed outlier: 3.687A pdb=" N LEU f 710 " --> pdb=" O ILE f 706 " (cutoff:3.500A) Processing helix chain 'f' and resid 721 through 735 removed outlier: 5.276A pdb=" N SER f 725 " --> pdb=" O VAL f 721 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE f 726 " --> pdb=" O SER f 722 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE f 727 " --> pdb=" O TYR f 723 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA f 728 " --> pdb=" O ASN f 724 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY f 733 " --> pdb=" O MET f 729 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER f 734 " --> pdb=" O GLY f 730 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 755 removed outlier: 3.902A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG f 746 " --> pdb=" O ALA f 742 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR f 751 " --> pdb=" O GLN f 747 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS f 754 " --> pdb=" O GLN f 750 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP f 755 " --> pdb=" O TYR f 751 " (cutoff:3.500A) Processing helix chain 'f' and resid 776 through 787 Proline residue: f 780 - end of helix removed outlier: 4.473A pdb=" N ASP f 784 " --> pdb=" O PRO f 780 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU f 787 " --> pdb=" O SER f 783 " (cutoff:3.500A) Processing helix chain 'f' and resid 797 through 803 removed outlier: 4.015A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE f 803 " --> pdb=" O VAL f 799 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 104 removed outlier: 3.691A pdb=" N TYR f 103 " --> pdb=" O ARG f 100 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY f 104 " --> pdb=" O PRO f 101 " (cutoff:3.500A) Processing helix chain 'f' and resid 353 through 358 removed outlier: 3.667A pdb=" N ASN f 356 " --> pdb=" O LEU f 353 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.767A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.494A 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: 4.811A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.429A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.332A 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: 3.841A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 187 removed outlier: 3.890A pdb=" N LYS g 184 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE g 187 " --> pdb=" O VAL g 183 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 Processing helix chain 'g' and resid 231 through 245 removed outlier: 3.817A pdb=" N ARG g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 32 removed outlier: 4.179A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLY i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.849A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.939A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR i 122 " --> pdb=" O LYS i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 removed outlier: 3.693A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 202 removed outlier: 4.220A pdb=" N ASP i 202 " --> pdb=" O ASN i 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 212 removed outlier: 4.036A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU i 212 " --> pdb=" O ALA i 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 207 through 212' Processing helix chain 'i' and resid 229 through 251 Processing helix chain 'k' and resid 21 through 34 removed outlier: 4.070A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.752A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 3.760A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.792A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 211 through 216 removed outlier: 3.946A pdb=" N ILE k 215 " --> pdb=" O ASN k 211 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU k 216 " --> pdb=" O ALA k 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 211 through 216' Processing helix chain 'k' and resid 230 through 241 Processing helix chain 'k' and resid 60 through 65 removed outlier: 5.051A pdb=" N GLU k 65 " --> pdb=" O SER k 62 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 33 removed outlier: 4.040A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) removed outlier: 5.482A 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 123 removed outlier: 4.070A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 3.686A pdb=" N ARG l 122 " --> pdb=" O ILE l 118 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR l 123 " --> pdb=" O PRO l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 164 through 180 removed outlier: 4.637A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 3.821A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 3.989A 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 206 through 211 removed outlier: 4.103A pdb=" N VAL l 210 " --> pdb=" O THR l 206 " (cutoff:3.500A) removed outlier: 6.277A 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 235 removed outlier: 4.715A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 5.373A pdb=" N GLY l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 5.646A pdb=" N ASP l 7 " --> pdb=" O ASN l 4 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN l 8 " --> pdb=" O GLN l 5 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP l 9 " --> pdb=" O TYR l 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 9' Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.631A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 Processing helix chain 'm' and resid 107 through 124 removed outlier: 4.098A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 4.278A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 180 through 185 removed outlier: 4.318A pdb=" N MET m 184 " --> pdb=" O GLN m 180 " (cutoff:3.500A) removed outlier: 6.117A 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 207 removed outlier: 4.557A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU m 192 " --> pdb=" O ASP m 188 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP m 202 " --> pdb=" O TYR m 198 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLU m 203 " --> pdb=" O ILE m 199 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N VAL m 204 " --> pdb=" O VAL m 200 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS m 205 " --> pdb=" O HIS m 201 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP m 206 " --> pdb=" O ASP m 202 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS m 207 " --> pdb=" O GLU m 203 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 5 through 10 removed outlier: 6.020A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER m 10 " --> pdb=" O TYR m 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 5 through 10' Processing helix chain 'n' and resid 48 through 71 Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.608A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.651A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 removed outlier: 3.595A pdb=" N ARG n 166 " --> pdb=" O LEU n 162 " (cutoff:3.500A) Processing helix chain 'x' and resid 25 through 37 Processing helix chain 'x' and resid 93 through 103 removed outlier: 5.619A pdb=" N LEU x 97 " --> pdb=" O THR x 93 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 126 removed outlier: 4.128A pdb=" N VAL x 126 " --> pdb=" O CYS x 122 " (cutoff:3.500A) Processing helix chain 'x' and resid 127 through 137 removed outlier: 5.365A pdb=" N ALA x 137 " --> pdb=" O LEU x 133 " (cutoff:3.500A) Processing helix chain 'x' and resid 147 through 167 removed outlier: 3.789A pdb=" N TYR x 151 " --> pdb=" O ALA x 147 " (cutoff:3.500A) removed outlier: 4.817A 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 214 removed outlier: 4.004A pdb=" N CYS x 203 " --> pdb=" O ASP x 199 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 246 Processing helix chain 'x' and resid 285 through 295 removed outlier: 4.379A pdb=" N GLN x 295 " --> pdb=" O LYS x 291 " (cutoff:3.500A) Processing helix chain 'x' and resid 360 through 380 removed outlier: 4.854A pdb=" N SER x 369 " --> pdb=" O GLU x 365 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE x 370 " --> pdb=" O LYS x 366 " (cutoff:3.500A) Processing helix chain 'x' and resid 381 through 386 removed outlier: 4.731A pdb=" N GLN x 385 " --> pdb=" O LYS x 381 " (cutoff:3.500A) Proline residue: x 386 - end of helix No H-bonds generated for 'chain 'x' and resid 381 through 386' Processing helix chain 'x' and resid 459 through 467 removed outlier: 3.738A pdb=" N ILE x 463 " --> pdb=" O THR x 459 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER x 467 " --> pdb=" O ILE x 463 " (cutoff:3.500A) Processing helix chain 'y' and resid 22 through 34 removed outlier: 4.124A pdb=" N VAL y 26 " --> pdb=" O THR y 22 " (cutoff:3.500A) Processing helix chain 'y' and resid 37 through 42 removed outlier: 3.626A pdb=" N GLN y 41 " --> pdb=" O PRO y 37 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG y 42 " --> pdb=" O PRO y 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 37 through 42' Processing helix chain 'y' and resid 55 through 60 Processing helix chain 'W' and resid 20 through 38 removed outlier: 4.269A pdb=" N VAL W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 4.626A pdb=" N GLY W 38 " --> pdb=" O LEU W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 58 Processing helix chain 'W' and resid 59 through 78 removed outlier: 4.639A pdb=" N THR W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS W 78 " --> pdb=" O CYS W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 94 removed outlier: 4.393A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 115 removed outlier: 4.568A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU W 114 " --> pdb=" O THR W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 135 removed outlier: 3.716A pdb=" N GLY W 134 " --> pdb=" O MET W 130 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS W 135 " --> pdb=" O VAL W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 156 removed outlier: 5.701A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS W 153 " --> pdb=" O LEU W 149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU W 154 " --> pdb=" O ALA W 150 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN W 156 " --> pdb=" O ILE W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 177 removed outlier: 6.004A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET W 177 " --> pdb=" O THR W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 197 removed outlier: 3.956A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 213 removed outlier: 3.780A pdb=" N THR W 211 " --> pdb=" O LYS W 207 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS W 212 " --> pdb=" O LYS W 208 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE W 213 " --> pdb=" O ILE W 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 215 through 220 removed outlier: 4.418A pdb=" N THR W 219 " --> pdb=" O GLN W 215 " (cutoff:3.500A) removed outlier: 5.045A 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 227 through 238 removed outlier: 4.498A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 257 removed outlier: 4.698A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 259 through 277 Processing helix chain 'W' and resid 280 through 291 Processing helix chain 'W' and resid 295 through 300 removed outlier: 4.363A pdb=" N ILE W 299 " --> pdb=" O LYS W 295 " (cutoff:3.500A) Proline residue: W 300 - end of helix No H-bonds generated for 'chain 'W' and resid 295 through 300' Processing helix chain 'W' and resid 301 through 307 removed outlier: 4.345A pdb=" N LEU W 305 " --> pdb=" O LYS W 301 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU W 306 " --> pdb=" O TYR W 302 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS W 307 " --> pdb=" O LYS W 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 301 through 307' Processing helix chain 'W' and resid 316 through 330 removed outlier: 6.020A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 4.320A pdb=" N GLU W 348 " --> pdb=" O THR W 344 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS W 368 " --> pdb=" O ARG W 364 " (cutoff:3.500A) removed outlier: 4.544A 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 removed outlier: 3.859A pdb=" N LYS W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 454 Processing helix chain 'W' and resid 221 through 226 removed outlier: 5.291A pdb=" N TYR W 226 " --> pdb=" O LYS W 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 221 through 226' Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 91 through 106 Proline residue: V 102 - end of helix removed outlier: 4.830A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 120 removed outlier: 3.513A pdb=" N LEU V 113 " --> pdb=" O ASN V 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.752A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 5.158A 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: 3.687A pdb=" N ALA V 184 " --> pdb=" O ARG V 180 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 222 removed outlier: 4.301A pdb=" N ASP V 204 " --> pdb=" O ARG V 200 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.238A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.826A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 removed outlier: 3.572A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.512A 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: 4.755A pdb=" N PHE V 348 " --> pdb=" O ASP V 344 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG V 349 " --> pdb=" O ARG V 345 " (cutoff:3.500A) removed outlier: 4.151A 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 402 removed outlier: 3.868A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 403 through 415 removed outlier: 3.512A pdb=" N TYR V 414 " --> pdb=" O ILE V 410 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 3.618A pdb=" N LEU V 426 " --> pdb=" O ILE V 422 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 Processing helix chain 'V' and resid 470 through 494 removed outlier: 3.613A pdb=" N LEU V 474 " --> pdb=" O ARG V 470 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET V 494 " --> pdb=" O SER V 490 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 64 removed outlier: 5.268A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 4.048A pdb=" N ASP e 45 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP e 46 " --> pdb=" O TRP e 43 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN e 47 " --> pdb=" O ASP e 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 42 through 47' Processing sheet with id= 1, first strand: chain 'A' and resid 96 through 99 removed outlier: 6.588A pdb=" N GLY A 141 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN A 148 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 111 through 114 removed outlier: 3.678A pdb=" N TYR A 111 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 123 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 236 through 240 removed outlier: 4.327A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP A 275 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS A 270 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 212 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 114 through 117 removed outlier: 3.640A pdb=" N GLU B 114 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 122 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 246 through 251 removed outlier: 5.325A pdb=" N THR B 246 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER B 280 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 120 through 125 removed outlier: 4.763A pdb=" N SER B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 71 through 77 removed outlier: 4.207A pdb=" N CYS C 112 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 84 through 88 Processing sheet with id= 9, first strand: chain 'C' and resid 209 through 215 removed outlier: 3.558A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS C 184 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.806A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA D 128 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER D 129 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.670A pdb=" N ALA D 310 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG D 200 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 55 through 58 Processing sheet with id= 13, first strand: chain 'E' and resid 68 through 73 Processing sheet with id= 14, first strand: chain 'E' and resid 170 through 175 Processing sheet with id= 15, first strand: chain 'E' and resid 228 through 233 Processing sheet with id= 16, first strand: chain 'F' and resid 95 through 98 removed outlier: 3.554A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 246 through 251 removed outlier: 4.613A pdb=" N THR F 247 " --> pdb=" O PRO F 280 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER F 281 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 283 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LYS F 221 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL F 223 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA F 330 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 332 " --> pdb=" O MET F 225 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 4.825A 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: 3.868A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.088A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 155 " --> pdb=" O TYR G 159 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.926A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.526A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS H 137 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 160 through 164 removed outlier: 5.602A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN H 214 " --> pdb=" O GLY H 217 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.477A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY h 73 " --> pdb=" O CYS h 137 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER h 133 " --> pdb=" O SER h 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU h 134 " --> pdb=" O SER h 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY h 138 " --> pdb=" O TYR h 145 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'h' and resid 160 through 164 removed outlier: 5.522A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 64 through 68 removed outlier: 6.337A pdb=" N LYS I 64 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 161 through 165 removed outlier: 5.107A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY I 42 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.194A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 158 through 162 removed outlier: 5.037A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU J 208 " --> pdb=" O LEU J 220 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS J 218 " --> pdb=" O VAL J 210 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'j' and resid 62 through 65 removed outlier: 3.598A pdb=" N LEU j 65 " --> pdb=" O VAL j 69 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN j 68 " --> pdb=" O PHE j 136 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'j' and resid 158 through 162 removed outlier: 4.711A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE j 40 " --> pdb=" O GLY j 37 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.426A pdb=" N LYS K 66 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU K 141 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU K 153 " --> pdb=" O CYS K 165 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 167 through 171 removed outlier: 4.995A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.476A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 158 through 162 removed outlier: 4.678A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'M' and resid 66 through 69 removed outlier: 6.535A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER M 141 " --> pdb=" O GLY M 145 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.800A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.544A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.394A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.486A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.340A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.463A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'o' and resid 124 through 128 removed outlier: 5.986A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'P' and resid 42 through 45 removed outlier: 5.910A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'P' and resid 136 through 140 removed outlier: 5.888A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.516A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'p' and resid 136 through 140 removed outlier: 5.920A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.467A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Q' and resid 129 through 132 removed outlier: 3.747A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.491A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'q' and resid 129 through 132 removed outlier: 3.830A pdb=" N LEU q 4 " --> pdb=" O HIS q 132 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'R' and resid 34 through 37 removed outlier: 3.508A pdb=" N ILE R 37 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 99 through 104 removed outlier: 3.878A pdb=" N VAL R 114 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.319A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER R 18 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'r' and resid 34 through 37 removed outlier: 3.646A pdb=" N ILE r 37 " --> pdb=" O LEU r 41 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 99 through 104 Processing sheet with id= 56, first strand: chain 'r' and resid 125 through 129 removed outlier: 5.937A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.638A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.646A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 's' and resid 43 through 46 removed outlier: 6.634A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 's' and resid 135 through 139 removed outlier: 5.734A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.498A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER T 54 " --> pdb=" O THR T 109 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.392A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 't' and resid 42 through 45 removed outlier: 6.959A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY t 113 " --> pdb=" O MET t 50 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 136 through 139 removed outlier: 4.425A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 800 through 803 removed outlier: 6.578A pdb=" N VAL U 800 " --> pdb=" O ASN U 880 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'X' and resid 376 through 380 removed outlier: 3.557A pdb=" N ASP X 379 " --> pdb=" O VAL X 384 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Y' and resid 345 through 349 removed outlier: 3.651A pdb=" N ILE Y 353 " --> pdb=" O ASP Y 348 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Z' and resid 47 through 50 removed outlier: 4.097A pdb=" N SER Z 140 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER Z 119 " --> pdb=" O SER Z 140 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS Z 96 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR Z 97 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL Z 38 " --> pdb=" O PHE Z 54 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 320 through 326 removed outlier: 3.935A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP a 325 " --> pdb=" O ARG a 330 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'b' and resid 3 through 11 removed outlier: 4.049A pdb=" N GLU b 4 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU b 54 " --> pdb=" O VAL b 10 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'b' and resid 107 through 114 removed outlier: 4.740A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL b 173 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'c' and resid 65 through 69 removed outlier: 4.419A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL c 31 " --> pdb=" O THR c 204 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'c' and resid 141 through 145 Processing sheet with id= 74, first strand: chain 'f' and resid 811 through 815 removed outlier: 3.799A pdb=" N ALA f 880 " --> pdb=" O GLY f 812 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER f 814 " --> pdb=" O ALA f 880 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU f 882 " --> pdb=" O SER f 814 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.327A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'g' and resid 165 through 169 removed outlier: 5.979A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'i' and resid 65 through 68 removed outlier: 6.518A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN i 155 " --> pdb=" O ASP i 151 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'i' and resid 161 through 165 removed outlier: 4.821A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'k' and resid 66 through 70 removed outlier: 6.627A pdb=" N LYS k 66 " --> pdb=" O MET k 78 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU k 141 " --> pdb=" O MET k 156 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU k 153 " --> pdb=" O CYS k 165 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR k 161 " --> pdb=" O ASP k 157 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'k' and resid 167 through 171 removed outlier: 5.681A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.497A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE l 154 " --> pdb=" O GLN l 146 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'l' and resid 158 through 162 removed outlier: 3.599A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'm' and resid 66 through 69 removed outlier: 6.499A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER m 141 " --> pdb=" O GLY m 145 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU m 148 " --> pdb=" O TYR m 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR m 158 " --> pdb=" O MET m 150 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'm' and resid 162 through 166 removed outlier: 4.999A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU m 212 " --> pdb=" O VAL m 49 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.554A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.569A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'x' and resid 44 through 47 Processing sheet with id= 88, first strand: chain 'x' and resid 274 through 278 removed outlier: 3.721A pdb=" N GLN x 327 " --> pdb=" O LEU x 275 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'x' and resid 296 through 301 Processing sheet with id= 90, first strand: chain 'x' and resid 331 through 335 Processing sheet with id= 91, first strand: chain 'x' and resid 422 through 428 removed outlier: 6.655A pdb=" N GLU x 446 " --> pdb=" O ARG x 442 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'y' and resid 11 through 16 removed outlier: 4.490A pdb=" N LYS y 11 " --> pdb=" O THR y 7 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER y 65 " --> pdb=" O GLN y 2 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'W' and resid 404 through 408 Processing sheet with id= 94, first strand: chain 'V' and resid 449 through 453 removed outlier: 3.609A pdb=" N TYR V 457 " --> pdb=" O ASN V 452 " (cutoff:3.500A) 5824 hydrogen bonds defined for protein. 17361 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: 48.46 Time building geometry restraints manager: 35.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 20023 1.32 - 1.45: 27295 1.45 - 1.58: 64234 1.58 - 1.70: 27 1.70 - 1.83: 1071 Bond restraints: 112650 Sorted by residual: bond pdb=" C ILE d 237 " pdb=" N PRO d 238 " ideal model delta sigma weight residual 1.334 1.391 -0.058 8.40e-03 1.42e+04 4.72e+01 bond pdb=" CA HIS f 815 " pdb=" CB HIS f 815 " ideal model delta sigma weight residual 1.523 1.576 -0.053 1.27e-02 6.20e+03 1.74e+01 bond pdb=" C LEU E 111 " pdb=" N PRO E 112 " ideal model delta sigma weight residual 1.334 1.374 -0.040 1.11e-02 8.12e+03 1.31e+01 bond pdb=" C ALA f 20 " pdb=" N PRO f 21 " ideal model delta sigma weight residual 1.333 1.379 -0.046 1.44e-02 4.82e+03 1.03e+01 bond pdb=" C LYS f 858 " pdb=" N PRO f 859 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.86e+00 ... (remaining 112645 not shown) Histogram of bond angle deviations from ideal: 94.86 - 103.85: 1438 103.85 - 112.83: 60589 112.83 - 121.81: 66459 121.81 - 130.80: 23244 130.80 - 139.78: 449 Bond angle restraints: 152179 Sorted by residual: angle pdb=" N THR f 24 " pdb=" CA THR f 24 " pdb=" C THR f 24 " ideal model delta sigma weight residual 111.28 102.83 8.45 1.09e+00 8.42e-01 6.00e+01 angle pdb=" C GLU g 223 " pdb=" N ASN g 224 " pdb=" CA ASN g 224 " ideal model delta sigma weight residual 122.26 130.07 -7.81 1.10e+00 8.26e-01 5.04e+01 angle pdb=" C ALA e 28 " pdb=" CA ALA e 28 " pdb=" CB ALA e 28 " ideal model delta sigma weight residual 116.54 109.90 6.64 1.15e+00 7.56e-01 3.33e+01 angle pdb=" C LEU E 111 " pdb=" N PRO E 112 " pdb=" CA PRO E 112 " ideal model delta sigma weight residual 120.13 113.64 6.49 1.13e+00 7.83e-01 3.30e+01 angle pdb=" N ALA Z 164 " pdb=" CA ALA Z 164 " pdb=" C ALA Z 164 " ideal model delta sigma weight residual 109.69 117.19 -7.50 1.44e+00 4.82e-01 2.71e+01 ... (remaining 152174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.67: 66012 27.67 - 55.33: 2613 55.33 - 83.00: 248 83.00 - 110.67: 16 110.67 - 138.34: 1 Dihedral angle restraints: 68890 sinusoidal: 27913 harmonic: 40977 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 161.66 138.34 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" CA ASP X 316 " pdb=" C ASP X 316 " pdb=" N PRO X 317 " pdb=" CA PRO X 317 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ILE C 251 " pdb=" C ILE C 251 " pdb=" N ASP C 252 " pdb=" CA ASP C 252 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 68887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 14464 0.065 - 0.129: 2513 0.129 - 0.194: 224 0.194 - 0.258: 22 0.258 - 0.323: 5 Chirality restraints: 17228 Sorted by residual: chirality pdb=" CA TYR W 111 " pdb=" N TYR W 111 " pdb=" C TYR W 111 " pdb=" CB TYR W 111 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB THR X 263 " pdb=" CA THR X 263 " pdb=" OG1 THR X 263 " pdb=" CG2 THR X 263 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE A 65 " pdb=" CA ILE A 65 " pdb=" CG1 ILE A 65 " pdb=" CG2 ILE A 65 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 17225 not shown) Planarity restraints: 19621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 215 " 0.027 2.00e-02 2.50e+03 2.85e-02 2.04e+01 pdb=" CG TRP M 215 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP M 215 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP M 215 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 215 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 215 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 215 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 215 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP M 215 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 215 " 0.021 2.00e-02 2.50e+03 1.98e-02 9.77e+00 pdb=" CG TRP m 215 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP m 215 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP m 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP m 215 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 215 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 215 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP m 215 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 38 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO R 39 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO R 39 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 39 " 0.043 5.00e-02 4.00e+02 ... (remaining 19618 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 2251 2.69 - 3.24: 103718 3.24 - 3.79: 175468 3.79 - 4.35: 222972 4.35 - 4.90: 375696 Nonbonded interactions: 880105 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 2.137 2.230 nonbonded pdb=" OH TYR f 349 " pdb=" O TYR f 751 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR g 231 " pdb=" OE1 GLU g 234 " model vdw 2.231 2.440 nonbonded pdb=" O MET V 463 " pdb=" OH TYR V 467 " model vdw 2.234 2.440 nonbonded pdb=" O THR f 537 " pdb=" OG1 THR f 541 " model vdw 2.234 2.440 ... (remaining 880100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 6 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 195 or (resid 196 and (n \ ame N or name CA or name C or name O or name CB )) or resid 197 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 245)) selection = (chain 'g' and resid 6 through 245) } ncs_group { reference = (chain 'H' and (resid 3 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB )) or resid 201 through 234)) selection = (chain 'h' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 234)) } ncs_group { reference = (chain 'I' and (resid 4 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB )) or resid 200 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 251)) selection = (chain 'i' and (resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 228 or (resid 229 and (name N or na \ me CA or name C or name O or name CB )) or resid 230 or (resid 231 and (name N o \ r name CA or name C or name O or name CB )) or resid 232 through 238 or (resid 2 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 251)) } ncs_group { reference = (chain 'J' and (resid 2 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 223 or (resid 22 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or re \ sid 233 through 238 or (resid 239 through 240 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'j' and (resid 2 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 173 or (resid 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 188 \ or (resid 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 217 or (resid 218 and (name N or name CA or name C or name O or nam \ e CB )) or resid 219 through 240)) } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)))) selection = (chain 'k' and (resid 8 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 207 or (resid 208 an \ d (name N or name CA or name C or name O or name CB )) or resid 209 through 241) \ ) } ncs_group { reference = (chain 'L' and (resid 4 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 241)) selection = (chain 'l' and (resid 4 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 241)) } ncs_group { reference = (chain 'M' and resid 5 through 244) selection = (chain 'm' and (resid 5 through 187 or (resid 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 244)) } ncs_group { reference = (chain 'N' and (resid 1 through 149 or (resid 150 and (name N or name CA or name \ C or name O or name CB )) or resid 151 through 202)) selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and (resid 1 through 179 or (resid 180 and (name N or name CA or name \ C or name O or name CB )) or resid 181 through 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 202 or (resid 20 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 204 through \ 220)) } ncs_group { reference = chain 'P' selection = (chain 'p' and (resid 2 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 205)) } ncs_group { reference = (chain 'Q' and (resid 1 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 199)) selection = chain 'q' } ncs_group { reference = (chain 'R' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 88 or (resid 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 through 201)) selection = chain 'r' } ncs_group { reference = (chain 'S' and (resid 1 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 213)) selection = (chain 's' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 213)) } ncs_group { reference = chain 'T' selection = (chain 't' and (resid 1 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 216)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.420 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: 52.240 Check model and map are aligned: 1.300 Set scattering table: 0.820 Process input model: 291.350 Find NCS groups from input model: 6.870 Set up NCS constraints: 0.570 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 366.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 112650 Z= 0.228 Angle : 0.756 13.362 152179 Z= 0.398 Chirality : 0.047 0.323 17228 Planarity : 0.005 0.078 19621 Dihedral : 14.166 138.337 42506 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.75 % Rotamer: Outliers : 0.31 % Allowed : 0.39 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % 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: -0.51 (0.07), residues: 13974 helix: 0.69 (0.06), residues: 6516 sheet: 0.25 (0.12), residues: 2017 loop : -1.85 (0.08), residues: 5441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP M 215 HIS 0.020 0.001 HIS f 202 PHE 0.027 0.001 PHE n 83 TYR 0.036 0.001 TYR W 226 ARG 0.007 0.000 ARG Q 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 465 time to evaluate : 10.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 MET cc_start: 0.8531 (ttp) cc_final: 0.8082 (tmm) REVERT: C 399 MET cc_start: 0.9026 (tpp) cc_final: 0.8817 (tpp) REVERT: D 204 MET cc_start: 0.9437 (ttt) cc_final: 0.8675 (tmm) REVERT: E 1 MET cc_start: 0.7765 (mmp) cc_final: 0.7535 (mmp) REVERT: E 218 MET cc_start: 0.8773 (tpt) cc_final: 0.8536 (mmp) REVERT: E 232 MET cc_start: 0.8164 (mpp) cc_final: 0.7906 (mpp) REVERT: F 36 MET cc_start: 0.7979 (mmp) cc_final: 0.7530 (mmm) REVERT: F 206 MET cc_start: 0.7504 (tpp) cc_final: 0.7285 (tpp) REVERT: F 310 MET cc_start: 0.7783 (mtm) cc_final: 0.7537 (ttt) REVERT: F 366 MET cc_start: 0.9373 (mpp) cc_final: 0.8939 (mpp) REVERT: F 405 MET cc_start: 0.9557 (mmp) cc_final: 0.8971 (mmt) REVERT: G 131 MET cc_start: 0.8944 (pmm) cc_final: 0.8523 (pmm) REVERT: U 351 MET cc_start: 0.9126 (ppp) cc_final: 0.8845 (ppp) REVERT: U 556 MET cc_start: 0.7993 (tpp) cc_final: 0.7363 (tpp) REVERT: U 725 MET cc_start: 0.8041 (ppp) cc_final: 0.7648 (ppp) REVERT: a 280 MET cc_start: 0.8876 (mpp) cc_final: 0.8488 (mpp) REVERT: a 349 MET cc_start: 0.9244 (pmm) cc_final: 0.8916 (pmm) REVERT: c 51 MET cc_start: 0.8694 (pmm) cc_final: 0.8396 (ppp) REVERT: c 57 MET cc_start: 0.8266 (pmm) cc_final: 0.7869 (pmm) REVERT: c 167 MET cc_start: 0.6461 (tpt) cc_final: 0.6148 (tpp) REVERT: c 226 MET cc_start: 0.8319 (mmm) cc_final: 0.8083 (mmm) REVERT: c 292 MET cc_start: 0.9512 (mmp) cc_final: 0.9230 (mmm) REVERT: f 113 MET cc_start: 0.8388 (ppp) cc_final: 0.7884 (pmm) REVERT: f 321 MET cc_start: 0.6621 (ppp) cc_final: 0.6169 (ppp) REVERT: f 825 MET cc_start: 0.7948 (tpt) cc_final: 0.7611 (tpp) REVERT: x 181 MET cc_start: 0.7656 (mtp) cc_final: 0.6885 (mtt) REVERT: y 4 PHE cc_start: 0.0175 (m-80) cc_final: -0.0111 (m-10) REVERT: W 113 GLU cc_start: 0.2079 (OUTLIER) cc_final: 0.1356 (mm-30) REVERT: W 177 MET cc_start: 0.0312 (mtt) cc_final: -0.2980 (mpp) REVERT: W 230 MET cc_start: 0.7901 (pmm) cc_final: 0.7673 (pmm) REVERT: W 451 MET cc_start: 0.5177 (tpt) cc_final: 0.4230 (tmm) REVERT: V 139 MET cc_start: 0.5782 (mpp) cc_final: 0.5063 (ptp) REVERT: V 309 MET cc_start: 0.7183 (ppp) cc_final: 0.6894 (ppp) REVERT: V 463 MET cc_start: 0.6737 (mmp) cc_final: 0.6050 (ttt) REVERT: V 494 MET cc_start: 0.8116 (tpp) cc_final: 0.7864 (tpp) outliers start: 37 outliers final: 5 residues processed: 498 average time/residue: 0.9035 time to fit residues: 802.0154 Evaluate side-chains 450 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 444 time to evaluate : 9.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain h residue 184 LEU Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 113 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1174 optimal weight: 20.0000 chunk 1054 optimal weight: 30.0000 chunk 585 optimal weight: 20.0000 chunk 360 optimal weight: 20.0000 chunk 711 optimal weight: 50.0000 chunk 563 optimal weight: 8.9990 chunk 1090 optimal weight: 9.9990 chunk 421 optimal weight: 30.0000 chunk 662 optimal weight: 20.0000 chunk 811 optimal weight: 20.0000 chunk 1263 optimal weight: 50.0000 overall best weight: 15.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 120 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS F 255 GLN ** I 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN U 734 GLN U 768 GLN X 296 ASN Y 77 ASN ** Y 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 351 ASN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 30 GLN ** c 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 GLN ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 371 ASN f 405 HIS ** f 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 868 HIS h 71 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 169 GLN r 162 GLN s 79 ASN x 121 GLN x 274 GLN W 96 GLN W 433 ASN ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 282 ASN V 452 ASN ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 112650 Z= 0.412 Angle : 0.642 10.417 152179 Z= 0.338 Chirality : 0.042 0.172 17228 Planarity : 0.005 0.083 19621 Dihedral : 5.767 128.920 15521 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.28 % Favored : 93.66 % Rotamer: Outliers : 0.27 % Allowed : 7.12 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 13974 helix: 1.59 (0.07), residues: 6526 sheet: 0.11 (0.11), residues: 1991 loop : -1.65 (0.08), residues: 5457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP M 215 HIS 0.010 0.001 HIS q 132 PHE 0.031 0.002 PHE q 171 TYR 0.025 0.002 TYR M 7 ARG 0.007 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 448 time to evaluate : 10.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.4379 (mmt) cc_final: 0.4114 (mmt) REVERT: B 309 MET cc_start: 0.8695 (ttp) cc_final: 0.8242 (tmm) REVERT: D 163 MET cc_start: 0.9100 (tpp) cc_final: 0.8691 (tpt) REVERT: D 384 MET cc_start: 0.8849 (mmp) cc_final: 0.8564 (tpp) REVERT: E 1 MET cc_start: 0.7909 (mmp) cc_final: 0.7599 (mmp) REVERT: E 218 MET cc_start: 0.8874 (tpt) cc_final: 0.8608 (mmp) REVERT: E 232 MET cc_start: 0.8382 (mpp) cc_final: 0.7886 (mpp) REVERT: E 275 MET cc_start: 0.7568 (ppp) cc_final: 0.7032 (ppp) REVERT: E 277 MET cc_start: 0.8657 (mpp) cc_final: 0.8067 (mpp) REVERT: E 352 MET cc_start: 0.8939 (mpp) cc_final: 0.8625 (mpp) REVERT: F 36 MET cc_start: 0.8066 (mmp) cc_final: 0.7696 (mmm) REVERT: F 175 MET cc_start: 0.2315 (mmt) cc_final: 0.1960 (tpt) REVERT: F 366 MET cc_start: 0.9394 (mpp) cc_final: 0.9017 (mpp) REVERT: G 131 MET cc_start: 0.8969 (pmm) cc_final: 0.8388 (pmm) REVERT: I 25 MET cc_start: 0.9211 (mmm) cc_final: 0.9007 (mtt) REVERT: L 26 MET cc_start: 0.7773 (tpt) cc_final: 0.6995 (tpt) REVERT: T 110 MET cc_start: 0.8536 (mmm) cc_final: 0.8203 (mmm) REVERT: U 725 MET cc_start: 0.8197 (ppp) cc_final: 0.7910 (ppp) REVERT: a 349 MET cc_start: 0.9295 (pmm) cc_final: 0.8952 (pmm) REVERT: b 107 MET cc_start: 0.8380 (mmt) cc_final: 0.8043 (mmp) REVERT: c 167 MET cc_start: 0.6345 (tpt) cc_final: 0.6027 (tpp) REVERT: f 297 MET cc_start: -0.0677 (ptt) cc_final: -0.0909 (ptt) REVERT: f 321 MET cc_start: 0.7246 (ppp) cc_final: 0.6542 (ppp) REVERT: h 233 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8447 (mp) REVERT: l 26 MET cc_start: 0.7878 (tpt) cc_final: 0.7604 (tpt) REVERT: r 93 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8649 (mtm) REVERT: x 101 MET cc_start: 0.6733 (tpp) cc_final: 0.6383 (mmt) REVERT: x 181 MET cc_start: 0.7642 (mtp) cc_final: 0.6942 (mtt) REVERT: W 113 GLU cc_start: 0.1986 (OUTLIER) cc_final: 0.1253 (mm-30) REVERT: W 177 MET cc_start: 0.0365 (mtt) cc_final: -0.2906 (mpp) REVERT: W 451 MET cc_start: 0.5246 (tpt) cc_final: 0.4033 (tmm) REVERT: V 139 MET cc_start: 0.5728 (mpp) cc_final: 0.4956 (ptp) REVERT: V 309 MET cc_start: 0.7158 (ppp) cc_final: 0.6930 (ppp) REVERT: V 494 MET cc_start: 0.7916 (tpp) cc_final: 0.7609 (tpp) outliers start: 32 outliers final: 16 residues processed: 465 average time/residue: 0.8776 time to fit residues: 739.0029 Evaluate side-chains 463 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 444 time to evaluate : 9.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain U residue 202 VAL Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain Y residue 235 ASP Chi-restraints excluded: chain d residue 19 CYS Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain m residue 184 MET Chi-restraints excluded: chain n residue 188 VAL Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain x residue 352 MET Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 113 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 702 optimal weight: 30.0000 chunk 392 optimal weight: 20.0000 chunk 1051 optimal weight: 7.9990 chunk 860 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 1265 optimal weight: 0.2980 chunk 1367 optimal weight: 7.9990 chunk 1127 optimal weight: 3.9990 chunk 1254 optimal weight: 8.9990 chunk 431 optimal weight: 20.0000 chunk 1015 optimal weight: 10.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 ASN ** Q 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 734 GLN Y 196 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 71 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 GLN ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 112650 Z= 0.175 Angle : 0.511 10.070 152179 Z= 0.268 Chirality : 0.040 0.174 17228 Planarity : 0.004 0.079 19621 Dihedral : 5.512 128.864 15517 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 0.35 % Allowed : 9.74 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.07), residues: 13974 helix: 1.95 (0.07), residues: 6505 sheet: 0.28 (0.11), residues: 2017 loop : -1.57 (0.08), residues: 5452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 215 HIS 0.009 0.001 HIS f 202 PHE 0.022 0.001 PHE W 309 TYR 0.016 0.001 TYR M 7 ARG 0.004 0.000 ARG V 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 446 time to evaluate : 10.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 MET cc_start: 0.8635 (ttp) cc_final: 0.8171 (tmm) REVERT: C 399 MET cc_start: 0.9054 (tpp) cc_final: 0.8820 (tpp) REVERT: D 163 MET cc_start: 0.9089 (tpp) cc_final: 0.8859 (tpp) REVERT: D 384 MET cc_start: 0.8845 (mmp) cc_final: 0.8598 (tpp) REVERT: E 1 MET cc_start: 0.7843 (mmp) cc_final: 0.7528 (mmp) REVERT: E 218 MET cc_start: 0.8820 (tpt) cc_final: 0.8596 (mmp) REVERT: E 232 MET cc_start: 0.8353 (mpp) cc_final: 0.7802 (mpp) REVERT: E 275 MET cc_start: 0.7751 (ppp) cc_final: 0.7233 (ppp) REVERT: E 277 MET cc_start: 0.8686 (mpp) cc_final: 0.8014 (mpp) REVERT: F 36 MET cc_start: 0.8036 (mmp) cc_final: 0.7696 (mmm) REVERT: F 175 MET cc_start: 0.2200 (mmt) cc_final: 0.1816 (tpt) REVERT: F 366 MET cc_start: 0.9402 (mpp) cc_final: 0.9032 (mpp) REVERT: G 131 MET cc_start: 0.8977 (pmm) cc_final: 0.8401 (pmm) REVERT: U 185 MET cc_start: 0.7042 (mmp) cc_final: 0.6368 (mmp) REVERT: U 725 MET cc_start: 0.8175 (ppp) cc_final: 0.7930 (ppp) REVERT: b 107 MET cc_start: 0.8419 (mmt) cc_final: 0.8195 (mmp) REVERT: c 167 MET cc_start: 0.6313 (tpt) cc_final: 0.6035 (tpp) REVERT: c 226 MET cc_start: 0.8728 (mmm) cc_final: 0.8506 (mmm) REVERT: f 297 MET cc_start: -0.0560 (OUTLIER) cc_final: -0.1002 (ptm) REVERT: f 321 MET cc_start: 0.7187 (ppp) cc_final: 0.6837 (ppp) REVERT: g 131 MET cc_start: 0.8343 (ppp) cc_final: 0.7869 (ppp) REVERT: h 233 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (mp) REVERT: l 26 MET cc_start: 0.7790 (tpt) cc_final: 0.7468 (tpt) REVERT: r 93 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8540 (mtm) REVERT: x 1 MET cc_start: 0.5839 (tmm) cc_final: 0.5570 (tmm) REVERT: x 67 MET cc_start: 0.4981 (tmm) cc_final: 0.4515 (tmm) REVERT: x 101 MET cc_start: 0.6723 (tpp) cc_final: 0.6420 (mmt) REVERT: x 181 MET cc_start: 0.7623 (mtp) cc_final: 0.6906 (mtt) REVERT: W 113 GLU cc_start: 0.2118 (OUTLIER) cc_final: 0.1296 (mm-30) REVERT: W 177 MET cc_start: 0.0542 (mtt) cc_final: -0.0885 (ttt) REVERT: W 230 MET cc_start: 0.7806 (pmm) cc_final: 0.7332 (pmm) REVERT: W 375 MET cc_start: 0.8202 (mmp) cc_final: 0.7795 (mtp) REVERT: W 451 MET cc_start: 0.5255 (tpt) cc_final: 0.4324 (tmm) REVERT: V 100 MET cc_start: 0.8441 (ppp) cc_final: 0.8214 (ppp) REVERT: V 139 MET cc_start: 0.5772 (mpp) cc_final: 0.4990 (ptp) REVERT: V 463 MET cc_start: 0.6969 (mmm) cc_final: 0.6297 (ttt) outliers start: 42 outliers final: 18 residues processed: 472 average time/residue: 0.8704 time to fit residues: 745.9084 Evaluate side-chains 465 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 443 time to evaluate : 10.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain d residue 19 CYS Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 113 GLU Chi-restraints excluded: chain W residue 190 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1250 optimal weight: 50.0000 chunk 951 optimal weight: 9.9990 chunk 656 optimal weight: 30.0000 chunk 140 optimal weight: 50.0000 chunk 603 optimal weight: 6.9990 chunk 849 optimal weight: 40.0000 chunk 1269 optimal weight: 4.9990 chunk 1344 optimal weight: 6.9990 chunk 663 optimal weight: 8.9990 chunk 1203 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN U 464 GLN U 734 GLN ** U 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 71 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 112650 Z= 0.212 Angle : 0.513 12.252 152179 Z= 0.268 Chirality : 0.040 0.168 17228 Planarity : 0.003 0.077 19621 Dihedral : 5.331 127.608 15517 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 0.71 % Allowed : 11.25 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.07), residues: 13974 helix: 2.08 (0.07), residues: 6521 sheet: 0.28 (0.11), residues: 2033 loop : -1.53 (0.08), residues: 5420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 215 HIS 0.008 0.001 HIS f 202 PHE 0.021 0.001 PHE P 69 TYR 0.016 0.001 TYR M 7 ARG 0.004 0.000 ARG V 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 446 time to evaluate : 10.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 MET cc_start: 0.8647 (ttp) cc_final: 0.8181 (tmm) REVERT: C 139 MET cc_start: 0.6062 (mmt) cc_final: 0.5861 (mmt) REVERT: C 293 MET cc_start: 0.8470 (mmm) cc_final: 0.8256 (tpp) REVERT: C 399 MET cc_start: 0.9078 (tpp) cc_final: 0.8857 (tpp) REVERT: D 163 MET cc_start: 0.9125 (tpp) cc_final: 0.8898 (tpp) REVERT: D 410 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6954 (p0) REVERT: E 1 MET cc_start: 0.7838 (mmp) cc_final: 0.7472 (mmp) REVERT: E 232 MET cc_start: 0.8266 (mpp) cc_final: 0.7676 (mpp) REVERT: E 275 MET cc_start: 0.7788 (ppp) cc_final: 0.7244 (ppp) REVERT: E 277 MET cc_start: 0.8619 (mpp) cc_final: 0.7841 (mpp) REVERT: E 352 MET cc_start: 0.8934 (mpp) cc_final: 0.8542 (mpp) REVERT: F 36 MET cc_start: 0.8089 (mmp) cc_final: 0.7755 (mmm) REVERT: F 175 MET cc_start: 0.2161 (mmt) cc_final: 0.1863 (tpt) REVERT: F 366 MET cc_start: 0.9422 (mpp) cc_final: 0.9119 (mpp) REVERT: G 131 MET cc_start: 0.8997 (pmm) cc_final: 0.8467 (pmm) REVERT: R 56 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: R 100 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8483 (mtt) REVERT: U 188 MET cc_start: 0.7811 (ppp) cc_final: 0.6812 (ppp) REVERT: f 294 MET cc_start: 0.7341 (pmm) cc_final: 0.6718 (pmm) REVERT: f 297 MET cc_start: -0.0456 (OUTLIER) cc_final: -0.0907 (ptm) REVERT: f 321 MET cc_start: 0.7290 (ppp) cc_final: 0.6958 (ppp) REVERT: g 131 MET cc_start: 0.8180 (ppp) cc_final: 0.7773 (ppp) REVERT: h 233 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8495 (mp) REVERT: l 26 MET cc_start: 0.7885 (tpt) cc_final: 0.7535 (tpt) REVERT: r 93 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8689 (mtm) REVERT: x 1 MET cc_start: 0.5701 (tmm) cc_final: 0.5466 (tmm) REVERT: x 101 MET cc_start: 0.6818 (tpp) cc_final: 0.6519 (mmt) REVERT: x 181 MET cc_start: 0.7606 (mtp) cc_final: 0.6961 (mtt) REVERT: W 113 GLU cc_start: 0.2308 (OUTLIER) cc_final: 0.1362 (mm-30) REVERT: W 177 MET cc_start: 0.0459 (mtt) cc_final: -0.2782 (mpp) REVERT: W 375 MET cc_start: 0.8224 (mmp) cc_final: 0.7886 (mtp) REVERT: W 451 MET cc_start: 0.5297 (tpt) cc_final: 0.4326 (tmm) REVERT: V 139 MET cc_start: 0.5766 (mpp) cc_final: 0.4947 (ptp) REVERT: V 309 MET cc_start: 0.6945 (ppp) cc_final: 0.6703 (ppp) outliers start: 85 outliers final: 38 residues processed: 508 average time/residue: 0.8595 time to fit residues: 789.3889 Evaluate side-chains 487 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 442 time to evaluate : 9.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 609 VAL Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain p residue 135 ASP Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 113 GLU Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain e residue 61 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1119 optimal weight: 20.0000 chunk 763 optimal weight: 6.9990 chunk 19 optimal weight: 50.0000 chunk 1001 optimal weight: 8.9990 chunk 554 optimal weight: 10.0000 chunk 1147 optimal weight: 5.9990 chunk 929 optimal weight: 40.0000 chunk 1 optimal weight: 50.0000 chunk 686 optimal weight: 20.0000 chunk 1206 optimal weight: 6.9990 chunk 339 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 HIS ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN U 389 ASN ** U 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 131 GLN x 112 ASN ** x 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 112650 Z= 0.213 Angle : 0.517 11.402 152179 Z= 0.269 Chirality : 0.040 0.214 17228 Planarity : 0.003 0.077 19621 Dihedral : 5.233 126.244 15517 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 0.95 % Allowed : 12.41 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.07), residues: 13974 helix: 2.15 (0.07), residues: 6531 sheet: 0.30 (0.11), residues: 2034 loop : -1.49 (0.08), residues: 5409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 255 HIS 0.007 0.001 HIS f 202 PHE 0.021 0.001 PHE W 309 TYR 0.017 0.001 TYR M 7 ARG 0.011 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 445 time to evaluate : 10.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 MET cc_start: 0.8665 (ttp) cc_final: 0.8185 (tmm) REVERT: C 293 MET cc_start: 0.8409 (mmm) cc_final: 0.8087 (tpt) REVERT: C 399 MET cc_start: 0.9071 (tpp) cc_final: 0.8844 (tpp) REVERT: D 163 MET cc_start: 0.9142 (tpp) cc_final: 0.8900 (tpp) REVERT: D 410 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.6995 (p0) REVERT: E 1 MET cc_start: 0.7840 (mmp) cc_final: 0.7394 (mmp) REVERT: E 122 MET cc_start: 0.6194 (mpp) cc_final: 0.5366 (mpp) REVERT: E 232 MET cc_start: 0.8272 (mpp) cc_final: 0.7594 (mpp) REVERT: E 275 MET cc_start: 0.7788 (ppp) cc_final: 0.7223 (ppp) REVERT: E 277 MET cc_start: 0.8602 (mpp) cc_final: 0.7780 (mpp) REVERT: F 36 MET cc_start: 0.8087 (mmp) cc_final: 0.7724 (mmm) REVERT: F 366 MET cc_start: 0.9403 (mpp) cc_final: 0.9113 (mpp) REVERT: G 131 MET cc_start: 0.9006 (pmm) cc_final: 0.8448 (pmm) REVERT: R 56 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: R 100 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8477 (mtt) REVERT: T 110 MET cc_start: 0.8584 (mmm) cc_final: 0.8157 (mmm) REVERT: U 725 MET cc_start: 0.8265 (ppp) cc_final: 0.7998 (ppp) REVERT: a 165 THR cc_start: 0.5695 (OUTLIER) cc_final: 0.5470 (p) REVERT: a 280 MET cc_start: 0.8876 (mpp) cc_final: 0.8539 (mpp) REVERT: a 341 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7502 (tt) REVERT: f 294 MET cc_start: 0.7402 (pmm) cc_final: 0.6838 (pmm) REVERT: f 297 MET cc_start: -0.0340 (OUTLIER) cc_final: -0.0882 (ptm) REVERT: f 321 MET cc_start: 0.7371 (ppp) cc_final: 0.7068 (ppp) REVERT: l 26 MET cc_start: 0.7918 (tpt) cc_final: 0.7482 (tpt) REVERT: r 93 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8690 (mtm) REVERT: x 1 MET cc_start: 0.5615 (tmm) cc_final: 0.5385 (tmm) REVERT: x 181 MET cc_start: 0.7592 (mtp) cc_final: 0.6910 (mpp) REVERT: W 113 GLU cc_start: 0.2360 (OUTLIER) cc_final: 0.1421 (mm-30) REVERT: W 177 MET cc_start: 0.0399 (mtt) cc_final: -0.2784 (mpp) REVERT: W 230 MET cc_start: 0.8059 (pmm) cc_final: 0.7444 (pmm) REVERT: W 375 MET cc_start: 0.8303 (mmp) cc_final: 0.7983 (mtp) REVERT: W 451 MET cc_start: 0.5357 (tpt) cc_final: 0.4383 (tmm) REVERT: V 139 MET cc_start: 0.5758 (mpp) cc_final: 0.4937 (ptp) REVERT: V 309 MET cc_start: 0.6886 (ppp) cc_final: 0.6545 (ppp) REVERT: V 463 MET cc_start: 0.6950 (mmm) cc_final: 0.6153 (ttt) outliers start: 114 outliers final: 60 residues processed: 538 average time/residue: 0.9108 time to fit residues: 893.4173 Evaluate side-chains 509 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 441 time to evaluate : 10.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain U residue 389 ASN Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 894 MET Chi-restraints excluded: chain U residue 925 VAL Chi-restraints excluded: chain X residue 319 ILE Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain Y residue 235 ASP Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 328 ASP Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 750 GLN Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 135 ASP Chi-restraints excluded: chain r residue 31 VAL Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 113 GLU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain e residue 61 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 452 optimal weight: 10.0000 chunk 1210 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 789 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 1345 optimal weight: 30.0000 chunk 1117 optimal weight: 30.0000 chunk 623 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 706 optimal weight: 0.0040 overall best weight: 6.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 647 HIS ** U 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 262 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 HIS ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 131 GLN ** x 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 112650 Z= 0.197 Angle : 0.516 11.572 152179 Z= 0.267 Chirality : 0.040 0.236 17228 Planarity : 0.003 0.077 19621 Dihedral : 5.171 125.218 15517 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 1.07 % Allowed : 13.20 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.07), residues: 13974 helix: 2.19 (0.07), residues: 6536 sheet: 0.32 (0.12), residues: 2030 loop : -1.48 (0.08), residues: 5408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 255 HIS 0.007 0.001 HIS f 202 PHE 0.020 0.001 PHE P 69 TYR 0.015 0.001 TYR M 7 ARG 0.004 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 445 time to evaluate : 10.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9173 (pp) REVERT: B 309 MET cc_start: 0.8670 (ttp) cc_final: 0.8185 (tmm) REVERT: C 293 MET cc_start: 0.8237 (mmm) cc_final: 0.7886 (tpp) REVERT: C 399 MET cc_start: 0.9075 (tpp) cc_final: 0.8852 (tpp) REVERT: D 163 MET cc_start: 0.9162 (tpp) cc_final: 0.8916 (tpp) REVERT: D 410 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7015 (p0) REVERT: E 1 MET cc_start: 0.7862 (mmp) cc_final: 0.7360 (mmp) REVERT: E 218 MET cc_start: 0.8823 (tpt) cc_final: 0.8526 (mmp) REVERT: E 232 MET cc_start: 0.8252 (mpp) cc_final: 0.7843 (mpp) REVERT: E 275 MET cc_start: 0.7720 (ppp) cc_final: 0.7307 (ppp) REVERT: E 277 MET cc_start: 0.8628 (mpp) cc_final: 0.8047 (mpp) REVERT: F 36 MET cc_start: 0.8096 (mmp) cc_final: 0.7732 (mmm) REVERT: F 175 MET cc_start: 0.1670 (tpt) cc_final: 0.1327 (tpt) REVERT: F 366 MET cc_start: 0.9381 (mpp) cc_final: 0.9127 (mpp) REVERT: G 131 MET cc_start: 0.9017 (pmm) cc_final: 0.8459 (pmm) REVERT: R 56 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: R 100 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8478 (mtt) REVERT: T 110 MET cc_start: 0.8626 (mmm) cc_final: 0.8053 (mmm) REVERT: U 188 MET cc_start: 0.7891 (ppp) cc_final: 0.6785 (ppp) REVERT: U 340 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8626 (tp40) REVERT: U 459 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8556 (p0) REVERT: X 254 MET cc_start: 0.8927 (tpt) cc_final: 0.8517 (tpt) REVERT: a 165 THR cc_start: 0.5699 (OUTLIER) cc_final: 0.5476 (p) REVERT: a 280 MET cc_start: 0.8858 (mpp) cc_final: 0.8567 (mpp) REVERT: a 341 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7509 (tt) REVERT: c 57 MET cc_start: 0.8227 (pmm) cc_final: 0.7823 (pmm) REVERT: f 294 MET cc_start: 0.7459 (pmm) cc_final: 0.7077 (pmm) REVERT: f 297 MET cc_start: -0.0126 (OUTLIER) cc_final: -0.0707 (ptm) REVERT: f 321 MET cc_start: 0.7470 (ppp) cc_final: 0.7167 (ppp) REVERT: l 26 MET cc_start: 0.7928 (tpt) cc_final: 0.7493 (tpt) REVERT: r 93 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8671 (mtm) REVERT: x 1 MET cc_start: 0.5597 (tmm) cc_final: 0.5374 (tmm) REVERT: x 181 MET cc_start: 0.7604 (mtp) cc_final: 0.6968 (mtt) REVERT: W 177 MET cc_start: 0.0341 (mtt) cc_final: -0.2827 (mpp) REVERT: W 375 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: W 451 MET cc_start: 0.5382 (tpt) cc_final: 0.4228 (tmm) REVERT: V 139 MET cc_start: 0.5778 (mpp) cc_final: 0.4933 (ptp) outliers start: 128 outliers final: 75 residues processed: 550 average time/residue: 0.9150 time to fit residues: 910.1656 Evaluate side-chains 526 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 440 time to evaluate : 9.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain U residue 340 GLN Chi-restraints excluded: chain U residue 389 ASN Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 894 MET Chi-restraints excluded: chain U residue 925 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 319 ILE Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain Y residue 235 ASP Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 328 ASP Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 240 HIS Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 476 THR Chi-restraints excluded: chain f residue 609 VAL Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain l residue 193 ARG Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 188 VAL Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain p residue 135 ASP Chi-restraints excluded: chain r residue 31 VAL Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain e residue 61 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1297 optimal weight: 0.3980 chunk 151 optimal weight: 10.0000 chunk 766 optimal weight: 8.9990 chunk 982 optimal weight: 30.0000 chunk 761 optimal weight: 8.9990 chunk 1132 optimal weight: 30.0000 chunk 751 optimal weight: 8.9990 chunk 1340 optimal weight: 60.0000 chunk 839 optimal weight: 6.9990 chunk 817 optimal weight: 8.9990 chunk 618 optimal weight: 40.0000 overall best weight: 6.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 131 GLN s 151 ASN s 152 GLN ** x 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 112650 Z= 0.200 Angle : 0.522 12.810 152179 Z= 0.269 Chirality : 0.040 0.239 17228 Planarity : 0.003 0.077 19621 Dihedral : 5.097 124.110 15514 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 1.11 % Allowed : 13.79 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.08), residues: 13974 helix: 2.22 (0.07), residues: 6530 sheet: 0.30 (0.11), residues: 2060 loop : -1.46 (0.09), residues: 5384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 255 HIS 0.007 0.001 HIS f 202 PHE 0.020 0.001 PHE P 69 TYR 0.016 0.001 TYR X 229 ARG 0.006 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 444 time to evaluate : 10.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9173 (pp) REVERT: B 309 MET cc_start: 0.8695 (ttp) cc_final: 0.8193 (tmm) REVERT: C 293 MET cc_start: 0.8188 (mmm) cc_final: 0.7903 (tpt) REVERT: C 399 MET cc_start: 0.9069 (tpp) cc_final: 0.8843 (tpp) REVERT: D 163 MET cc_start: 0.9167 (tpp) cc_final: 0.8918 (tpp) REVERT: D 410 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7022 (p0) REVERT: E 1 MET cc_start: 0.7850 (mmp) cc_final: 0.7293 (mmp) REVERT: E 218 MET cc_start: 0.8811 (tpt) cc_final: 0.8520 (mmp) REVERT: E 232 MET cc_start: 0.8271 (mpp) cc_final: 0.7816 (mpp) REVERT: E 275 MET cc_start: 0.7671 (ppp) cc_final: 0.7255 (ppp) REVERT: E 277 MET cc_start: 0.8641 (mpp) cc_final: 0.8058 (mpp) REVERT: F 36 MET cc_start: 0.8100 (mmp) cc_final: 0.7748 (mmm) REVERT: F 366 MET cc_start: 0.9369 (mpp) cc_final: 0.9126 (mpp) REVERT: F 405 MET cc_start: 0.9304 (mtp) cc_final: 0.8984 (mtt) REVERT: G 131 MET cc_start: 0.9024 (pmm) cc_final: 0.8458 (pmm) REVERT: H 186 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (p0) REVERT: H 203 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7691 (mtm) REVERT: L 26 MET cc_start: 0.7790 (tpt) cc_final: 0.6994 (tpt) REVERT: R 56 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: R 100 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8485 (mtt) REVERT: T 110 MET cc_start: 0.8642 (mmm) cc_final: 0.8062 (mmm) REVERT: U 188 MET cc_start: 0.7935 (ppp) cc_final: 0.6861 (ppp) REVERT: U 340 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8632 (tp40) REVERT: U 459 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8545 (p0) REVERT: X 254 MET cc_start: 0.8905 (tpt) cc_final: 0.8455 (tpt) REVERT: Y 282 MET cc_start: 0.9011 (ttp) cc_final: 0.8676 (ttm) REVERT: Z 81 MET cc_start: 0.9097 (mpp) cc_final: 0.8700 (mtp) REVERT: a 165 THR cc_start: 0.5704 (OUTLIER) cc_final: 0.5484 (p) REVERT: a 341 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7508 (tt) REVERT: c 57 MET cc_start: 0.8239 (pmm) cc_final: 0.7854 (pmm) REVERT: f 294 MET cc_start: 0.7469 (pmm) cc_final: 0.7206 (pmm) REVERT: f 297 MET cc_start: -0.0009 (OUTLIER) cc_final: -0.0617 (ptm) REVERT: f 321 MET cc_start: 0.7487 (ppp) cc_final: 0.7197 (ppp) REVERT: f 715 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8209 (p90) REVERT: h 203 MET cc_start: 0.8061 (ptt) cc_final: 0.7808 (ptt) REVERT: l 26 MET cc_start: 0.7926 (tpt) cc_final: 0.7505 (tpt) REVERT: r 93 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8669 (mtm) REVERT: x 181 MET cc_start: 0.7582 (mtp) cc_final: 0.6977 (mtt) REVERT: W 177 MET cc_start: 0.0375 (OUTLIER) cc_final: -0.2789 (mpp) REVERT: W 375 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8042 (mtp) REVERT: W 451 MET cc_start: 0.5408 (tpt) cc_final: 0.4391 (tmm) REVERT: V 139 MET cc_start: 0.5757 (mpp) cc_final: 0.4931 (ptp) outliers start: 132 outliers final: 82 residues processed: 551 average time/residue: 0.8491 time to fit residues: 848.1420 Evaluate side-chains 537 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 440 time to evaluate : 9.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain U residue 340 GLN Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 894 MET Chi-restraints excluded: chain U residue 925 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 315 ASP Chi-restraints excluded: chain X residue 319 ILE Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 389 ASP Chi-restraints excluded: chain Y residue 31 HIS Chi-restraints excluded: chain Y residue 235 ASP Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 240 HIS Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 476 THR Chi-restraints excluded: chain f residue 609 VAL Chi-restraints excluded: chain f residue 715 HIS Chi-restraints excluded: chain f residue 750 GLN Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain l residue 193 ARG Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 188 VAL Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain p residue 135 ASP Chi-restraints excluded: chain r residue 31 VAL Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 177 MET Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain W residue 378 MET Chi-restraints excluded: chain e residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 829 optimal weight: 6.9990 chunk 535 optimal weight: 8.9990 chunk 800 optimal weight: 7.9990 chunk 403 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 852 optimal weight: 0.0070 chunk 913 optimal weight: 20.0000 chunk 662 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 1053 optimal weight: 10.0000 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 15 ASN ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 131 GLN x 413 ASN ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 112650 Z= 0.164 Angle : 0.518 13.768 152179 Z= 0.265 Chirality : 0.040 0.237 17228 Planarity : 0.003 0.076 19621 Dihedral : 5.037 122.999 15514 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 0.98 % Allowed : 14.16 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.08), residues: 13974 helix: 2.25 (0.07), residues: 6538 sheet: 0.34 (0.11), residues: 2059 loop : -1.45 (0.09), residues: 5377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 255 HIS 0.006 0.001 HIS f 202 PHE 0.019 0.001 PHE W 309 TYR 0.016 0.001 TYR X 229 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 443 time to evaluate : 10.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8489 (mmm) cc_final: 0.7675 (ptp) REVERT: B 73 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9133 (pp) REVERT: B 309 MET cc_start: 0.8691 (ttp) cc_final: 0.8182 (tmm) REVERT: C 138 MET cc_start: 0.7835 (mmp) cc_final: 0.7587 (mmp) REVERT: C 293 MET cc_start: 0.8173 (mmm) cc_final: 0.7944 (tpt) REVERT: D 163 MET cc_start: 0.9166 (tpp) cc_final: 0.8918 (tpp) REVERT: E 1 MET cc_start: 0.7848 (mmp) cc_final: 0.7413 (mmp) REVERT: E 218 MET cc_start: 0.8813 (tpt) cc_final: 0.8531 (mmp) REVERT: E 232 MET cc_start: 0.8281 (mpp) cc_final: 0.7832 (mpp) REVERT: E 275 MET cc_start: 0.7679 (ppp) cc_final: 0.7261 (ppp) REVERT: E 277 MET cc_start: 0.8645 (mpp) cc_final: 0.8047 (mpp) REVERT: F 366 MET cc_start: 0.9343 (mpp) cc_final: 0.9112 (mpp) REVERT: G 131 MET cc_start: 0.9030 (pmm) cc_final: 0.8472 (pmm) REVERT: H 186 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8103 (p0) REVERT: H 203 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7660 (mtm) REVERT: L 26 MET cc_start: 0.7817 (tpt) cc_final: 0.6971 (tpt) REVERT: R 56 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: R 100 MET cc_start: 0.8777 (mmm) cc_final: 0.8432 (mtt) REVERT: T 110 MET cc_start: 0.8649 (mmm) cc_final: 0.8077 (mmm) REVERT: U 188 MET cc_start: 0.7886 (ppp) cc_final: 0.6817 (ppp) REVERT: U 459 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8537 (p0) REVERT: X 254 MET cc_start: 0.8874 (tpt) cc_final: 0.8392 (tpt) REVERT: Y 282 MET cc_start: 0.9004 (ttp) cc_final: 0.8667 (ttm) REVERT: Z 81 MET cc_start: 0.9077 (mpp) cc_final: 0.8722 (mtp) REVERT: a 165 THR cc_start: 0.5720 (OUTLIER) cc_final: 0.5494 (p) REVERT: a 341 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7493 (tt) REVERT: c 284 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8796 (mt) REVERT: c 303 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7837 (ttt) REVERT: f 294 MET cc_start: 0.7470 (pmm) cc_final: 0.7089 (pmm) REVERT: f 297 MET cc_start: 0.0018 (OUTLIER) cc_final: -0.0576 (ptm) REVERT: f 321 MET cc_start: 0.7454 (ppp) cc_final: 0.7200 (ppp) REVERT: f 715 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8142 (p90) REVERT: l 26 MET cc_start: 0.7965 (tpt) cc_final: 0.7582 (tpt) REVERT: r 93 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8645 (mtm) REVERT: x 181 MET cc_start: 0.7593 (mtp) cc_final: 0.6987 (mtt) REVERT: W 177 MET cc_start: 0.0462 (OUTLIER) cc_final: -0.2728 (mpp) REVERT: W 230 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7427 (pmm) REVERT: W 375 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: W 451 MET cc_start: 0.5356 (tpt) cc_final: 0.4309 (tmm) REVERT: V 139 MET cc_start: 0.5757 (mpp) cc_final: 0.4912 (ptp) REVERT: V 309 MET cc_start: 0.7063 (ppp) cc_final: 0.6651 (ppp) outliers start: 117 outliers final: 80 residues processed: 538 average time/residue: 0.8997 time to fit residues: 876.8121 Evaluate side-chains 534 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 439 time to evaluate : 9.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 894 MET Chi-restraints excluded: chain U residue 925 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 389 ASP Chi-restraints excluded: chain Y residue 31 HIS Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain a residue 141 MET Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 240 HIS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 476 THR Chi-restraints excluded: chain f residue 715 HIS Chi-restraints excluded: chain f residue 750 GLN Chi-restraints excluded: chain h residue 184 LEU Chi-restraints excluded: chain i residue 11 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain l residue 193 ARG Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 188 VAL Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain r residue 31 VAL Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 133 ASP Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 177 MET Chi-restraints excluded: chain W residue 230 MET Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain W residue 378 MET Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain e residue 61 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 1219 optimal weight: 5.9990 chunk 1284 optimal weight: 10.0000 chunk 1171 optimal weight: 9.9990 chunk 1249 optimal weight: 20.0000 chunk 751 optimal weight: 6.9990 chunk 544 optimal weight: 20.0000 chunk 981 optimal weight: 7.9990 chunk 383 optimal weight: 2.9990 chunk 1128 optimal weight: 30.0000 chunk 1181 optimal weight: 20.0000 chunk 1244 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 GLN ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 131 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 112650 Z= 0.199 Angle : 0.535 14.173 152179 Z= 0.273 Chirality : 0.040 0.236 17228 Planarity : 0.003 0.076 19621 Dihedral : 5.034 122.208 15514 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.60 % Rotamer: Outliers : 1.10 % Allowed : 14.28 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.08), residues: 13974 helix: 2.25 (0.07), residues: 6536 sheet: 0.32 (0.12), residues: 2056 loop : -1.44 (0.09), residues: 5382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP T 107 HIS 0.006 0.001 HIS f 202 PHE 0.020 0.001 PHE P 69 TYR 0.015 0.001 TYR X 229 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 440 time to evaluate : 10.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 MET cc_start: 0.8702 (ttp) cc_final: 0.8180 (tmm) REVERT: C 138 MET cc_start: 0.7935 (mmp) cc_final: 0.7675 (mmp) REVERT: D 163 MET cc_start: 0.9169 (tpp) cc_final: 0.8928 (tpp) REVERT: E 218 MET cc_start: 0.8834 (tpt) cc_final: 0.8542 (mmp) REVERT: F 366 MET cc_start: 0.9359 (mpp) cc_final: 0.9123 (mpp) REVERT: G 131 MET cc_start: 0.9034 (pmm) cc_final: 0.8474 (pmm) REVERT: H 203 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7799 (mtm) REVERT: R 44 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9102 (p) REVERT: R 56 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: R 100 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8473 (mtt) REVERT: T 110 MET cc_start: 0.8673 (mmm) cc_final: 0.8092 (mmm) REVERT: U 459 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8546 (p0) REVERT: X 254 MET cc_start: 0.8859 (tpt) cc_final: 0.8372 (tpt) REVERT: Y 282 MET cc_start: 0.9018 (ttp) cc_final: 0.8679 (ttm) REVERT: a 165 THR cc_start: 0.5695 (OUTLIER) cc_final: 0.5464 (p) REVERT: a 341 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7854 (tt) REVERT: c 226 MET cc_start: 0.8584 (mmm) cc_final: 0.8360 (mmm) REVERT: c 284 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8798 (mt) REVERT: c 303 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7803 (ttt) REVERT: f 294 MET cc_start: 0.7508 (pmm) cc_final: 0.7053 (pmm) REVERT: f 297 MET cc_start: 0.0074 (OUTLIER) cc_final: -0.0524 (ptm) REVERT: f 321 MET cc_start: 0.7518 (ppp) cc_final: 0.7255 (ppp) REVERT: f 715 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8126 (p90) REVERT: h 203 MET cc_start: 0.7933 (ptt) cc_final: 0.7650 (ptt) REVERT: l 26 MET cc_start: 0.7987 (tpt) cc_final: 0.7599 (tpt) REVERT: r 93 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: x 181 MET cc_start: 0.7602 (mtp) cc_final: 0.7029 (mtt) REVERT: W 177 MET cc_start: 0.0349 (OUTLIER) cc_final: -0.2794 (mpp) REVERT: W 230 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7457 (pmm) REVERT: W 375 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (mtp) REVERT: W 451 MET cc_start: 0.5473 (tpt) cc_final: 0.4406 (tmm) REVERT: V 139 MET cc_start: 0.5785 (mpp) cc_final: 0.4930 (ptp) REVERT: V 309 MET cc_start: 0.7021 (ppp) cc_final: 0.6503 (ppp) REVERT: V 494 MET cc_start: 0.7926 (tpp) cc_final: 0.7684 (tpp) outliers start: 131 outliers final: 95 residues processed: 546 average time/residue: 0.8524 time to fit residues: 845.6064 Evaluate side-chains 550 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 440 time to evaluate : 10.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 894 MET Chi-restraints excluded: chain U residue 925 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 315 ASP Chi-restraints excluded: chain X residue 319 ILE Chi-restraints excluded: chain X residue 389 ASP Chi-restraints excluded: chain Y residue 31 HIS Chi-restraints excluded: chain Y residue 235 ASP Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 347 ILE Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 240 HIS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 476 THR Chi-restraints excluded: chain f residue 609 VAL Chi-restraints excluded: chain f residue 715 HIS Chi-restraints excluded: chain f residue 750 GLN Chi-restraints excluded: chain h residue 184 LEU Chi-restraints excluded: chain i residue 11 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain l residue 193 ARG Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 188 VAL Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain p residue 135 ASP Chi-restraints excluded: chain r residue 31 VAL Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 133 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 177 MET Chi-restraints excluded: chain W residue 230 MET Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain W residue 378 MET Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain e residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 820 optimal weight: 20.0000 chunk 1321 optimal weight: 40.0000 chunk 806 optimal weight: 7.9990 chunk 626 optimal weight: 40.0000 chunk 918 optimal weight: 6.9990 chunk 1385 optimal weight: 7.9990 chunk 1275 optimal weight: 7.9990 chunk 1103 optimal weight: 7.9990 chunk 114 optimal weight: 40.0000 chunk 852 optimal weight: 9.9990 chunk 676 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 131 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 112650 Z= 0.220 Angle : 0.552 14.778 152179 Z= 0.282 Chirality : 0.040 0.285 17228 Planarity : 0.003 0.076 19621 Dihedral : 5.074 121.131 15514 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.54 % Rotamer: Outliers : 1.08 % Allowed : 14.40 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.89 (0.08), residues: 13974 helix: 2.24 (0.07), residues: 6531 sheet: 0.31 (0.12), residues: 2044 loop : -1.44 (0.09), residues: 5399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP T 107 HIS 0.020 0.001 HIS b 94 PHE 0.021 0.001 PHE P 69 TYR 0.017 0.001 TYR M 7 ARG 0.003 0.000 ARG A 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27948 Ramachandran restraints generated. 13974 Oldfield, 0 Emsley, 13974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 441 time to evaluate : 10.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8491 (mmm) cc_final: 0.7699 (ptp) REVERT: B 309 MET cc_start: 0.8721 (ttp) cc_final: 0.8190 (tmm) REVERT: C 138 MET cc_start: 0.7937 (mmp) cc_final: 0.7674 (mmp) REVERT: D 163 MET cc_start: 0.9167 (tpp) cc_final: 0.8929 (tpp) REVERT: E 218 MET cc_start: 0.8851 (tpt) cc_final: 0.8554 (mmp) REVERT: E 275 MET cc_start: 0.7645 (ppp) cc_final: 0.7171 (ppp) REVERT: F 366 MET cc_start: 0.9351 (mpp) cc_final: 0.9117 (mpp) REVERT: G 131 MET cc_start: 0.9032 (pmm) cc_final: 0.8469 (pmm) REVERT: H 203 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7826 (mtm) REVERT: L 26 MET cc_start: 0.7710 (tpt) cc_final: 0.7095 (tpt) REVERT: R 44 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9115 (p) REVERT: R 56 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: R 100 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8505 (mtt) REVERT: T 110 MET cc_start: 0.8689 (mmm) cc_final: 0.8114 (mmm) REVERT: U 188 MET cc_start: 0.8188 (ppp) cc_final: 0.7218 (ppp) REVERT: U 459 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8566 (p0) REVERT: X 254 MET cc_start: 0.8879 (tpt) cc_final: 0.8396 (tpt) REVERT: Y 282 MET cc_start: 0.9011 (ttp) cc_final: 0.8668 (ttm) REVERT: a 165 THR cc_start: 0.5730 (OUTLIER) cc_final: 0.5503 (p) REVERT: c 57 MET cc_start: 0.8293 (pmm) cc_final: 0.7289 (pmm) REVERT: c 284 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8801 (mt) REVERT: c 303 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7829 (ttt) REVERT: f 294 MET cc_start: 0.7541 (pmm) cc_final: 0.7083 (pmm) REVERT: f 297 MET cc_start: 0.0089 (OUTLIER) cc_final: -0.0514 (ptm) REVERT: f 321 MET cc_start: 0.7578 (ppp) cc_final: 0.7302 (ppp) REVERT: f 715 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8143 (p90) REVERT: h 203 MET cc_start: 0.8025 (ptt) cc_final: 0.7782 (ptt) REVERT: l 26 MET cc_start: 0.7993 (tpt) cc_final: 0.7602 (tpt) REVERT: r 93 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8627 (mtm) REVERT: x 181 MET cc_start: 0.7635 (mtp) cc_final: 0.7073 (mtt) REVERT: x 488 MET cc_start: 0.6326 (tpt) cc_final: 0.4242 (ttt) REVERT: W 177 MET cc_start: 0.0418 (OUTLIER) cc_final: -0.2753 (mpp) REVERT: W 230 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7474 (pmm) REVERT: W 375 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (mtp) REVERT: W 451 MET cc_start: 0.5518 (tpt) cc_final: 0.4466 (tmm) REVERT: V 139 MET cc_start: 0.5806 (mpp) cc_final: 0.4944 (ptp) REVERT: V 309 MET cc_start: 0.7066 (ppp) cc_final: 0.6534 (ppp) REVERT: V 494 MET cc_start: 0.7922 (tpp) cc_final: 0.7685 (tpp) outliers start: 129 outliers final: 102 residues processed: 546 average time/residue: 0.9206 time to fit residues: 912.0874 Evaluate side-chains 556 residues out of total 12029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 440 time to evaluate : 10.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 583 MET Chi-restraints excluded: chain U residue 588 MET Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 894 MET Chi-restraints excluded: chain U residue 925 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 315 ASP Chi-restraints excluded: chain X residue 319 ILE Chi-restraints excluded: chain X residue 389 ASP Chi-restraints excluded: chain Y residue 31 HIS Chi-restraints excluded: chain Y residue 235 ASP Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 347 ILE Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain a residue 141 MET Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 240 HIS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain f residue 297 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 476 THR Chi-restraints excluded: chain f residue 609 VAL Chi-restraints excluded: chain f residue 715 HIS Chi-restraints excluded: chain f residue 750 GLN Chi-restraints excluded: chain h residue 118 MET Chi-restraints excluded: chain h residue 184 LEU Chi-restraints excluded: chain i residue 11 ILE Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain j residue 41 VAL Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 78 MET Chi-restraints excluded: chain l residue 193 ARG Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain m residue 156 VAL Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 188 VAL Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain p residue 135 ASP Chi-restraints excluded: chain r residue 31 VAL Chi-restraints excluded: chain r residue 93 MET Chi-restraints excluded: chain r residue 174 VAL Chi-restraints excluded: chain s residue 133 ASP Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain x residue 89 VAL Chi-restraints excluded: chain y residue 39 ASP Chi-restraints excluded: chain W residue 111 TYR Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 177 MET Chi-restraints excluded: chain W residue 230 MET Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain W residue 378 MET Chi-restraints excluded: chain W residue 412 ILE Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain e residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1391 random chunks: chunk 876 optimal weight: 1.9990 chunk 1175 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 1017 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 306 optimal weight: 6.9990 chunk 1105 optimal weight: 20.0000 chunk 462 optimal weight: 10.0000 chunk 1134 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 792 ASN Y 306 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 131 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.033582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.028744 restraints weight = 2197468.913| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.42 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 112650 Z= 0.155 Angle : 0.530 14.640 152179 Z= 0.269 Chirality : 0.040 0.237 17228 Planarity : 0.003 0.076 19621 Dihedral : 4.997 119.844 15514 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.85 % Rotamer: Outliers : 0.95 % Allowed : 14.66 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.08), residues: 13974 helix: 2.29 (0.07), residues: 6526 sheet: 0.35 (0.12), residues: 2056 loop : -1.44 (0.09), residues: 5392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 107 HIS 0.023 0.001 HIS b 94 PHE 0.019 0.001 PHE W 309 TYR 0.017 0.001 TYR X 229 ARG 0.004 0.000 ARG A 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19760.61 seconds wall clock time: 350 minutes 1.76 seconds (21001.76 seconds total)