Starting phenix.real_space_refine on Mon Feb 19 04:53:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r87_4753/02_2024/6r87_4753.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r87_4753/02_2024/6r87_4753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r87_4753/02_2024/6r87_4753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r87_4753/02_2024/6r87_4753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r87_4753/02_2024/6r87_4753.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r87_4753/02_2024/6r87_4753.pdb" } resolution = 3.4 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= 0.015 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: 7 Type Number sf(0) Gaussians Se 1 7.20 5 Zn 1 6.06 5 P 3671 5.49 5 S 126 5.16 5 C 70966 2.51 5 N 24872 2.21 5 O 35618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 443": "NH1" <-> "NH2" Residue "R ARG 461": "NH1" <-> "NH2" Residue "R ARG 503": "NH1" <-> "NH2" Residue "R ARG 506": "NH1" <-> "NH2" Residue "R ARG 513": "NH1" <-> "NH2" Residue "R ARG 518": "NH1" <-> "NH2" Residue "R ARG 525": "NH1" <-> "NH2" Residue "J ARG 30": "NH1" <-> "NH2" Residue "J PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 105": "NH1" <-> "NH2" Residue "K PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "7 TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 23": "NH1" <-> "NH2" Residue "7 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 91": "NH1" <-> "NH2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 3": "NH1" <-> "NH2" Residue "5 TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 126": "NH1" <-> "NH2" Residue "5 ARG 128": "NH1" <-> "NH2" Residue "5 ARG 175": "NH1" <-> "NH2" Residue "5 ARG 181": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 176": "NH1" <-> "NH2" Residue "S ARG 178": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "s ARG 109": "NH1" <-> "NH2" Residue "s ARG 152": "NH1" <-> "NH2" Residue "s ARG 153": "NH1" <-> "NH2" Residue "s ARG 177": "NH1" <-> "NH2" Residue "s PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 117": "NH1" <-> "NH2" Residue "U TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 155": "NH1" <-> "NH2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 108": "NH1" <-> "NH2" Residue "V ARG 139": "NH1" <-> "NH2" Residue "V PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 125": "NH1" <-> "NH2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "a ARG 121": "NH1" <-> "NH2" Residue "b PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 84": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "e PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "f ARG 70": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 326": "NH1" <-> "NH2" Residue "g PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 140": "NH1" <-> "NH2" Residue "h TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 135255 Number of models: 1 Model: "" Number of chains: 50 Chain: "R" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2777 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 11, 'TRANS': 343} Chain breaks: 10 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'UNK:plan-1': 40} Unresolved non-hydrogen planarities: 40 Chain: "X" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1633 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "i" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "j" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "K" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "7" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "l" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "M" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "m" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "n" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "O" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "o" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "p" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "Q" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "5" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "s" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 209} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1228 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain: "U" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1445 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "V" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "W" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 737 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 180 Chain: "r" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "x" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 59, 'rna3p_pyr': 57} Link IDs: {'rna2p': 5, 'rna3p': 115} Chain: "Y" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 513 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 69, 'rna3p_pyr': 75} Link IDs: {'rna2p': 14, 'rna3p': 143} Chain: "Z" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "a" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 28, 'rna3p_pyr': 32} Link IDs: {'rna2p': 15, 'rna3p': 60} Chain: "b" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 847 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "c" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "E" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1914 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "F" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2375 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "h" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "1" Number of atoms: 70924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3316, 70924 Classifications: {'RNA': 3316} Modifications used: {'rna2p_pur': 205, 'rna2p_pyr': 137, 'rna3p_pur': 1626, 'rna3p_pyr': 1348} Link IDs: {'rna2p': 342, 'rna3p': 2973} Chain breaks: 4 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 196 SG CYS R 74 38.257 82.281 114.025 1.00247.67 S ATOM 215 SG CYS R 77 38.118 83.831 116.620 1.00252.25 S Time building chain proxies: 53.07, per 1000 atoms: 0.39 Number of scatterers: 135255 At special positions: 0 Unit cell: (237.396, 208.128, 276.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Se 1 33.99 Zn 1 29.99 S 126 16.00 P 3671 15.00 O 35618 8.00 N 24872 7.00 C 70966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 57.93 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 601 " pdb="ZN ZN R 601 " - pdb=" ND1 HIS R 96 " pdb="ZN ZN R 601 " - pdb=" SG CYS R 77 " pdb="ZN ZN R 601 " - pdb=" SG CYS R 74 " 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13500 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 72 sheets defined 35.0% alpha, 13.4% beta 1140 base pairs and 1962 stacking pairs defined. Time for finding SS restraints: 47.28 Creating SS restraints... Processing helix chain 'R' and resid 14 through 23 removed outlier: 3.994A pdb=" N TYR R 19 " --> pdb=" O ASN R 16 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE R 20 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE R 21 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU R 23 " --> pdb=" O ILE R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 30 Processing helix chain 'R' and resid 93 through 105 removed outlier: 3.724A pdb=" N LEU R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 123 Processing helix chain 'R' and resid 157 through 173 removed outlier: 3.689A pdb=" N UNK R 173 " --> pdb=" O UNK R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 211 No H-bonds generated for 'chain 'R' and resid 209 through 211' Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.966A pdb=" N SER R 217 " --> pdb=" O LYS R 213 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 227 removed outlier: 3.760A pdb=" N ALA R 222 " --> pdb=" O ASN R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 311 through 331 Processing helix chain 'R' and resid 331 through 337 Processing helix chain 'R' and resid 347 through 354 removed outlier: 3.829A pdb=" N PHE R 354 " --> pdb=" O ASP R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 390 Processing helix chain 'R' and resid 435 through 442 Processing helix chain 'R' and resid 444 through 454 removed outlier: 4.128A pdb=" N ILE R 448 " --> pdb=" O ALA R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 459 through 463 Processing helix chain 'R' and resid 473 through 482 Processing helix chain 'R' and resid 483 through 493 Processing helix chain 'R' and resid 507 through 515 Processing helix chain 'R' and resid 517 through 527 removed outlier: 3.500A pdb=" N PHE R 521 " --> pdb=" O VAL R 517 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN R 527 " --> pdb=" O ILE R 523 " (cutoff:3.500A) Processing helix chain 'R' and resid 536 through 545 Processing helix chain 'X' and resid 31 through 42 removed outlier: 3.580A pdb=" N TYR X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA X 37 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE X 38 " --> pdb=" O PHE X 34 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU X 41 " --> pdb=" O ALA X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 88 Processing helix chain 'X' and resid 103 through 108 removed outlier: 3.671A pdb=" N VAL X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 133 removed outlier: 3.809A pdb=" N LEU X 128 " --> pdb=" O GLU X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 178 Processing helix chain 'X' and resid 211 through 222 removed outlier: 3.518A pdb=" N VAL X 217 " --> pdb=" O PRO X 213 " (cutoff:3.500A) Processing helix chain 'i' and resid 60 through 64 Processing helix chain 'i' and resid 66 through 70 Processing helix chain 'i' and resid 81 through 105 removed outlier: 3.884A pdb=" N ALA i 92 " --> pdb=" O ARG i 88 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU i 96 " --> pdb=" O ALA i 92 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 72 Processing helix chain 'J' and resid 96 through 106 Processing helix chain 'J' and resid 120 through 130 removed outlier: 3.565A pdb=" N LEU J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 151 removed outlier: 3.565A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 removed outlier: 4.209A pdb=" N ILE J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 180 through 190 Processing helix chain 'J' and resid 194 through 202 Processing helix chain 'J' and resid 234 through 244 removed outlier: 4.332A pdb=" N LYS J 238 " --> pdb=" O GLU J 234 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 10 Processing helix chain 'j' and resid 13 through 36 removed outlier: 3.771A pdb=" N SER j 19 " --> pdb=" O GLU j 15 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU j 36 " --> pdb=" O LYS j 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 70 removed outlier: 4.210A pdb=" N SER j 50 " --> pdb=" O THR j 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN j 59 " --> pdb=" O LEU j 55 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA j 65 " --> pdb=" O GLN j 61 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL j 66 " --> pdb=" O GLN j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 81 Processing helix chain 'j' and resid 85 through 90 removed outlier: 3.622A pdb=" N ARG j 89 " --> pdb=" O THR j 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 99 Processing helix chain 'j' and resid 101 through 111 Processing helix chain 'K' and resid 53 through 69 Processing helix chain 'K' and resid 83 through 96 Processing helix chain 'K' and resid 101 through 119 removed outlier: 3.654A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 145 Processing helix chain 'K' and resid 159 through 163 Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'K' and resid 182 through 189 removed outlier: 3.773A pdb=" N LEU K 186 " --> pdb=" O GLY K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 222 Processing helix chain 'K' and resid 225 through 232 Processing helix chain 'K' and resid 239 through 255 removed outlier: 3.547A pdb=" N ASP K 254 " --> pdb=" O ALA K 250 " (cutoff:3.500A) Processing helix chain 'k' and resid 34 through 49 Processing helix chain 'k' and resid 51 through 64 removed outlier: 3.782A pdb=" N ARG k 62 " --> pdb=" O ILE k 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 77 removed outlier: 3.639A pdb=" N LYS k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 98 removed outlier: 3.641A pdb=" N ALA k 85 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER k 97 " --> pdb=" O ILE k 93 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 84 Processing helix chain '7' and resid 116 through 120 Processing helix chain '7' and resid 150 through 164 removed outlier: 3.525A pdb=" N VAL 7 154 " --> pdb=" O SER 7 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 Processing helix chain 'l' and resid 52 through 57 Processing helix chain 'l' and resid 66 through 69 Processing helix chain 'l' and resid 70 through 76 removed outlier: 3.654A pdb=" N ASN l 76 " --> pdb=" O ARG l 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 42 Processing helix chain 'M' and resid 72 through 87 removed outlier: 3.769A pdb=" N ALA M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.763A pdb=" N LEU M 112 " --> pdb=" O HIS M 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY M 113 " --> pdb=" O ILE M 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 109 through 113' Processing helix chain 'M' and resid 155 through 166 removed outlier: 3.597A pdb=" N GLN M 165 " --> pdb=" O SER M 161 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS M 166 " --> pdb=" O TRP M 162 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 16 Processing helix chain 'm' and resid 58 through 68 removed outlier: 4.216A pdb=" N LYS m 64 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN m 67 " --> pdb=" O LYS m 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 21 Processing helix chain 'N' and resid 27 through 46 removed outlier: 3.819A pdb=" N ALA N 43 " --> pdb=" O ARG N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 Processing helix chain 'N' and resid 86 through 94 Processing helix chain 'N' and resid 105 through 122 Processing helix chain 'N' and resid 166 through 179 removed outlier: 4.104A pdb=" N GLU N 176 " --> pdb=" O LEU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 192 removed outlier: 3.931A pdb=" N ALA N 187 " --> pdb=" O ARG N 183 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'n' and resid 6 through 19 Processing helix chain 'n' and resid 24 through 30 removed outlier: 3.543A pdb=" N LEU n 29 " --> pdb=" O TRP n 26 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG n 30 " --> pdb=" O ILE n 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 89 Processing helix chain 'O' and resid 89 through 96 removed outlier: 3.544A pdb=" N LYS O 93 " --> pdb=" O ALA O 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 110 removed outlier: 3.667A pdb=" N LYS O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 135 Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.907A pdb=" N LEU o 85 " --> pdb=" O SER o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 12 removed outlier: 3.887A pdb=" N LEU p 7 " --> pdb=" O ALA p 3 " (cutoff:3.500A) Processing helix chain 'p' and resid 16 through 32 Processing helix chain 'p' and resid 44 through 50 Processing helix chain 'p' and resid 75 through 79 removed outlier: 3.794A pdb=" N ALA p 79 " --> pdb=" O PRO p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 87 removed outlier: 3.918A pdb=" N GLN p 87 " --> pdb=" O PRO p 84 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 110 Processing helix chain 'p' and resid 139 through 144 removed outlier: 3.561A pdb=" N ARG p 144 " --> pdb=" O LYS p 140 " (cutoff:3.500A) Processing helix chain 'p' and resid 148 through 157 removed outlier: 3.739A pdb=" N ILE p 151 " --> pdb=" O TYR p 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP p 153 " --> pdb=" O TRP p 150 " (cutoff:3.500A) Proline residue: p 154 - end of helix removed outlier: 3.694A pdb=" N LYS p 157 " --> pdb=" O PRO p 154 " (cutoff:3.500A) Processing helix chain 'p' and resid 165 through 172 removed outlier: 3.504A pdb=" N LYS p 169 " --> pdb=" O THR p 165 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS p 170 " --> pdb=" O ALA p 166 " (cutoff:3.500A) Processing helix chain 'p' and resid 186 through 193 Processing helix chain 'Q' and resid 15 through 28 removed outlier: 3.752A pdb=" N VAL Q 22 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 58 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 92 through 101 removed outlier: 3.536A pdb=" N ARG Q 101 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 129 Processing helix chain 'Q' and resid 138 through 146 Processing helix chain 'Q' and resid 149 through 185 removed outlier: 4.475A pdb=" N VAL Q 162 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE Q 174 " --> pdb=" O LYS Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 197 Processing helix chain '5' and resid 10 through 12 No H-bonds generated for 'chain '5' and resid 10 through 12' Processing helix chain '5' and resid 25 through 36 removed outlier: 4.629A pdb=" N GLU 5 31 " --> pdb=" O LYS 5 27 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 53 removed outlier: 3.797A pdb=" N GLU 5 49 " --> pdb=" O GLN 5 45 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN 5 50 " --> pdb=" O LYS 5 46 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU 5 52 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP 5 53 " --> pdb=" O GLU 5 49 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 75 Processing helix chain '5' and resid 84 through 105 removed outlier: 4.343A pdb=" N LEU 5 94 " --> pdb=" O PHE 5 90 " (cutoff:3.500A) Processing helix chain '5' and resid 108 through 110 No H-bonds generated for 'chain '5' and resid 108 through 110' Processing helix chain '5' and resid 169 through 177 removed outlier: 4.132A pdb=" N ARG 5 175 " --> pdb=" O ARG 5 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 40 removed outlier: 3.939A pdb=" N PHE S 35 " --> pdb=" O LYS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 54 removed outlier: 4.005A pdb=" N LYS S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL S 48 " --> pdb=" O PHE S 44 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 73 Processing helix chain 'S' and resid 107 through 117 Processing helix chain 'S' and resid 123 through 131 Processing helix chain 'S' and resid 148 through 152 Processing helix chain 's' and resid 4 through 8 Processing helix chain 's' and resid 61 through 77 removed outlier: 3.621A pdb=" N ARG s 68 " --> pdb=" O LEU s 64 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET s 75 " --> pdb=" O ALA s 71 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 83 removed outlier: 3.691A pdb=" N ALA s 83 " --> pdb=" O GLY s 80 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 80 through 83' Processing helix chain 's' and resid 140 through 142 No H-bonds generated for 'chain 's' and resid 140 through 142' Processing helix chain 's' and resid 143 through 155 removed outlier: 3.838A pdb=" N VAL s 147 " --> pdb=" O ASN s 143 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU s 149 " --> pdb=" O ASP s 145 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG s 152 " --> pdb=" O VAL s 148 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG s 153 " --> pdb=" O GLU s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 156 through 158 No H-bonds generated for 'chain 's' and resid 156 through 158' Processing helix chain 's' and resid 176 through 187 Processing helix chain 's' and resid 204 through 212 removed outlier: 3.703A pdb=" N ASN s 208 " --> pdb=" O SER s 204 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 16 Processing helix chain 'T' and resid 28 through 35 Processing helix chain 'T' and resid 37 through 47 removed outlier: 4.103A pdb=" N LYS T 43 " --> pdb=" O ASN T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 72 removed outlier: 3.511A pdb=" N GLU T 72 " --> pdb=" O GLN T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 89 Processing helix chain 'T' and resid 90 through 112 removed outlier: 3.668A pdb=" N VAL T 101 " --> pdb=" O ARG T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.719A pdb=" N LYS T 125 " --> pdb=" O HIS T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 152 Processing helix chain 'U' and resid 33 through 46 removed outlier: 3.596A pdb=" N ALA U 37 " --> pdb=" O ASN U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 114 removed outlier: 3.515A pdb=" N ALA U 111 " --> pdb=" O TYR U 107 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA U 112 " --> pdb=" O GLN U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 142 Processing helix chain 'V' and resid 54 through 58 removed outlier: 3.583A pdb=" N GLN V 58 " --> pdb=" O LYS V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 99 through 123 removed outlier: 3.827A pdb=" N GLN V 103 " --> pdb=" O SER V 99 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA V 121 " --> pdb=" O ALA V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 24 removed outlier: 3.583A pdb=" N THR W 23 " --> pdb=" O VAL W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 38 removed outlier: 3.616A pdb=" N TYR W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 87 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.775A pdb=" N LYS P 31 " --> pdb=" O LEU P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 47 removed outlier: 3.590A pdb=" N ALA P 47 " --> pdb=" O GLY P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 84 Processing helix chain 'P' and resid 108 through 113 removed outlier: 3.558A pdb=" N ALA P 113 " --> pdb=" O ILE P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 133 removed outlier: 3.552A pdb=" N THR P 129 " --> pdb=" O LEU P 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 4 through 20 Processing helix chain 'r' and resid 34 through 43 removed outlier: 3.504A pdb=" N GLU r 40 " --> pdb=" O GLN r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 65 removed outlier: 4.040A pdb=" N ARG r 61 " --> pdb=" O THR r 57 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 76 removed outlier: 3.524A pdb=" N PHE r 73 " --> pdb=" O LEU r 70 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS r 75 " --> pdb=" O ASP r 72 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU r 76 " --> pdb=" O PHE r 73 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 103 removed outlier: 3.766A pdb=" N LYS r 97 " --> pdb=" O LEU r 93 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER r 102 " --> pdb=" O ASN r 98 " (cutoff:3.500A) Processing helix chain 'x' and resid 119 through 124 Processing helix chain 'x' and resid 126 through 132 Processing helix chain 'Y' and resid 33 through 41 removed outlier: 3.705A pdb=" N ALA Y 37 " --> pdb=" O ASN Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 49 removed outlier: 3.673A pdb=" N ILE Y 49 " --> pdb=" O PRO Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 59 Processing helix chain 'Z' and resid 58 through 62 Processing helix chain 'Z' and resid 69 through 80 removed outlier: 3.883A pdb=" N ASN Z 80 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 103 removed outlier: 3.685A pdb=" N LYS Z 96 " --> pdb=" O LYS Z 92 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS Z 97 " --> pdb=" O TYR Z 93 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS Z 100 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 140 removed outlier: 3.682A pdb=" N ARG Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 21 Processing helix chain 'a' and resid 23 through 31 removed outlier: 4.337A pdb=" N VAL a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU a 31 " --> pdb=" O ARG a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 43 Processing helix chain 'a' and resid 100 through 102 No H-bonds generated for 'chain 'a' and resid 100 through 102' Processing helix chain 'a' and resid 113 through 122 Processing helix chain 'b' and resid 58 through 64 Processing helix chain 'b' and resid 65 through 67 No H-bonds generated for 'chain 'b' and resid 65 through 67' Processing helix chain 'b' and resid 105 through 123 removed outlier: 4.022A pdb=" N GLU b 109 " --> pdb=" O SER b 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'c' and resid 41 through 46 Processing helix chain 'c' and resid 64 through 69 removed outlier: 3.646A pdb=" N TRP c 69 " --> pdb=" O ALA c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 92 removed outlier: 3.830A pdb=" N ASP c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN c 89 " --> pdb=" O ASP c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 142 removed outlier: 3.654A pdb=" N GLU c 136 " --> pdb=" O LYS c 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.632A pdb=" N THR D 11 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 35 removed outlier: 3.638A pdb=" N LEU D 29 " --> pdb=" O GLN D 25 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.724A pdb=" N THR D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 17 removed outlier: 3.566A pdb=" N ALA d 16 " --> pdb=" O GLN d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 58 removed outlier: 3.559A pdb=" N LYS d 52 " --> pdb=" O HIS d 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA d 57 " --> pdb=" O ALA d 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 Processing helix chain 'E' and resid 33 through 38 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 141 through 143 No H-bonds generated for 'chain 'E' and resid 141 through 143' Processing helix chain 'E' and resid 173 through 177 removed outlier: 3.705A pdb=" N LYS E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 190 removed outlier: 3.578A pdb=" N ALA E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 21 Processing helix chain 'e' and resid 26 through 36 Processing helix chain 'e' and resid 49 through 64 removed outlier: 3.869A pdb=" N LEU e 62 " --> pdb=" O TYR e 58 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER e 63 " --> pdb=" O TYR e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'F' and resid 133 through 138 removed outlier: 3.640A pdb=" N TYR F 137 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.801A pdb=" N VAL F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 234 removed outlier: 3.660A pdb=" N TRP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'f' and resid 24 through 26 No H-bonds generated for 'chain 'f' and resid 24 through 26' Processing helix chain 'f' and resid 27 through 45 removed outlier: 3.603A pdb=" N ARG f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS f 38 " --> pdb=" O LYS f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 60 removed outlier: 3.556A pdb=" N TRP f 60 " --> pdb=" O ASN f 56 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 63 No H-bonds generated for 'chain 'f' and resid 61 through 63' Processing helix chain 'G' and resid 31 through 44 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 132 through 138 Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 161 through 173 removed outlier: 3.757A pdb=" N ALA G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 181 removed outlier: 3.715A pdb=" N VAL G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 195 removed outlier: 3.814A pdb=" N LYS G 193 " --> pdb=" O GLY G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 220 removed outlier: 3.609A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 239 Processing helix chain 'G' and resid 240 through 243 Processing helix chain 'G' and resid 252 through 263 removed outlier: 3.719A pdb=" N GLY G 263 " --> pdb=" O ASP G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.800A pdb=" N ALA G 298 " --> pdb=" O GLU G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 327 removed outlier: 4.058A pdb=" N LEU G 327 " --> pdb=" O VAL G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 335 removed outlier: 4.138A pdb=" N VAL G 333 " --> pdb=" O PRO G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 360 Processing helix chain 'g' and resid 54 through 58 Processing helix chain 'g' and resid 78 through 83 Processing helix chain 'g' and resid 84 through 86 No H-bonds generated for 'chain 'g' and resid 84 through 86' Processing helix chain 'g' and resid 101 through 116 removed outlier: 4.097A pdb=" N VAL g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL g 107 " --> pdb=" O LYS g 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 29 through 38 removed outlier: 4.109A pdb=" N ARG H 35 " --> pdb=" O TYR H 31 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 86 Proline residue: H 84 - end of helix No H-bonds generated for 'chain 'H' and resid 81 through 86' Processing helix chain 'H' and resid 94 through 113 Processing helix chain 'H' and resid 157 through 170 removed outlier: 3.606A pdb=" N GLY H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY H 170 " --> pdb=" O ALA H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 180 removed outlier: 4.250A pdb=" N ARG H 179 " --> pdb=" O SER H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 200 removed outlier: 4.060A pdb=" N PHE H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 215 through 222 removed outlier: 3.567A pdb=" N PHE H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'H' and resid 235 through 250 removed outlier: 3.863A pdb=" N ALA H 243 " --> pdb=" O ILE H 239 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 270 removed outlier: 3.905A pdb=" N TYR H 265 " --> pdb=" O THR H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 293 Processing helix chain 'h' and resid 41 through 45 removed outlier: 3.536A pdb=" N LEU h 45 " --> pdb=" O GLN h 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.811A pdb=" N LYS I 100 " --> pdb=" O ASN I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 150 removed outlier: 3.978A pdb=" N VAL I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 161 removed outlier: 3.689A pdb=" N SER I 160 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 124 removed outlier: 3.511A pdb=" N LEU L 123 " --> pdb=" O GLN L 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 119 through 124' Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 179 through 184 removed outlier: 3.589A pdb=" N ILE L 183 " --> pdb=" O LEU L 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'R' and resid 276 through 283 removed outlier: 6.074A pdb=" N PHE R 276 " --> pdb=" O SER R 252 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER R 252 " --> pdb=" O PHE R 276 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE R 235 " --> pdb=" O CYS R 338 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN R 340 " --> pdb=" O ILE R 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 17 through 19 removed outlier: 6.900A pdb=" N CYS X 24 " --> pdb=" O VAL X 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'X' and resid 109 through 110 removed outlier: 5.887A pdb=" N ALA X 115 " --> pdb=" O PHE X 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 152 through 154 removed outlier: 6.902A pdb=" N GLY X 159 " --> pdb=" O VAL X 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 20 through 24 Processing sheet with id=AA8, first strand: chain 'J' and resid 74 through 76 removed outlier: 3.638A pdb=" N TYR J 75 " --> pdb=" O VAL V 141 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL V 141 " --> pdb=" O TYR J 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'J' and resid 205 through 206 removed outlier: 4.387A pdb=" N SER J 113 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AB2, first strand: chain 'j' and resid 116 through 117 Processing sheet with id=AB3, first strand: chain 'K' and resid 177 through 180 removed outlier: 6.535A pdb=" N VAL K 151 " --> pdb=" O ALA K 178 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL K 180 " --> pdb=" O VAL K 151 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE K 153 " --> pdb=" O VAL K 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '7' and resid 3 through 11 removed outlier: 6.794A pdb=" N ILE 7 4 " --> pdb=" O ASN 7 59 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU 7 52 " --> pdb=" O VAL 7 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '7' and resid 17 through 21 Processing sheet with id=AB6, first strand: chain '7' and resid 132 through 135 removed outlier: 6.388A pdb=" N LYS 7 87 " --> pdb=" O LYS 7 184 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS 7 184 " --> pdb=" O LYS 7 87 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS 7 89 " --> pdb=" O SER 7 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '7' and resid 100 through 104 Processing sheet with id=AB8, first strand: chain 'l' and resid 16 through 17 Processing sheet with id=AB9, first strand: chain 'M' and resid 46 through 48 removed outlier: 7.030A pdb=" N VAL M 130 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU M 17 " --> pdb=" O TYR M 128 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR M 128 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU M 19 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP M 126 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE M 21 " --> pdb=" O GLY M 124 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLY M 124 " --> pdb=" O ILE M 21 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 51 through 56 removed outlier: 4.733A pdb=" N THR m 22 " --> pdb=" O ARG m 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 23 through 24 removed outlier: 6.352A pdb=" N LYS N 23 " --> pdb=" O LEU p 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'N' and resid 57 through 59 Processing sheet with id=AC4, first strand: chain 'N' and resid 156 through 157 removed outlier: 7.273A pdb=" N LYS c 126 " --> pdb=" O PRO c 100 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE c 102 " --> pdb=" O LYS c 126 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL c 125 " --> pdb=" O GLU c 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 14 through 15 removed outlier: 3.508A pdb=" N PHE U 150 " --> pdb=" O VAL O 15 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 56 through 59 removed outlier: 4.519A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL O 20 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'o' and resid 102 through 103 Processing sheet with id=AC8, first strand: chain 'p' and resid 36 through 39 removed outlier: 4.339A pdb=" N ILE p 61 " --> pdb=" O ALA p 39 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU p 131 " --> pdb=" O TRP p 120 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP p 120 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.174A pdb=" N VAL Q 7 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL Q 36 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE Q 9 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL Q 118 " --> pdb=" O VAL Q 6 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL Q 8 " --> pdb=" O VAL Q 118 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 42 through 44 Processing sheet with id=AD2, first strand: chain '5' and resid 14 through 17 removed outlier: 6.581A pdb=" N HIS 5 145 " --> pdb=" O VAL 5 119 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL 5 119 " --> pdb=" O HIS 5 145 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU 5 147 " --> pdb=" O ILE 5 117 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE 5 117 " --> pdb=" O GLU 5 147 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL 5 149 " --> pdb=" O SER 5 115 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '5' and resid 58 through 59 Processing sheet with id=AD4, first strand: chain '5' and resid 126 through 131 removed outlier: 3.891A pdb=" N ARG 5 135 " --> pdb=" O ARG 5 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 62 through 63 removed outlier: 6.137A pdb=" N VAL S 62 " --> pdb=" O THR S 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'S' and resid 121 through 122 removed outlier: 6.305A pdb=" N VAL S 81 " --> pdb=" O ALA S 102 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR S 80 " --> pdb=" O LEU S 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 's' and resid 34 through 36 Processing sheet with id=AD8, first strand: chain 's' and resid 51 through 52 Processing sheet with id=AD9, first strand: chain 's' and resid 57 through 60 removed outlier: 5.501A pdb=" N ILE s 98 " --> pdb=" O PRO s 121 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY s 123 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 's' and resid 189 through 192 Processing sheet with id=AE2, first strand: chain 'T' and resid 23 through 24 removed outlier: 3.644A pdb=" N TRP T 23 " --> pdb=" O VAL T 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL T 51 " --> pdb=" O TRP T 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'U' and resid 58 through 64 removed outlier: 6.493A pdb=" N ILE U 10 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE U 61 " --> pdb=" O GLN U 8 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN U 8 " --> pdb=" O ILE U 61 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN U 63 " --> pdb=" O GLU U 6 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU U 6 " --> pdb=" O GLN U 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 87 through 96 removed outlier: 6.927A pdb=" N ASN U 74 " --> pdb=" O GLU U 128 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU U 128 " --> pdb=" O ASN U 74 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY U 76 " --> pdb=" O VAL U 126 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL U 126 " --> pdb=" O GLY U 76 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP U 78 " --> pdb=" O LEU U 124 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 84 through 92 removed outlier: 3.699A pdb=" N ASN V 66 " --> pdb=" O GLY V 73 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE V 75 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL V 64 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ASN V 77 " --> pdb=" O GLY V 62 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLY V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 54 through 57 removed outlier: 3.539A pdb=" N VAL W 66 " --> pdb=" O THR W 55 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR W 103 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR W 16 " --> pdb=" O TYR W 103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 12 through 16 Processing sheet with id=AE8, first strand: chain 'r' and resid 50 through 52 removed outlier: 3.811A pdb=" N VAL r 190 " --> pdb=" O PHE r 197 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN r 195 " --> pdb=" O ASP r 192 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'x' and resid 35 through 39 removed outlier: 6.696A pdb=" N MET x 59 " --> pdb=" O ILE x 37 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL x 39 " --> pdb=" O MET x 57 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET x 57 " --> pdb=" O VAL x 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'x' and resid 85 through 86 removed outlier: 3.512A pdb=" N TRP x 85 " --> pdb=" O LEU x 93 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU x 93 " --> pdb=" O TRP x 85 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE x 92 " --> pdb=" O LEU Y 20 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL Y 22 " --> pdb=" O PHE x 92 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR x 94 " --> pdb=" O VAL Y 22 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 4 through 5 removed outlier: 3.649A pdb=" N GLU Y 4 " --> pdb=" O ILE Y 13 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 63 through 66 removed outlier: 4.173A pdb=" N LYS Z 109 " --> pdb=" O ARG Z 125 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 32 through 34 Processing sheet with id=AF5, first strand: chain 'a' and resid 79 through 82 removed outlier: 6.960A pdb=" N ALA a 79 " --> pdb=" O VAL a 73 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL a 73 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN a 81 " --> pdb=" O SER a 71 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU a 57 " --> pdb=" O ILE a 106 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE a 106 " --> pdb=" O LEU a 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 86 through 88 Processing sheet with id=AF7, first strand: chain 'b' and resid 69 through 76 removed outlier: 6.555A pdb=" N LYS b 69 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N HIS b 40 " --> pdb=" O PRO b 28 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU b 42 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE b 46 " --> pdb=" O LYS b 22 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS b 22 " --> pdb=" O ILE b 46 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS b 21 " --> pdb=" O VAL b 13 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS b 9 " --> pdb=" O ILE b 25 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL b 10 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'C' and resid 23 through 27 removed outlier: 4.783A pdb=" N VAL C 68 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 72 through 74 removed outlier: 5.751A pdb=" N LEU c 73 " --> pdb=" O LEU c 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.774A pdb=" N ILE D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 71 through 77 removed outlier: 4.219A pdb=" N GLN E 47 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL E 62 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL E 45 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ARG E 64 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLY E 43 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 101 through 103 removed outlier: 6.192A pdb=" N ILE E 136 " --> pdb=" O ARG E 149 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG E 149 " --> pdb=" O ILE E 136 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 224 through 225 Processing sheet with id=AG6, first strand: chain 'e' and resid 22 through 25 removed outlier: 6.718A pdb=" N THR e 24 " --> pdb=" O ILE e 92 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE e 92 " --> pdb=" O THR e 24 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE e 42 " --> pdb=" O TYR e 68 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 356 through 359 removed outlier: 7.523A pdb=" N LEU F 356 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASP F 59 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE F 335 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL F 220 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA F 217 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE F 278 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA F 219 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR F 276 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS F 281 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET F 323 " --> pdb=" O TYR F 283 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL F 285 " --> pdb=" O PHE F 321 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE F 321 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG F 70 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP F 59 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL F 72 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL F 57 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU F 74 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR F 55 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F 76 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET F 53 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 78 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 98 through 106 removed outlier: 3.841A pdb=" N GLY F 98 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY F 91 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR F 104 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL F 89 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP F 106 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL F 87 " --> pdb=" O TRP F 106 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL F 86 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS F 163 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 157 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AH1, first strand: chain 'f' and resid 49 through 51 removed outlier: 6.884A pdb=" N ARG f 50 " --> pdb=" O VAL f 93 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 13 through 20 removed outlier: 7.034A pdb=" N THR G 16 " --> pdb=" O SER G 10 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER G 10 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN G 18 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL G 151 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU G 150 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU G 206 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR G 251 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL G 208 " --> pdb=" O THR G 251 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 186 through 187 Processing sheet with id=AH4, first strand: chain 'g' and resid 72 through 76 removed outlier: 6.045A pdb=" N LYS g 72 " --> pdb=" O ALA g 93 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU g 95 " --> pdb=" O LYS g 72 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE g 74 " --> pdb=" O GLU g 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'H' and resid 73 through 79 removed outlier: 6.665A pdb=" N ILE H 64 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA H 77 " --> pdb=" O CYS H 62 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N CYS H 62 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR H 79 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE H 60 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'h' and resid 8 through 18 removed outlier: 10.155A pdb=" N VAL h 9 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE h 32 " --> pdb=" O VAL h 9 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLY h 11 " --> pdb=" O ILE h 30 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE h 30 " --> pdb=" O GLY h 11 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N HIS h 13 " --> pdb=" O SER h 28 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N SER h 28 " --> pdb=" O HIS h 13 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N SER h 15 " --> pdb=" O ASN h 26 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ASN h 26 " --> pdb=" O SER h 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN h 17 " --> pdb=" O ASN h 24 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASN h 26 " --> pdb=" O PHE h 85 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N PHE h 85 " --> pdb=" O ASN h 26 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL h 80 " --> pdb=" O THR h 74 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR h 74 " --> pdb=" O VAL h 80 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG h 82 " --> pdb=" O THR h 72 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS h 63 " --> pdb=" O ALA h 55 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG h 48 " --> pdb=" O PHE h 101 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL h 52 " --> pdb=" O SER h 97 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N SER h 97 " --> pdb=" O VAL h 52 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 77 through 80 removed outlier: 6.578A pdb=" N THR I 62 " --> pdb=" O HIS I 57 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS I 57 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU I 64 " --> pdb=" O LEU I 55 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR I 38 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR I 89 " --> pdb=" O VAL I 39 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE I 41 " --> pdb=" O THR I 87 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR I 87 " --> pdb=" O ILE I 41 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 163 through 164 removed outlier: 3.510A pdb=" N LEU L 163 " --> pdb=" O ASN L 40 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL L 205 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 70 through 71 1926 hydrogen bonds defined for protein. 5400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2809 hydrogen bonds 4506 hydrogen bond angles 0 basepair planarities 1140 basepair parallelities 1962 stacking parallelities Total time for adding SS restraints: 238.05 Time building geometry restraints manager: 62.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.26: 12567 1.26 - 1.43: 62727 1.43 - 1.61: 69712 1.61 - 1.78: 443 1.78 - 1.95: 135 Bond restraints: 145584 Sorted by residual: bond pdb=" O3' G B 3 " pdb=" P C B 4 " ideal model delta sigma weight residual 1.607 1.952 -0.345 1.50e-02 4.44e+03 5.29e+02 bond pdb=" C LYS F 237 " pdb=" N LEU F 238 " ideal model delta sigma weight residual 1.329 1.090 0.239 3.03e-02 1.09e+03 6.21e+01 bond pdb=" C ALA V 133 " pdb=" N GLN V 134 " ideal model delta sigma weight residual 1.331 1.232 0.099 1.48e-02 4.57e+03 4.46e+01 bond pdb=" C ALA a 47 " pdb=" N LEU a 48 " ideal model delta sigma weight residual 1.325 1.262 0.063 1.25e-02 6.40e+03 2.57e+01 bond pdb=" C PRO H 139 " pdb=" N ARG H 140 " ideal model delta sigma weight residual 1.331 1.199 0.132 2.83e-02 1.25e+03 2.16e+01 ... (remaining 145579 not shown) Histogram of bond angle deviations from ideal: 89.40 - 99.58: 40 99.58 - 109.76: 60074 109.76 - 119.95: 96320 119.95 - 130.13: 55997 130.13 - 140.31: 2083 Bond angle restraints: 214514 Sorted by residual: angle pdb=" C3' G B 3 " pdb=" O3' G B 3 " pdb=" P C B 4 " ideal model delta sigma weight residual 120.20 101.06 19.14 1.50e+00 4.44e-01 1.63e+02 angle pdb=" C PRO N 48 " pdb=" N ARG N 49 " pdb=" CA ARG N 49 " ideal model delta sigma weight residual 122.48 140.31 -17.83 1.62e+00 3.81e-01 1.21e+02 angle pdb=" N PHE s 172 " pdb=" CA PHE s 172 " pdb=" C PHE s 172 " ideal model delta sigma weight residual 113.72 102.93 10.79 1.30e+00 5.92e-01 6.89e+01 angle pdb=" N VAL L 191 " pdb=" CA VAL L 191 " pdb=" C VAL L 191 " ideal model delta sigma weight residual 112.29 104.59 7.70 9.40e-01 1.13e+00 6.71e+01 angle pdb=" N CYS s 104 " pdb=" CA CYS s 104 " pdb=" C CYS s 104 " ideal model delta sigma weight residual 113.18 102.83 10.35 1.33e+00 5.65e-01 6.05e+01 ... (remaining 214509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 82609 35.97 - 71.94: 8806 71.94 - 107.91: 892 107.91 - 143.88: 60 143.88 - 179.85: 95 Dihedral angle restraints: 92462 sinusoidal: 71547 harmonic: 20915 Sorted by residual: dihedral pdb=" CA ASN J 157 " pdb=" C ASN J 157 " pdb=" N LYS J 158 " pdb=" CA LYS J 158 " ideal model delta harmonic sigma weight residual -180.00 -106.25 -73.75 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA LYS H 259 " pdb=" C LYS H 259 " pdb=" N PHE H 260 " pdb=" CA PHE H 260 " ideal model delta harmonic sigma weight residual -180.00 -112.57 -67.43 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" CA SER s 103 " pdb=" C SER s 103 " pdb=" N CYS s 104 " pdb=" CA CYS s 104 " ideal model delta harmonic sigma weight residual 180.00 116.13 63.87 0 5.00e+00 4.00e-02 1.63e+02 ... (remaining 92459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 24911 0.121 - 0.242: 1815 0.242 - 0.362: 187 0.362 - 0.483: 47 0.483 - 0.604: 14 Chirality restraints: 26974 Sorted by residual: chirality pdb=" C3' G 3 77 " pdb=" C4' G 3 77 " pdb=" O3' G 3 77 " pdb=" C2' G 3 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" C3' A 11900 " pdb=" C4' A 11900 " pdb=" O3' A 11900 " pdb=" C2' A 11900 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CB ILE p 133 " pdb=" CA ILE p 133 " pdb=" CG1 ILE p 133 " pdb=" CG2 ILE p 133 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.07e+00 ... (remaining 26971 not shown) Planarity restraints: 13552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 69 " 0.060 2.00e-02 2.50e+03 4.87e-02 7.13e+01 pdb=" N9 G B 69 " -0.050 2.00e-02 2.50e+03 pdb=" C8 G B 69 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 69 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 69 " -0.019 2.00e-02 2.50e+03 pdb=" C6 G B 69 " -0.111 2.00e-02 2.50e+03 pdb=" O6 G B 69 " 0.092 2.00e-02 2.50e+03 pdb=" N1 G B 69 " 0.030 2.00e-02 2.50e+03 pdb=" C2 G B 69 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G B 69 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G B 69 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 924 " 0.074 2.00e-02 2.50e+03 3.36e-02 3.39e+01 pdb=" N9 G 1 924 " -0.087 2.00e-02 2.50e+03 pdb=" C8 G 1 924 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 1 924 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 1 924 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G 1 924 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G 1 924 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G 1 924 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 1 924 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G 1 924 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G 1 924 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G 1 924 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP c 46 " -0.023 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C ASP c 46 " 0.080 2.00e-02 2.50e+03 pdb=" O ASP c 46 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS c 47 " -0.027 2.00e-02 2.50e+03 ... (remaining 13549 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.76: 4 1.76 - 2.55: 1447 2.55 - 3.33: 151199 3.33 - 4.12: 420440 4.12 - 4.90: 635712 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1208802 Sorted by model distance: nonbonded pdb=" O THR R 286 " pdb=" N2 G B 73 " model vdw 0.981 2.520 nonbonded pdb=" ND1 HIS R 245 " pdb=" ND1 HIS R 283 " model vdw 1.300 3.200 nonbonded pdb=" NH1 ARG R 284 " pdb=" C8 G B 1 " model vdw 1.670 3.340 nonbonded pdb=" N2 G B 2 " pdb=" O2 C B 71 " model vdw 1.673 2.496 nonbonded pdb=" N1 G B 2 " pdb=" N3 C B 71 " model vdw 1.918 2.560 ... (remaining 1208797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 2.770 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: 17.500 Check model and map are aligned: 1.570 Set scattering table: 0.930 Process input model: 519.390 Find NCS groups from input model: 3.410 Set up NCS constraints: 0.380 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: 0.030 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 548.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.012 0.345 145584 Z= 0.764 Angle : 1.284 19.136 214514 Z= 0.675 Chirality : 0.070 0.604 26974 Planarity : 0.008 0.094 13552 Dihedral : 23.198 179.848 78962 Min Nonbonded Distance : 0.981 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.27 % Favored : 91.40 % Rotamer: Outliers : 0.66 % Allowed : 2.44 % Favored : 96.89 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.47 % 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: -3.94 (0.08), residues: 7085 helix: -2.97 (0.08), residues: 2263 sheet: -2.01 (0.15), residues: 935 loop : -2.58 (0.08), residues: 3887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP F 255 HIS 0.021 0.004 HIS b 57 PHE 0.050 0.004 PHE S 153 TYR 0.049 0.005 TYR D 14 ARG 0.029 0.002 ARG H 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2288 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 2249 time to evaluate : 6.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 15 LYS cc_start: 0.9521 (tttt) cc_final: 0.9232 (mmtm) REVERT: R 19 TYR cc_start: 0.8945 (t80) cc_final: 0.8071 (t80) REVERT: R 98 MET cc_start: 0.7719 (mmm) cc_final: 0.7129 (ptt) REVERT: R 212 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7388 (t0) REVERT: R 233 MET cc_start: 0.8025 (pmm) cc_final: 0.7545 (pmm) REVERT: R 282 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5584 (p90) REVERT: R 361 ASN cc_start: 0.7391 (m110) cc_final: 0.6481 (p0) REVERT: R 379 VAL cc_start: 0.9252 (t) cc_final: 0.8925 (m) REVERT: X 42 LEU cc_start: 0.7913 (mt) cc_final: 0.7626 (tt) REVERT: X 46 ILE cc_start: 0.8923 (pt) cc_final: 0.8597 (pt) REVERT: X 66 ASN cc_start: 0.5121 (p0) cc_final: 0.3254 (p0) REVERT: X 127 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7967 (mt-10) REVERT: X 156 ASN cc_start: 0.7212 (m-40) cc_final: 0.5775 (m-40) REVERT: i 106 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8787 (tppt) REVERT: J 51 TYR cc_start: 0.9255 (m-10) cc_final: 0.8859 (m-80) REVERT: J 64 GLN cc_start: 0.8738 (tp40) cc_final: 0.8398 (tp40) REVERT: J 68 ASP cc_start: 0.8820 (m-30) cc_final: 0.8613 (m-30) REVERT: J 183 ASP cc_start: 0.8350 (m-30) cc_final: 0.7598 (m-30) REVERT: J 244 ASN cc_start: 0.7889 (t0) cc_final: 0.7593 (t0) REVERT: j 113 GLN cc_start: 0.8902 (tp40) cc_final: 0.8669 (mm-40) REVERT: j 118 ILE cc_start: 0.9036 (mt) cc_final: 0.8814 (tt) REVERT: K 63 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8574 (mmmm) REVERT: K 124 ASP cc_start: 0.8781 (m-30) cc_final: 0.8576 (m-30) REVERT: K 134 TYR cc_start: 0.8491 (p90) cc_final: 0.8284 (p90) REVERT: K 172 LYS cc_start: 0.9160 (tptt) cc_final: 0.8849 (tppp) REVERT: K 219 ASP cc_start: 0.8521 (m-30) cc_final: 0.8112 (m-30) REVERT: K 224 ASP cc_start: 0.8809 (m-30) cc_final: 0.8487 (p0) REVERT: k 40 VAL cc_start: 0.9440 (t) cc_final: 0.9165 (p) REVERT: k 59 ASP cc_start: 0.8306 (m-30) cc_final: 0.7834 (m-30) REVERT: k 92 ASN cc_start: 0.9073 (m-40) cc_final: 0.8846 (m-40) REVERT: 7 42 ASP cc_start: 0.8023 (m-30) cc_final: 0.7819 (m-30) REVERT: 7 107 ASP cc_start: 0.8397 (m-30) cc_final: 0.8168 (t0) REVERT: M 34 SER cc_start: 0.9484 (t) cc_final: 0.9247 (p) REVERT: M 47 GLN cc_start: 0.8760 (mt0) cc_final: 0.7979 (mt0) REVERT: M 61 ARG cc_start: 0.8549 (ttt90) cc_final: 0.8283 (ttm110) REVERT: M 62 ASN cc_start: 0.8446 (m-40) cc_final: 0.7572 (t0) REVERT: M 75 LYS cc_start: 0.9290 (ttmt) cc_final: 0.8790 (ttpt) REVERT: M 89 TYR cc_start: 0.8729 (m-10) cc_final: 0.8310 (m-10) REVERT: M 93 ASP cc_start: 0.8059 (t70) cc_final: 0.7794 (p0) REVERT: M 131 MET cc_start: 0.8589 (mmm) cc_final: 0.8098 (mmm) REVERT: M 167 TYR cc_start: 0.8123 (m-80) cc_final: 0.6884 (m-10) REVERT: m 64 LYS cc_start: 0.9380 (mptt) cc_final: 0.9143 (mtmt) REVERT: N 107 GLU cc_start: 0.8056 (mp0) cc_final: 0.7848 (mp0) REVERT: N 117 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8696 (mmtm) REVERT: N 189 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8344 (mt-10) REVERT: O 116 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7778 (mt-10) REVERT: o 83 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8655 (ttpt) REVERT: o 98 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8475 (mtpp) REVERT: p 86 ASN cc_start: 0.8326 (m-40) cc_final: 0.8069 (m110) REVERT: Q 42 ASN cc_start: 0.8798 (m110) cc_final: 0.8596 (m110) REVERT: Q 125 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.8177 (ttp-170) REVERT: 5 80 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8256 (mtpp) REVERT: S 100 THR cc_start: 0.9316 (m) cc_final: 0.8953 (p) REVERT: S 122 ILE cc_start: 0.8730 (mm) cc_final: 0.8434 (mt) REVERT: S 123 THR cc_start: 0.7922 (p) cc_final: 0.7649 (t) REVERT: S 146 SER cc_start: 0.9129 (m) cc_final: 0.8748 (p) REVERT: S 155 MET cc_start: 0.8267 (tpt) cc_final: 0.7496 (tpt) REVERT: S 176 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7992 (ttt180) REVERT: s 22 ASN cc_start: 0.8420 (t0) cc_final: 0.8050 (t0) REVERT: s 99 ASN cc_start: 0.8777 (t0) cc_final: 0.8530 (t0) REVERT: s 213 PRO cc_start: 0.9316 (Cg_exo) cc_final: 0.8456 (Cg_endo) REVERT: s 214 GLU cc_start: 0.7783 (mp0) cc_final: 0.7409 (mp0) REVERT: T 143 ILE cc_start: 0.9324 (mt) cc_final: 0.9108 (mt) REVERT: T 144 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8133 (tm-30) REVERT: T 148 ASP cc_start: 0.8454 (m-30) cc_final: 0.7568 (m-30) REVERT: U 104 GLU cc_start: 0.8266 (tp30) cc_final: 0.7916 (tt0) REVERT: U 137 ARG cc_start: 0.8416 (mmt180) cc_final: 0.8088 (mmt180) REVERT: U 160 THR cc_start: 0.8961 (m) cc_final: 0.8730 (t) REVERT: V 128 LEU cc_start: 0.9376 (pp) cc_final: 0.9066 (pp) REVERT: W 16 THR cc_start: 0.8930 (p) cc_final: 0.8323 (p) REVERT: W 28 PHE cc_start: 0.9036 (t80) cc_final: 0.8685 (t80) REVERT: W 98 THR cc_start: 0.8190 (m) cc_final: 0.7938 (p) REVERT: W 101 ASN cc_start: 0.9473 (m-40) cc_final: 0.8776 (m-40) REVERT: W 107 PHE cc_start: 0.8024 (t80) cc_final: 0.7740 (t80) REVERT: r 38 MET cc_start: 0.8336 (mmm) cc_final: 0.7861 (mmm) REVERT: x 68 GLU cc_start: 0.7609 (mp0) cc_final: 0.7376 (mp0) REVERT: x 72 LYS cc_start: 0.8423 (ptmt) cc_final: 0.8200 (ptpp) REVERT: x 121 GLU cc_start: 0.7718 (mp0) cc_final: 0.7183 (mp0) REVERT: x 124 ASP cc_start: 0.7300 (m-30) cc_final: 0.7040 (m-30) REVERT: Y 33 ASN cc_start: 0.8965 (p0) cc_final: 0.8404 (p0) REVERT: Z 63 ILE cc_start: 0.9047 (pp) cc_final: 0.8818 (mm) REVERT: Z 68 THR cc_start: 0.8199 (p) cc_final: 0.7933 (p) REVERT: Z 97 LYS cc_start: 0.8890 (tttt) cc_final: 0.8685 (ttpp) REVERT: Z 101 GLU cc_start: 0.8653 (tt0) cc_final: 0.8357 (tt0) REVERT: a 42 GLN cc_start: 0.8923 (tp40) cc_final: 0.8474 (tm-30) REVERT: b 106 GLN cc_start: 0.8220 (tt0) cc_final: 0.7200 (tt0) REVERT: C 7 THR cc_start: 0.9012 (p) cc_final: 0.8709 (t) REVERT: C 22 GLN cc_start: 0.8490 (tp40) cc_final: 0.8149 (tp40) REVERT: D 83 ILE cc_start: 0.8888 (mm) cc_final: 0.8615 (mm) REVERT: D 89 MET cc_start: 0.8124 (mtm) cc_final: 0.7893 (tmm) REVERT: d 38 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8854 (mtpt) REVERT: d 44 LYS cc_start: 0.9325 (tttt) cc_final: 0.8989 (tptt) REVERT: E 68 LYS cc_start: 0.8282 (tttt) cc_final: 0.7647 (ptmt) REVERT: e 16 LEU cc_start: 0.9017 (tp) cc_final: 0.8776 (tp) REVERT: e 38 LYS cc_start: 0.8975 (mttm) cc_final: 0.7773 (mttm) REVERT: e 66 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7782 (mtmm) REVERT: e 93 LEU cc_start: 0.8784 (pp) cc_final: 0.8290 (pp) REVERT: F 6 TYR cc_start: 0.8882 (m-80) cc_final: 0.8630 (m-10) REVERT: F 305 ILE cc_start: 0.9214 (pt) cc_final: 0.8750 (tt) REVERT: f 9 THR cc_start: 0.9084 (m) cc_final: 0.8772 (p) REVERT: G 9 HIS cc_start: 0.8347 (m-70) cc_final: 0.7556 (m90) REVERT: G 58 HIS cc_start: 0.7827 (m-70) cc_final: 0.7601 (m-70) REVERT: G 99 MET cc_start: 0.7817 (ptp) cc_final: 0.7565 (ptp) REVERT: G 179 LEU cc_start: 0.8676 (mt) cc_final: 0.8444 (mt) REVERT: G 304 GLN cc_start: 0.8359 (tt0) cc_final: 0.8105 (tt0) REVERT: g 55 ILE cc_start: 0.9426 (tp) cc_final: 0.9023 (tp) REVERT: g 92 TYR cc_start: 0.9015 (m-80) cc_final: 0.8744 (m-80) REVERT: g 111 ARG cc_start: 0.8963 (tpt170) cc_final: 0.8572 (tpp80) REVERT: H 32 GLN cc_start: 0.8694 (tt0) cc_final: 0.8090 (tt0) REVERT: H 57 ASN cc_start: 0.7824 (m-40) cc_final: 0.7150 (m110) REVERT: H 92 LEU cc_start: 0.8767 (pp) cc_final: 0.8454 (mp) REVERT: H 168 ASP cc_start: 0.8271 (m-30) cc_final: 0.7987 (m-30) REVERT: I 92 SER cc_start: 0.8965 (t) cc_final: 0.8702 (p) REVERT: I 158 TYR cc_start: 0.9094 (t80) cc_final: 0.8767 (t80) outliers start: 39 outliers final: 14 residues processed: 2273 average time/residue: 1.3451 time to fit residues: 5109.2691 Evaluate side-chains 1555 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1539 time to evaluate : 6.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain x residue 73 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain g residue 27 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 902 optimal weight: 0.7980 chunk 810 optimal weight: 5.9990 chunk 449 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 546 optimal weight: 0.9980 chunk 432 optimal weight: 5.9990 chunk 837 optimal weight: 0.8980 chunk 324 optimal weight: 0.6980 chunk 509 optimal weight: 0.9980 chunk 623 optimal weight: 0.9980 chunk 970 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 ASN R 279 HIS X 6 GLN X 21 ASN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN i 52 GLN J 166 ASN j 16 GLN j 76 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 12 ASN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 59 ASN 7 183 HIS l 20 ASN M 95 ASN N 19 GLN N 137 GLN n 19 GLN O 56 GLN O 62 GLN o 119 ASN p 37 HIS p 123 GLN p 195 ASN Q 50 ASN Q 55 HIS 5 55 GLN 5 97 ASN 5 145 HIS S 9 GLN S 45 ASN S 73 GLN ** s 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 143 ASN s 162 GLN s 174 ASN T 130 ASN U 88 HIS U 122 HIS U 142 GLN V 90 ASN V 112 ASN r 56 ASN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 HIS a 120 GLN b 29 HIS b 36 HIS b 40 HIS b 57 HIS b 123 GLN C 22 GLN C 59 HIS C 82 GLN ** c 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 120 ASN d 12 GLN E 47 GLN E 97 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 209 HIS F 165 GLN F 173 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS f 57 GLN f 87 ASN G 5 GLN G 48 GLN G 59 GLN G 201 GLN G 221 ASN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN I 57 HIS L 44 GLN L 57 ASN L 108 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 145584 Z= 0.169 Angle : 0.714 12.510 214514 Z= 0.375 Chirality : 0.041 0.349 26974 Planarity : 0.005 0.061 13552 Dihedral : 24.284 179.852 64951 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.10 % Favored : 93.66 % Rotamer: Outliers : 3.09 % Allowed : 13.19 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.09), residues: 7085 helix: -1.24 (0.10), residues: 2297 sheet: -1.72 (0.15), residues: 933 loop : -2.08 (0.09), residues: 3855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP O 85 HIS 0.015 0.001 HIS M 68 PHE 0.027 0.002 PHE f 90 TYR 0.028 0.002 TYR W 33 ARG 0.009 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1933 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1751 time to evaluate : 6.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 19 TYR cc_start: 0.8736 (t80) cc_final: 0.8115 (t80) REVERT: R 34 MET cc_start: 0.6100 (tmm) cc_final: 0.5866 (tmm) REVERT: R 98 MET cc_start: 0.7693 (mmm) cc_final: 0.7138 (ptt) REVERT: R 312 LEU cc_start: 0.7197 (mt) cc_final: 0.6827 (pp) REVERT: R 361 ASN cc_start: 0.7094 (m110) cc_final: 0.6513 (p0) REVERT: R 379 VAL cc_start: 0.9318 (t) cc_final: 0.9052 (m) REVERT: R 388 GLU cc_start: 0.8343 (tp30) cc_final: 0.8080 (tp30) REVERT: R 483 MET cc_start: 0.1262 (tpp) cc_final: 0.0685 (ttm) REVERT: X 139 ARG cc_start: 0.5406 (mtt-85) cc_final: 0.4983 (mmt90) REVERT: i 65 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8833 (t) REVERT: i 86 LYS cc_start: 0.8395 (tttm) cc_final: 0.8116 (ttpt) REVERT: J 40 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8467 (ttmt) REVERT: J 51 TYR cc_start: 0.9205 (m-10) cc_final: 0.8911 (m-80) REVERT: J 81 HIS cc_start: 0.8074 (m90) cc_final: 0.7601 (m90) REVERT: J 183 ASP cc_start: 0.8228 (m-30) cc_final: 0.7802 (m-30) REVERT: J 244 ASN cc_start: 0.7861 (t0) cc_final: 0.7474 (t0) REVERT: j 94 LYS cc_start: 0.9268 (tppt) cc_final: 0.9034 (ttmt) REVERT: j 105 ARG cc_start: 0.8320 (tmm-80) cc_final: 0.7970 (tmm160) REVERT: K 138 HIS cc_start: 0.7944 (t-170) cc_final: 0.7424 (t-170) REVERT: K 219 ASP cc_start: 0.8499 (m-30) cc_final: 0.8039 (m-30) REVERT: K 246 MET cc_start: 0.8088 (tmm) cc_final: 0.7887 (ppp) REVERT: k 40 VAL cc_start: 0.9459 (t) cc_final: 0.9153 (p) REVERT: k 44 VAL cc_start: 0.9241 (t) cc_final: 0.9009 (m) REVERT: 7 92 TYR cc_start: 0.8545 (m-10) cc_final: 0.8181 (m-10) REVERT: 7 171 ASP cc_start: 0.7618 (t70) cc_final: 0.7245 (t70) REVERT: l 8 PHE cc_start: 0.9025 (m-10) cc_final: 0.8815 (m-80) REVERT: M 28 ASP cc_start: 0.8623 (t0) cc_final: 0.8359 (p0) REVERT: M 30 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8658 (tt) REVERT: M 34 SER cc_start: 0.9462 (t) cc_final: 0.9216 (p) REVERT: M 61 ARG cc_start: 0.8487 (ttt90) cc_final: 0.8241 (ttm110) REVERT: M 62 ASN cc_start: 0.8399 (m-40) cc_final: 0.7774 (t0) REVERT: M 89 TYR cc_start: 0.8731 (m-10) cc_final: 0.8486 (m-10) REVERT: M 125 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8333 (ttp) REVERT: m 17 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7734 (ttp-170) REVERT: m 39 ARG cc_start: 0.8968 (mmm-85) cc_final: 0.8677 (mmm-85) REVERT: m 65 LEU cc_start: 0.9358 (tt) cc_final: 0.9089 (tt) REVERT: N 107 GLU cc_start: 0.7985 (mp0) cc_final: 0.7760 (mp0) REVERT: N 153 ASP cc_start: 0.7871 (t0) cc_final: 0.7607 (t0) REVERT: N 189 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8519 (mt-10) REVERT: n 42 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8452 (ptm-80) REVERT: O 47 ASP cc_start: 0.6888 (t70) cc_final: 0.6604 (t70) REVERT: O 116 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7822 (mt-10) REVERT: o 98 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8517 (mtpp) REVERT: o 109 ASN cc_start: 0.9263 (m110) cc_final: 0.8945 (m-40) REVERT: o 112 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8070 (mmmt) REVERT: p 86 ASN cc_start: 0.8125 (m-40) cc_final: 0.7906 (m110) REVERT: p 138 GLN cc_start: 0.8080 (pm20) cc_final: 0.7796 (pm20) REVERT: Q 42 ASN cc_start: 0.8708 (m110) cc_final: 0.8443 (m110) REVERT: 5 25 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7813 (p) REVERT: 5 41 LEU cc_start: 0.8675 (tt) cc_final: 0.8472 (tt) REVERT: 5 80 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8337 (mtpp) REVERT: S 90 ASP cc_start: 0.8624 (t70) cc_final: 0.8389 (t0) REVERT: S 100 THR cc_start: 0.9239 (m) cc_final: 0.9024 (p) REVERT: S 155 MET cc_start: 0.8266 (tpt) cc_final: 0.7489 (tpt) REVERT: s 22 ASN cc_start: 0.8333 (t0) cc_final: 0.8088 (t0) REVERT: s 101 MET cc_start: 0.5066 (OUTLIER) cc_final: 0.4641 (mmt) REVERT: s 144 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (tttt) REVERT: s 179 GLU cc_start: 0.8148 (tp30) cc_final: 0.7815 (tp30) REVERT: s 188 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8157 (mp0) REVERT: T 140 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8026 (tp30) REVERT: U 63 GLN cc_start: 0.8906 (tt0) cc_final: 0.8598 (tt0) REVERT: U 104 GLU cc_start: 0.8128 (tp30) cc_final: 0.7773 (tt0) REVERT: U 137 ARG cc_start: 0.8507 (mmt180) cc_final: 0.7957 (mmt-90) REVERT: U 160 THR cc_start: 0.8792 (m) cc_final: 0.8564 (t) REVERT: W 20 SER cc_start: 0.8662 (p) cc_final: 0.8412 (p) REVERT: W 28 PHE cc_start: 0.8981 (t80) cc_final: 0.8502 (t80) REVERT: W 36 TYR cc_start: 0.8058 (t80) cc_final: 0.7703 (t80) REVERT: x 69 LEU cc_start: 0.9122 (mm) cc_final: 0.8914 (mt) REVERT: x 70 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7158 (mtp85) REVERT: Y 30 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7176 (mtt-85) REVERT: Y 32 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8471 (tm-30) REVERT: Y 60 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8242 (ptmt) REVERT: Z 97 LYS cc_start: 0.8745 (tttt) cc_final: 0.8455 (ttpp) REVERT: a 42 GLN cc_start: 0.8885 (tp40) cc_final: 0.8532 (tm-30) REVERT: b 66 THR cc_start: 0.9346 (p) cc_final: 0.8961 (t) REVERT: b 121 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8437 (mtt90) REVERT: b 123 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8613 (mm110) REVERT: C 68 VAL cc_start: 0.8496 (p) cc_final: 0.8223 (m) REVERT: C 71 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8105 (ttm110) REVERT: c 58 MET cc_start: 0.8452 (mtp) cc_final: 0.8213 (mtm) REVERT: c 90 TYR cc_start: 0.8582 (m-10) cc_final: 0.8253 (m-10) REVERT: d 21 ILE cc_start: 0.8659 (mm) cc_final: 0.8320 (mm) REVERT: d 44 LYS cc_start: 0.9134 (tttt) cc_final: 0.8886 (tptt) REVERT: E 68 LYS cc_start: 0.8163 (tttt) cc_final: 0.7336 (ptmm) REVERT: E 147 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7632 (mtm-85) REVERT: E 149 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.6941 (ttm-80) REVERT: E 155 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7814 (mtmm) REVERT: E 237 LEU cc_start: 0.8530 (mt) cc_final: 0.8315 (mp) REVERT: e 36 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7318 (tm-30) REVERT: e 40 LYS cc_start: 0.8376 (mttt) cc_final: 0.8110 (mttt) REVERT: e 66 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7710 (mtmm) REVERT: e 93 LEU cc_start: 0.8501 (pp) cc_final: 0.7878 (pp) REVERT: F 146 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8175 (ttp-110) REVERT: F 305 ILE cc_start: 0.9133 (pt) cc_final: 0.8910 (tt) REVERT: F 319 ASN cc_start: 0.8484 (m-40) cc_final: 0.8114 (m-40) REVERT: F 343 TYR cc_start: 0.8310 (p90) cc_final: 0.7973 (p90) REVERT: F 360 ASP cc_start: 0.7722 (t0) cc_final: 0.7488 (t0) REVERT: f 42 LEU cc_start: 0.8751 (tt) cc_final: 0.8406 (tp) REVERT: G 111 VAL cc_start: 0.9440 (t) cc_final: 0.9166 (p) REVERT: G 304 GLN cc_start: 0.8349 (tt0) cc_final: 0.7773 (pt0) REVERT: G 320 ASN cc_start: 0.8435 (t0) cc_final: 0.8167 (t0) REVERT: g 16 LYS cc_start: 0.7980 (tptt) cc_final: 0.7735 (mmpt) REVERT: g 60 ASN cc_start: 0.8792 (t0) cc_final: 0.8416 (t0) REVERT: g 83 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8421 (mt-10) REVERT: g 92 TYR cc_start: 0.8775 (m-80) cc_final: 0.8521 (m-80) REVERT: g 100 ILE cc_start: 0.8638 (mm) cc_final: 0.8399 (mm) REVERT: g 111 ARG cc_start: 0.8836 (tpt170) cc_final: 0.8409 (tpp80) REVERT: H 57 ASN cc_start: 0.7701 (m-40) cc_final: 0.7167 (m110) REVERT: H 92 LEU cc_start: 0.8643 (pp) cc_final: 0.8243 (mt) REVERT: H 168 ASP cc_start: 0.8183 (m-30) cc_final: 0.7905 (m-30) REVERT: H 179 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7884 (mmt180) REVERT: H 262 LYS cc_start: 0.9530 (OUTLIER) cc_final: 0.8881 (tmmt) REVERT: h 29 LEU cc_start: 0.8998 (mt) cc_final: 0.8791 (mt) REVERT: h 43 PHE cc_start: 0.9001 (t80) cc_final: 0.8723 (t80) REVERT: I 8 LYS cc_start: 0.7533 (tptp) cc_final: 0.7274 (tptt) REVERT: I 92 SER cc_start: 0.8771 (t) cc_final: 0.8506 (p) REVERT: I 102 ASN cc_start: 0.8480 (p0) cc_final: 0.7759 (p0) REVERT: L 47 LYS cc_start: 0.1579 (pttm) cc_final: 0.1096 (pttm) REVERT: L 156 LYS cc_start: 0.6349 (pptt) cc_final: 0.5903 (tptp) outliers start: 182 outliers final: 107 residues processed: 1841 average time/residue: 1.3294 time to fit residues: 4242.2065 Evaluate side-chains 1627 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1513 time to evaluate : 6.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 19 SER Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 189 ASP Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 25 SER Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain s residue 101 MET Chi-restraints excluded: chain s residue 144 LYS Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 65 ASN Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 99 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Z residue 67 ILE Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 120 ASN Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain g residue 27 ARG Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 86 THR Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 539 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 807 optimal weight: 10.0000 chunk 661 optimal weight: 0.0000 chunk 267 optimal weight: 0.7980 chunk 972 optimal weight: 8.9990 chunk 1050 optimal weight: 10.0000 chunk 866 optimal weight: 10.0000 chunk 964 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 780 optimal weight: 8.9990 overall best weight: 3.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 3 GLN J 166 ASN j 16 GLN j 34 GLN j 76 GLN j 104 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 157 ASN l 20 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 GLN p 117 ASN ** p 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 28 ASN 5 72 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 11 GLN s 143 ASN s 162 GLN s 208 ASN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN V 112 ASN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 GLN ** b 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 82 GLN E 97 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN F 165 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS f 87 ASN G 221 ASN g 98 HIS H 32 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN I 57 HIS I 138 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 145584 Z= 0.311 Angle : 0.706 12.904 214514 Z= 0.367 Chirality : 0.043 0.367 26974 Planarity : 0.005 0.065 13552 Dihedral : 23.953 179.985 64944 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.24 % Favored : 92.52 % Rotamer: Outliers : 4.46 % Allowed : 15.96 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.09), residues: 7085 helix: -0.63 (0.10), residues: 2313 sheet: -1.59 (0.15), residues: 987 loop : -1.89 (0.09), residues: 3785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 99 HIS 0.023 0.001 HIS Y 58 PHE 0.037 0.002 PHE M 163 TYR 0.023 0.002 TYR M 116 ARG 0.010 0.001 ARG H 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1808 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1545 time to evaluate : 7.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 19 TYR cc_start: 0.8679 (t80) cc_final: 0.8089 (t80) REVERT: R 34 MET cc_start: 0.5846 (tmm) cc_final: 0.5631 (tmm) REVERT: R 233 MET cc_start: 0.8367 (pmm) cc_final: 0.7739 (pmm) REVERT: R 240 MET cc_start: 0.8872 (mtt) cc_final: 0.8450 (mtp) REVERT: R 271 GLU cc_start: 0.8880 (pt0) cc_final: 0.8638 (pp20) REVERT: R 361 ASN cc_start: 0.7208 (m110) cc_final: 0.6618 (p0) REVERT: R 379 VAL cc_start: 0.9343 (t) cc_final: 0.9097 (m) REVERT: R 388 GLU cc_start: 0.8397 (tp30) cc_final: 0.8137 (tp30) REVERT: i 51 LEU cc_start: 0.9278 (pp) cc_final: 0.8920 (pp) REVERT: i 65 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8868 (t) REVERT: J 40 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8568 (ttmt) REVERT: J 51 TYR cc_start: 0.9175 (m-10) cc_final: 0.8877 (m-80) REVERT: J 64 GLN cc_start: 0.8763 (tp40) cc_final: 0.7757 (tp40) REVERT: J 183 ASP cc_start: 0.8510 (m-30) cc_final: 0.7939 (m-30) REVERT: j 94 LYS cc_start: 0.9372 (tppt) cc_final: 0.9026 (ttmt) REVERT: j 105 ARG cc_start: 0.8366 (tmm-80) cc_final: 0.7903 (tmm160) REVERT: j 113 GLN cc_start: 0.8701 (mm-40) cc_final: 0.7950 (tm-30) REVERT: K 138 HIS cc_start: 0.8182 (t-170) cc_final: 0.7746 (t-170) REVERT: K 202 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7963 (tm-30) REVERT: K 231 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8580 (mppt) REVERT: K 246 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8054 (ppp) REVERT: k 40 VAL cc_start: 0.9469 (t) cc_final: 0.9155 (p) REVERT: k 41 ARG cc_start: 0.8990 (mtt90) cc_final: 0.8775 (mtt90) REVERT: k 44 VAL cc_start: 0.9287 (t) cc_final: 0.9062 (m) REVERT: k 54 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7711 (mt-10) REVERT: k 59 ASP cc_start: 0.8233 (m-30) cc_final: 0.8016 (m-30) REVERT: 7 107 ASP cc_start: 0.8264 (t0) cc_final: 0.7978 (t0) REVERT: l 75 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8615 (tttm) REVERT: M 61 ARG cc_start: 0.8496 (ttt90) cc_final: 0.8220 (ttp-110) REVERT: M 62 ASN cc_start: 0.8288 (m-40) cc_final: 0.7563 (t0) REVERT: M 63 GLU cc_start: 0.8665 (tt0) cc_final: 0.7820 (tm-30) REVERT: M 101 ASN cc_start: 0.7603 (m-40) cc_final: 0.7326 (m-40) REVERT: M 109 HIS cc_start: 0.8918 (p-80) cc_final: 0.8698 (p-80) REVERT: M 125 MET cc_start: 0.8577 (ttp) cc_final: 0.8241 (ttp) REVERT: m 39 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8606 (mmm-85) REVERT: m 65 LEU cc_start: 0.9342 (tt) cc_final: 0.9102 (tt) REVERT: N 107 GLU cc_start: 0.7964 (mp0) cc_final: 0.7700 (mp0) REVERT: N 122 LYS cc_start: 0.8647 (mttp) cc_final: 0.8329 (mmmt) REVERT: N 189 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8690 (mp0) REVERT: O 47 ASP cc_start: 0.6921 (t70) cc_final: 0.6596 (t70) REVERT: O 116 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7848 (mt-10) REVERT: o 89 TYR cc_start: 0.8287 (m-10) cc_final: 0.8085 (m-80) REVERT: o 98 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8587 (mtpp) REVERT: o 109 ASN cc_start: 0.9268 (m110) cc_final: 0.8953 (m-40) REVERT: o 112 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8158 (mmmt) REVERT: p 86 ASN cc_start: 0.8417 (m-40) cc_final: 0.8077 (m110) REVERT: Q 4 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7249 (mt-10) REVERT: Q 42 ASN cc_start: 0.8742 (m110) cc_final: 0.8527 (m110) REVERT: Q 84 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8805 (tp) REVERT: Q 106 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: Q 182 ASN cc_start: 0.8684 (m-40) cc_final: 0.8470 (m110) REVERT: S 90 ASP cc_start: 0.8518 (t70) cc_final: 0.8273 (t0) REVERT: S 100 THR cc_start: 0.9165 (m) cc_final: 0.8914 (p) REVERT: S 122 ILE cc_start: 0.8486 (mm) cc_final: 0.7890 (mt) REVERT: S 155 MET cc_start: 0.8329 (tpt) cc_final: 0.7477 (tpt) REVERT: s 22 ASN cc_start: 0.8388 (t0) cc_final: 0.8092 (t0) REVERT: s 35 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8863 (pp) REVERT: s 101 MET cc_start: 0.5231 (mmt) cc_final: 0.4940 (mmt) REVERT: s 179 GLU cc_start: 0.8229 (tp30) cc_final: 0.7817 (tp30) REVERT: s 183 LYS cc_start: 0.9275 (mttt) cc_final: 0.8507 (mtpt) REVERT: s 185 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8769 (mm-30) REVERT: s 188 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8251 (mp0) REVERT: T 140 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8009 (tp30) REVERT: U 63 GLN cc_start: 0.9002 (tt0) cc_final: 0.8785 (tt0) REVERT: U 160 THR cc_start: 0.8785 (m) cc_final: 0.8553 (t) REVERT: V 13 TYR cc_start: 0.8674 (m-80) cc_final: 0.8402 (m-80) REVERT: W 20 SER cc_start: 0.8755 (p) cc_final: 0.8524 (p) REVERT: W 28 PHE cc_start: 0.8958 (t80) cc_final: 0.8463 (t80) REVERT: r 12 PHE cc_start: 0.5871 (m-10) cc_final: 0.5197 (m-80) REVERT: x 66 LYS cc_start: 0.9069 (ptmt) cc_final: 0.8650 (ptmm) REVERT: x 68 GLU cc_start: 0.7849 (mp0) cc_final: 0.7129 (mp0) REVERT: x 72 LYS cc_start: 0.8479 (ptmt) cc_final: 0.8184 (ptpp) REVERT: Y 30 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.6966 (mtt-85) REVERT: Y 32 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8521 (tm-30) REVERT: Y 60 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8239 (ptmm) REVERT: Z 97 LYS cc_start: 0.8812 (tttt) cc_final: 0.8491 (ttpp) REVERT: b 49 TYR cc_start: 0.8489 (m-80) cc_final: 0.8287 (m-10) REVERT: b 66 THR cc_start: 0.9420 (p) cc_final: 0.9007 (t) REVERT: b 123 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8604 (mm110) REVERT: c 58 MET cc_start: 0.8501 (mtp) cc_final: 0.8127 (mtm) REVERT: c 70 LYS cc_start: 0.8848 (mttm) cc_final: 0.8631 (mmmm) REVERT: d 21 ILE cc_start: 0.8753 (mm) cc_final: 0.8549 (mm) REVERT: d 44 LYS cc_start: 0.9179 (tttt) cc_final: 0.8885 (tptt) REVERT: d 52 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8486 (mmtp) REVERT: E 68 LYS cc_start: 0.8255 (tttt) cc_final: 0.7741 (ttpt) REVERT: E 189 TYR cc_start: 0.8593 (m-80) cc_final: 0.8231 (m-80) REVERT: e 12 GLN cc_start: 0.8843 (tp40) cc_final: 0.8579 (mp10) REVERT: e 36 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7481 (tm-30) REVERT: e 38 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8341 (mmtp) REVERT: e 66 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7706 (mtmm) REVERT: e 93 LEU cc_start: 0.8579 (pp) cc_final: 0.8286 (pp) REVERT: F 305 ILE cc_start: 0.9175 (pt) cc_final: 0.8881 (tt) REVERT: F 343 TYR cc_start: 0.8255 (p90) cc_final: 0.8003 (p90) REVERT: f 42 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8517 (tp) REVERT: f 50 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8299 (mtm-85) REVERT: G 226 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6910 (mt-10) REVERT: G 237 GLN cc_start: 0.8765 (mt0) cc_final: 0.8534 (mt0) REVERT: G 296 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8530 (mm110) REVERT: G 304 GLN cc_start: 0.8347 (tt0) cc_final: 0.8118 (tt0) REVERT: G 320 ASN cc_start: 0.8505 (t0) cc_final: 0.8151 (t0) REVERT: g 83 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8435 (mt-10) REVERT: g 111 ARG cc_start: 0.8861 (tpt170) cc_final: 0.8372 (tpp80) REVERT: H 32 GLN cc_start: 0.8108 (tt0) cc_final: 0.7834 (tt0) REVERT: H 57 ASN cc_start: 0.7885 (m-40) cc_final: 0.7297 (m110) REVERT: H 92 LEU cc_start: 0.8676 (pp) cc_final: 0.8317 (mt) REVERT: H 168 ASP cc_start: 0.8252 (m-30) cc_final: 0.7985 (m-30) REVERT: H 264 GLN cc_start: 0.9021 (mp10) cc_final: 0.8641 (mp10) REVERT: h 6 ARG cc_start: 0.8887 (ttp80) cc_final: 0.8504 (ttp80) REVERT: h 43 PHE cc_start: 0.8974 (t80) cc_final: 0.8694 (t80) REVERT: I 54 TYR cc_start: 0.8923 (t80) cc_final: 0.8623 (t80) REVERT: I 92 SER cc_start: 0.8778 (t) cc_final: 0.8533 (p) REVERT: I 133 GLU cc_start: 0.8741 (pm20) cc_final: 0.8537 (pm20) REVERT: I 134 ARG cc_start: 0.9123 (ttm-80) cc_final: 0.8888 (ttm-80) REVERT: I 138 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: I 142 ASP cc_start: 0.8319 (p0) cc_final: 0.8096 (p0) REVERT: I 143 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8752 (pttm) REVERT: I 175 LYS cc_start: 0.8194 (tptp) cc_final: 0.7933 (tptp) REVERT: L 47 LYS cc_start: 0.1556 (pttm) cc_final: 0.1056 (pttm) REVERT: L 174 MET cc_start: 0.4733 (tpp) cc_final: 0.3642 (mmm) outliers start: 263 outliers final: 189 residues processed: 1688 average time/residue: 1.2116 time to fit residues: 3527.0605 Evaluate side-chains 1658 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1460 time to evaluate : 6.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain j residue 11 THR Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 51 SER Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 80 THR Chi-restraints excluded: chain 7 residue 82 VAL Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 142 ASP Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain s residue 35 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain s residue 207 ASN Chi-restraints excluded: chain s residue 208 ASN Chi-restraints excluded: chain T residue 61 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 99 SER Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 68 THR Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain g residue 27 ARG Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 109 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 960 optimal weight: 8.9990 chunk 731 optimal weight: 40.0000 chunk 504 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 464 optimal weight: 8.9990 chunk 653 optimal weight: 10.0000 chunk 976 optimal weight: 50.0000 chunk 1033 optimal weight: 10.0000 chunk 509 optimal weight: 10.0000 chunk 925 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 159 GLN J 186 HIS j 16 GLN j 34 GLN j 76 GLN j 104 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 162 GLN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 HIS d 43 HIS d 45 HIS E 97 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 ASN G 221 ASN G 260 GLN G 307 GLN g 98 HIS ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 145584 Z= 0.435 Angle : 0.766 14.368 214514 Z= 0.396 Chirality : 0.046 0.375 26974 Planarity : 0.006 0.071 13552 Dihedral : 23.899 179.997 64942 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.79 % Favored : 91.97 % Rotamer: Outliers : 5.75 % Allowed : 16.91 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.09), residues: 7085 helix: -0.40 (0.11), residues: 2299 sheet: -1.42 (0.15), residues: 975 loop : -1.88 (0.09), residues: 3811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP O 99 HIS 0.008 0.002 HIS N 99 PHE 0.023 0.002 PHE S 44 TYR 0.028 0.002 TYR K 134 ARG 0.009 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1839 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1500 time to evaluate : 7.047 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 19 TYR cc_start: 0.8540 (t80) cc_final: 0.7793 (t80) REVERT: R 34 MET cc_start: 0.5887 (tmm) cc_final: 0.5636 (tmm) REVERT: R 240 MET cc_start: 0.8837 (mtt) cc_final: 0.8464 (mtm) REVERT: R 271 GLU cc_start: 0.8955 (pt0) cc_final: 0.8569 (pp20) REVERT: R 361 ASN cc_start: 0.7257 (m110) cc_final: 0.6680 (p0) REVERT: R 379 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9131 (m) REVERT: R 388 GLU cc_start: 0.8450 (tp30) cc_final: 0.8249 (tp30) REVERT: X 6 GLN cc_start: 0.7608 (mt0) cc_final: 0.7235 (mm-40) REVERT: X 42 LEU cc_start: 0.7880 (mt) cc_final: 0.7647 (tt) REVERT: i 36 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7938 (mmtt) REVERT: i 51 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8927 (pp) REVERT: i 65 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8818 (t) REVERT: J 40 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8725 (ttmt) REVERT: J 51 TYR cc_start: 0.9178 (m-10) cc_final: 0.8928 (m-80) REVERT: J 64 GLN cc_start: 0.8761 (tp40) cc_final: 0.7826 (tp40) REVERT: J 183 ASP cc_start: 0.8527 (m-30) cc_final: 0.7998 (m-30) REVERT: j 94 LYS cc_start: 0.9416 (tppt) cc_final: 0.9213 (tppt) REVERT: j 102 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: j 105 ARG cc_start: 0.8390 (tmm-80) cc_final: 0.7721 (tmm160) REVERT: j 113 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8111 (tm-30) REVERT: K 138 HIS cc_start: 0.8349 (t-170) cc_final: 0.8072 (t-170) REVERT: K 202 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7918 (tm-30) REVERT: K 231 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8596 (mppt) REVERT: k 40 VAL cc_start: 0.9489 (t) cc_final: 0.9205 (p) REVERT: 7 23 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.5901 (mpp80) REVERT: 7 38 LEU cc_start: 0.9018 (mp) cc_final: 0.8315 (mp) REVERT: 7 90 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.8000 (mtp) REVERT: 7 107 ASP cc_start: 0.8259 (t0) cc_final: 0.7908 (t0) REVERT: 7 153 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8005 (t0) REVERT: l 75 LYS cc_start: 0.8851 (ttpp) cc_final: 0.8603 (tttm) REVERT: M 25 GLU cc_start: 0.8199 (pm20) cc_final: 0.7697 (pm20) REVERT: M 61 ARG cc_start: 0.8522 (ttt90) cc_final: 0.8260 (ttm110) REVERT: M 62 ASN cc_start: 0.8445 (m-40) cc_final: 0.7756 (t0) REVERT: M 125 MET cc_start: 0.8557 (ttp) cc_final: 0.8242 (ttp) REVERT: M 131 MET cc_start: 0.8624 (mmm) cc_final: 0.8260 (mmm) REVERT: m 39 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8671 (mmm-85) REVERT: m 65 LEU cc_start: 0.9355 (tt) cc_final: 0.9064 (tt) REVERT: N 107 GLU cc_start: 0.7964 (mp0) cc_final: 0.7682 (mp0) REVERT: N 122 LYS cc_start: 0.8691 (mttp) cc_final: 0.8330 (mmmt) REVERT: N 149 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7893 (mp10) REVERT: N 189 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8767 (mt-10) REVERT: O 47 ASP cc_start: 0.6959 (t70) cc_final: 0.6653 (t70) REVERT: O 116 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7956 (mt-10) REVERT: o 89 TYR cc_start: 0.8480 (m-10) cc_final: 0.8010 (m-80) REVERT: o 109 ASN cc_start: 0.9290 (m110) cc_final: 0.8952 (m-40) REVERT: o 112 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8275 (mmmt) REVERT: Q 4 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7388 (mt-10) REVERT: Q 42 ASN cc_start: 0.8802 (m110) cc_final: 0.8552 (m110) REVERT: Q 106 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: Q 182 ASN cc_start: 0.8774 (m-40) cc_final: 0.8555 (m110) REVERT: S 6 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8176 (t) REVERT: S 25 TYR cc_start: 0.8189 (m-80) cc_final: 0.7929 (m-80) REVERT: S 90 ASP cc_start: 0.8474 (t70) cc_final: 0.8225 (t0) REVERT: S 100 THR cc_start: 0.9172 (m) cc_final: 0.8942 (p) REVERT: s 22 ASN cc_start: 0.8486 (t0) cc_final: 0.8225 (t0) REVERT: s 65 GLU cc_start: 0.7764 (tt0) cc_final: 0.7526 (tt0) REVERT: s 101 MET cc_start: 0.5381 (mmt) cc_final: 0.5180 (mmt) REVERT: s 143 ASN cc_start: 0.8981 (t0) cc_final: 0.8437 (t0) REVERT: s 179 GLU cc_start: 0.8427 (tp30) cc_final: 0.8106 (tp30) REVERT: s 183 LYS cc_start: 0.9269 (mttt) cc_final: 0.8886 (mtpt) REVERT: s 185 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8736 (mm-30) REVERT: s 188 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8142 (mp0) REVERT: T 130 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8654 (t0) REVERT: T 140 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8100 (tp30) REVERT: U 137 ARG cc_start: 0.8764 (mmt-90) cc_final: 0.7804 (mmt-90) REVERT: U 160 THR cc_start: 0.8651 (m) cc_final: 0.8437 (t) REVERT: V 13 TYR cc_start: 0.8717 (m-80) cc_final: 0.8434 (m-80) REVERT: W 28 PHE cc_start: 0.8949 (t80) cc_final: 0.8500 (t80) REVERT: r 12 PHE cc_start: 0.6136 (m-10) cc_final: 0.5312 (m-80) REVERT: x 66 LYS cc_start: 0.9135 (ptmt) cc_final: 0.8279 (ptmt) REVERT: x 68 GLU cc_start: 0.7988 (mp0) cc_final: 0.7177 (mp0) REVERT: x 71 LYS cc_start: 0.8926 (mttp) cc_final: 0.8633 (mttp) REVERT: x 72 LYS cc_start: 0.8666 (ptmt) cc_final: 0.8281 (ptpp) REVERT: Y 32 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8650 (tm-30) REVERT: Z 73 MET cc_start: 0.8063 (mpp) cc_final: 0.7854 (mpp) REVERT: b 66 THR cc_start: 0.9453 (p) cc_final: 0.8954 (t) REVERT: b 123 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8647 (mm110) REVERT: c 58 MET cc_start: 0.8592 (mtp) cc_final: 0.8213 (mtm) REVERT: c 70 LYS cc_start: 0.8957 (mttm) cc_final: 0.8747 (mmmt) REVERT: d 21 ILE cc_start: 0.8856 (mm) cc_final: 0.8648 (mm) REVERT: d 44 LYS cc_start: 0.9309 (tttt) cc_final: 0.8918 (tptt) REVERT: E 68 LYS cc_start: 0.8376 (tttt) cc_final: 0.7539 (ptmm) REVERT: e 12 GLN cc_start: 0.8959 (tp40) cc_final: 0.8563 (mp10) REVERT: F 261 MET cc_start: 0.8306 (mtm) cc_final: 0.8084 (mtm) REVERT: F 305 ILE cc_start: 0.9189 (pt) cc_final: 0.8892 (tt) REVERT: F 343 TYR cc_start: 0.8271 (p90) cc_final: 0.8011 (p90) REVERT: f 42 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8516 (tp) REVERT: f 50 ARG cc_start: 0.8508 (mtt180) cc_final: 0.8265 (mtm-85) REVERT: f 80 ASN cc_start: 0.5941 (t0) cc_final: 0.5718 (t0) REVERT: G 55 LYS cc_start: 0.7737 (pttm) cc_final: 0.7279 (pttm) REVERT: G 99 MET cc_start: 0.7728 (ptp) cc_final: 0.7520 (ptm) REVERT: G 136 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8872 (mm) REVERT: G 194 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8208 (p90) REVERT: G 296 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8508 (mm-40) REVERT: G 304 GLN cc_start: 0.8313 (tt0) cc_final: 0.8110 (tt0) REVERT: G 320 ASN cc_start: 0.8597 (t0) cc_final: 0.8205 (t0) REVERT: g 111 ARG cc_start: 0.8905 (tpt170) cc_final: 0.8400 (tpp80) REVERT: H 57 ASN cc_start: 0.8004 (m-40) cc_final: 0.7399 (m110) REVERT: H 92 LEU cc_start: 0.8751 (pp) cc_final: 0.8453 (mp) REVERT: H 168 ASP cc_start: 0.8277 (m-30) cc_final: 0.7938 (m-30) REVERT: h 6 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8592 (ttp80) REVERT: h 97 SER cc_start: 0.8449 (m) cc_final: 0.8134 (m) REVERT: I 92 SER cc_start: 0.8804 (t) cc_final: 0.7707 (p) REVERT: I 134 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8905 (ttm-80) REVERT: I 138 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8296 (tp-100) REVERT: I 143 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8826 (pttm) REVERT: L 47 LYS cc_start: 0.1668 (pttm) cc_final: 0.0984 (pttp) REVERT: L 174 MET cc_start: 0.4872 (tpp) cc_final: 0.3976 (mmm) outliers start: 339 outliers final: 253 residues processed: 1678 average time/residue: 1.2052 time to fit residues: 3506.7057 Evaluate side-chains 1677 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1409 time to evaluate : 6.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain X residue 68 ARG Chi-restraints excluded: chain X residue 121 ILE Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain X residue 193 VAL Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 105 VAL Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain j residue 11 THR Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 51 SER Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 80 THR Chi-restraints excluded: chain 7 residue 82 VAL Chi-restraints excluded: chain 7 residue 90 MET Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 153 ASP Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain n residue 34 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 99 TRP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 121 VAL Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 169 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 137 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain s residue 207 ASN Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 SER Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 109 TYR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 164 SER Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 99 SER Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 53 MET Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 68 THR Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain b residue 24 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain b residue 105 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 48 HIS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain g residue 9 ILE Chi-restraints excluded: chain g residue 27 ARG Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 88 ASN Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 860 optimal weight: 40.0000 chunk 586 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 769 optimal weight: 8.9990 chunk 426 optimal weight: 10.0000 chunk 881 optimal weight: 1.9990 chunk 714 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 527 optimal weight: 0.0670 chunk 927 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 overall best weight: 2.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 GLN j 34 GLN j 104 GLN K 155 ASN 7 157 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN ** s 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 162 GLN s 208 ASN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 106 GLN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN E 79 ASN E 97 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN g 98 HIS ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 77 ASN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 145584 Z= 0.238 Angle : 0.652 16.862 214514 Z= 0.340 Chirality : 0.040 0.336 26974 Planarity : 0.005 0.058 13552 Dihedral : 23.813 179.445 64942 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.21 % Favored : 92.55 % Rotamer: Outliers : 4.97 % Allowed : 19.23 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.10), residues: 7085 helix: -0.08 (0.11), residues: 2301 sheet: -1.25 (0.15), residues: 981 loop : -1.72 (0.10), residues: 3803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP O 99 HIS 0.007 0.001 HIS H 90 PHE 0.030 0.002 PHE s 172 TYR 0.028 0.002 TYR K 134 ARG 0.009 0.001 ARG m 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1810 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1517 time to evaluate : 7.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 19 TYR cc_start: 0.8572 (t80) cc_final: 0.7884 (t80) REVERT: R 240 MET cc_start: 0.8864 (mtt) cc_final: 0.8562 (mtm) REVERT: R 271 GLU cc_start: 0.8919 (pt0) cc_final: 0.8471 (pp20) REVERT: R 317 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7506 (mm-30) REVERT: R 361 ASN cc_start: 0.7313 (m110) cc_final: 0.6748 (p0) REVERT: R 379 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9077 (m) REVERT: R 388 GLU cc_start: 0.8449 (tp30) cc_final: 0.8240 (tp30) REVERT: R 474 MET cc_start: 0.5649 (ptp) cc_final: 0.5406 (ptt) REVERT: X 6 GLN cc_start: 0.7503 (mt0) cc_final: 0.7172 (mm-40) REVERT: X 42 LEU cc_start: 0.7779 (mt) cc_final: 0.7551 (tt) REVERT: i 36 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7985 (mmtt) REVERT: i 51 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8918 (pp) REVERT: i 65 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8784 (t) REVERT: J 40 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8646 (ttmt) REVERT: J 51 TYR cc_start: 0.9129 (m-10) cc_final: 0.8865 (m-80) REVERT: J 179 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8846 (pp) REVERT: J 183 ASP cc_start: 0.8516 (m-30) cc_final: 0.8015 (m-30) REVERT: j 94 LYS cc_start: 0.9390 (tppt) cc_final: 0.9124 (tppt) REVERT: j 102 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: j 105 ARG cc_start: 0.8381 (tmm-80) cc_final: 0.7996 (tmm-80) REVERT: j 113 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8038 (tm-30) REVERT: K 138 HIS cc_start: 0.8202 (t-170) cc_final: 0.7785 (t-170) REVERT: K 231 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8626 (mppt) REVERT: K 246 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7894 (ppp) REVERT: k 40 VAL cc_start: 0.9450 (t) cc_final: 0.9174 (p) REVERT: k 44 VAL cc_start: 0.9290 (t) cc_final: 0.9049 (m) REVERT: 7 90 MET cc_start: 0.8223 (mtp) cc_final: 0.7966 (mtp) REVERT: 7 107 ASP cc_start: 0.8179 (t0) cc_final: 0.7799 (t0) REVERT: 7 153 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7996 (t0) REVERT: l 75 LYS cc_start: 0.8868 (ttpp) cc_final: 0.8641 (tttm) REVERT: M 61 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8259 (ttp-110) REVERT: M 62 ASN cc_start: 0.8453 (m-40) cc_final: 0.7735 (t0) REVERT: M 131 MET cc_start: 0.8575 (mmm) cc_final: 0.8371 (mmm) REVERT: m 17 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7880 (ttp-170) REVERT: m 39 ARG cc_start: 0.8967 (mmm-85) cc_final: 0.8603 (mmm-85) REVERT: m 65 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9105 (tt) REVERT: N 121 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8413 (p) REVERT: N 122 LYS cc_start: 0.8666 (mttp) cc_final: 0.8261 (mmmt) REVERT: N 189 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8724 (mp0) REVERT: O 47 ASP cc_start: 0.6973 (t70) cc_final: 0.6662 (t70) REVERT: O 116 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7854 (mt-10) REVERT: O 125 LYS cc_start: 0.9286 (mtpp) cc_final: 0.8998 (mttt) REVERT: o 89 TYR cc_start: 0.8420 (m-10) cc_final: 0.8083 (m-80) REVERT: o 98 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8595 (mtpp) REVERT: o 109 ASN cc_start: 0.9187 (m110) cc_final: 0.8868 (m-40) REVERT: o 112 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8094 (mmmt) REVERT: Q 42 ASN cc_start: 0.8753 (m110) cc_final: 0.8497 (m110) REVERT: Q 106 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: Q 182 ASN cc_start: 0.8780 (m-40) cc_final: 0.8535 (m110) REVERT: S 6 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8168 (t) REVERT: S 29 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9007 (mm) REVERT: S 90 ASP cc_start: 0.8521 (t70) cc_final: 0.8266 (t0) REVERT: S 100 THR cc_start: 0.9137 (m) cc_final: 0.8861 (p) REVERT: s 22 ASN cc_start: 0.8446 (t0) cc_final: 0.8115 (t0) REVERT: s 143 ASN cc_start: 0.8839 (t0) cc_final: 0.8574 (t0) REVERT: s 174 ASN cc_start: 0.8559 (t0) cc_final: 0.8298 (t0) REVERT: s 183 LYS cc_start: 0.9267 (mttt) cc_final: 0.8908 (mtmt) REVERT: s 188 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8120 (mp0) REVERT: T 130 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8306 (t0) REVERT: T 135 LYS cc_start: 0.8833 (tttm) cc_final: 0.8529 (ttmm) REVERT: T 140 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8059 (tp30) REVERT: T 148 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: V 13 TYR cc_start: 0.8662 (m-80) cc_final: 0.8374 (m-80) REVERT: x 66 LYS cc_start: 0.9082 (ptmt) cc_final: 0.8753 (ptmt) REVERT: x 68 GLU cc_start: 0.7945 (mp0) cc_final: 0.7572 (mp0) REVERT: x 72 LYS cc_start: 0.8590 (ptmt) cc_final: 0.8270 (ptpp) REVERT: Y 32 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8593 (tm-30) REVERT: b 66 THR cc_start: 0.9454 (p) cc_final: 0.9012 (t) REVERT: b 123 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8652 (mm110) REVERT: C 7 THR cc_start: 0.8480 (t) cc_final: 0.7897 (t) REVERT: c 70 LYS cc_start: 0.8960 (mttm) cc_final: 0.8730 (mmmt) REVERT: d 44 LYS cc_start: 0.9241 (tttt) cc_final: 0.8824 (tptt) REVERT: d 52 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8568 (mmtp) REVERT: E 68 LYS cc_start: 0.8273 (tttt) cc_final: 0.7769 (ttpt) REVERT: E 128 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8378 (mtm180) REVERT: E 194 ASN cc_start: 0.8595 (t0) cc_final: 0.8251 (t0) REVERT: e 12 GLN cc_start: 0.8947 (tp40) cc_final: 0.8586 (mp10) REVERT: F 261 MET cc_start: 0.8278 (mtm) cc_final: 0.8072 (mtm) REVERT: F 319 ASN cc_start: 0.8389 (m110) cc_final: 0.7983 (m-40) REVERT: F 343 TYR cc_start: 0.8218 (p90) cc_final: 0.7927 (p90) REVERT: f 34 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8211 (mtpt) REVERT: f 42 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8449 (tp) REVERT: f 50 ARG cc_start: 0.8474 (mtt180) cc_final: 0.8252 (mtm-85) REVERT: f 62 ARG cc_start: 0.8725 (mtt-85) cc_final: 0.8265 (mtp85) REVERT: G 55 LYS cc_start: 0.7836 (pttm) cc_final: 0.7373 (pttm) REVERT: G 99 MET cc_start: 0.7650 (ptp) cc_final: 0.7412 (ptm) REVERT: G 237 GLN cc_start: 0.8730 (mt0) cc_final: 0.8504 (mt0) REVERT: G 304 GLN cc_start: 0.8269 (tt0) cc_final: 0.8064 (tt0) REVERT: G 306 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8517 (p) REVERT: G 320 ASN cc_start: 0.8526 (t0) cc_final: 0.8291 (t0) REVERT: g 111 ARG cc_start: 0.8837 (tpt170) cc_final: 0.8347 (tpp80) REVERT: H 92 LEU cc_start: 0.8669 (pp) cc_final: 0.8347 (mp) REVERT: H 168 ASP cc_start: 0.8253 (m-30) cc_final: 0.7904 (m-30) REVERT: h 6 ARG cc_start: 0.9002 (ttp80) cc_final: 0.8724 (ttp80) REVERT: h 43 PHE cc_start: 0.8886 (t80) cc_final: 0.8634 (t80) REVERT: h 97 SER cc_start: 0.8372 (m) cc_final: 0.8036 (m) REVERT: I 92 SER cc_start: 0.8971 (t) cc_final: 0.8446 (t) REVERT: I 134 ARG cc_start: 0.9159 (ttm-80) cc_final: 0.8875 (ttm-80) REVERT: I 137 ASP cc_start: 0.9222 (m-30) cc_final: 0.8903 (m-30) REVERT: I 143 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8869 (pttm) REVERT: L 47 LYS cc_start: 0.1717 (pttm) cc_final: 0.1126 (pttm) REVERT: L 174 MET cc_start: 0.4760 (OUTLIER) cc_final: 0.4558 (mmm) outliers start: 293 outliers final: 217 residues processed: 1664 average time/residue: 1.2113 time to fit residues: 3490.0680 Evaluate side-chains 1674 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1438 time to evaluate : 6.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain X residue 9 ASN Chi-restraints excluded: chain X residue 68 ARG Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain j residue 11 THR Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 51 SER Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 78 MET Chi-restraints excluded: chain 7 residue 80 THR Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 153 ASP Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 99 TRP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain s residue 35 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 82 ASP Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain s residue 207 ASN Chi-restraints excluded: chain s residue 208 ASN Chi-restraints excluded: chain T residue 61 SER Chi-restraints excluded: chain T residue 109 TYR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 65 ASN Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 99 SER Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain x residue 25 CYS Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Z residue 67 ILE Chi-restraints excluded: chain Z residue 68 THR Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 105 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 124 ILE Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 HIS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain g residue 9 ILE Chi-restraints excluded: chain g residue 27 ARG Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 109 LEU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain L residue 174 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 347 optimal weight: 0.9990 chunk 930 optimal weight: 30.0000 chunk 204 optimal weight: 3.9990 chunk 606 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 1034 optimal weight: 6.9990 chunk 858 optimal weight: 50.0000 chunk 478 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 chunk 342 optimal weight: 5.9990 chunk 542 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 454 ASN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 GLN j 34 GLN j 104 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 172 GLN ** s 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 162 GLN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 7 GLN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 106 GLN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN G 260 GLN ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS H 32 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 145584 Z= 0.314 Angle : 0.684 18.153 214514 Z= 0.354 Chirality : 0.041 0.427 26974 Planarity : 0.005 0.060 13552 Dihedral : 23.762 179.758 64942 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.89 % Favored : 91.88 % Rotamer: Outliers : 5.75 % Allowed : 19.39 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 7085 helix: 0.08 (0.11), residues: 2290 sheet: -1.20 (0.15), residues: 991 loop : -1.70 (0.10), residues: 3804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 99 HIS 0.008 0.001 HIS F 313 PHE 0.027 0.002 PHE M 163 TYR 0.032 0.002 TYR M 167 ARG 0.010 0.001 ARG m 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1797 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1458 time to evaluate : 7.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 19 TYR cc_start: 0.8556 (t80) cc_final: 0.7838 (t80) REVERT: R 240 MET cc_start: 0.8825 (mtt) cc_final: 0.8228 (mtm) REVERT: R 271 GLU cc_start: 0.8833 (pt0) cc_final: 0.8442 (pp20) REVERT: R 279 HIS cc_start: 0.8698 (p-80) cc_final: 0.7535 (p90) REVERT: R 344 ARG cc_start: 0.7084 (ttp-110) cc_final: 0.5406 (ttp80) REVERT: R 346 ARG cc_start: 0.7757 (mtm180) cc_final: 0.7516 (mtm180) REVERT: R 361 ASN cc_start: 0.7347 (m110) cc_final: 0.6839 (p0) REVERT: R 379 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9087 (m) REVERT: X 6 GLN cc_start: 0.7440 (mt0) cc_final: 0.7032 (mm-40) REVERT: X 42 LEU cc_start: 0.7821 (mt) cc_final: 0.7589 (tt) REVERT: i 36 LYS cc_start: 0.8283 (mmtt) cc_final: 0.8012 (mmtt) REVERT: i 51 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8872 (pp) REVERT: i 65 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8791 (t) REVERT: J 40 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8669 (ttmt) REVERT: J 51 TYR cc_start: 0.9119 (m-10) cc_final: 0.8878 (m-80) REVERT: J 158 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7427 (mmtm) REVERT: J 179 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8888 (pp) REVERT: J 183 ASP cc_start: 0.8575 (m-30) cc_final: 0.8075 (m-30) REVERT: j 94 LYS cc_start: 0.9380 (tppt) cc_final: 0.9120 (tppt) REVERT: j 102 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: j 105 ARG cc_start: 0.8387 (tmm-80) cc_final: 0.7792 (tmm160) REVERT: j 113 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8055 (tm-30) REVERT: K 138 HIS cc_start: 0.8411 (t-170) cc_final: 0.8057 (t-170) REVERT: k 34 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8722 (t) REVERT: k 40 VAL cc_start: 0.9466 (t) cc_final: 0.9170 (p) REVERT: k 44 VAL cc_start: 0.9304 (t) cc_final: 0.9068 (m) REVERT: 7 90 MET cc_start: 0.8245 (mtp) cc_final: 0.8010 (mtp) REVERT: 7 107 ASP cc_start: 0.8174 (t0) cc_final: 0.7793 (t0) REVERT: 7 153 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7963 (t0) REVERT: l 75 LYS cc_start: 0.8868 (ttpp) cc_final: 0.8631 (tttm) REVERT: l 79 GLN cc_start: 0.8096 (mt0) cc_final: 0.7603 (mm-40) REVERT: M 61 ARG cc_start: 0.8555 (ttt90) cc_final: 0.8303 (ttm110) REVERT: M 62 ASN cc_start: 0.8439 (m-40) cc_final: 0.7737 (t0) REVERT: M 125 MET cc_start: 0.8461 (ttp) cc_final: 0.8232 (ttp) REVERT: m 17 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7787 (ttp-170) REVERT: m 39 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8597 (mmm-85) REVERT: m 65 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9117 (tt) REVERT: N 11 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7959 (mtpp) REVERT: N 121 SER cc_start: 0.9131 (p) cc_final: 0.8646 (p) REVERT: N 122 LYS cc_start: 0.8627 (mttp) cc_final: 0.8230 (mmmt) REVERT: N 180 ARG cc_start: 0.7914 (tmt90) cc_final: 0.7682 (tmm-80) REVERT: N 189 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8706 (mp0) REVERT: O 47 ASP cc_start: 0.6895 (t70) cc_final: 0.6640 (t70) REVERT: O 116 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7853 (mt-10) REVERT: O 125 LYS cc_start: 0.9280 (mtpp) cc_final: 0.9007 (mttt) REVERT: o 89 TYR cc_start: 0.8471 (m-10) cc_final: 0.8177 (m-80) REVERT: o 98 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8611 (mtpp) REVERT: o 109 ASN cc_start: 0.9245 (m110) cc_final: 0.8959 (m-40) REVERT: o 112 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8136 (mmmt) REVERT: p 198 SER cc_start: 0.9303 (t) cc_final: 0.9068 (p) REVERT: Q 42 ASN cc_start: 0.8795 (m110) cc_final: 0.8551 (m110) REVERT: Q 106 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: Q 182 ASN cc_start: 0.8778 (m-40) cc_final: 0.8542 (m110) REVERT: S 6 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8160 (t) REVERT: S 90 ASP cc_start: 0.8523 (t70) cc_final: 0.8286 (t0) REVERT: S 100 THR cc_start: 0.9119 (m) cc_final: 0.8859 (p) REVERT: s 22 ASN cc_start: 0.8474 (t0) cc_final: 0.8135 (t0) REVERT: s 65 GLU cc_start: 0.7784 (tt0) cc_final: 0.7579 (tt0) REVERT: s 143 ASN cc_start: 0.8903 (t0) cc_final: 0.8502 (t0) REVERT: s 179 GLU cc_start: 0.8414 (tp30) cc_final: 0.7976 (tp30) REVERT: s 183 LYS cc_start: 0.9257 (mttt) cc_final: 0.8736 (mtmt) REVERT: s 185 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8557 (mm-30) REVERT: s 188 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8116 (mp0) REVERT: s 198 PHE cc_start: 0.8580 (m-80) cc_final: 0.8380 (m-80) REVERT: T 130 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8422 (t0) REVERT: T 135 LYS cc_start: 0.8848 (tttm) cc_final: 0.8531 (ttmm) REVERT: T 140 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8068 (tp30) REVERT: T 148 ASP cc_start: 0.8242 (m-30) cc_final: 0.7974 (m-30) REVERT: V 13 TYR cc_start: 0.8747 (m-80) cc_final: 0.8433 (m-80) REVERT: W 28 PHE cc_start: 0.8908 (t80) cc_final: 0.8316 (t80) REVERT: x 66 LYS cc_start: 0.9059 (ptmt) cc_final: 0.8572 (ptmt) REVERT: x 68 GLU cc_start: 0.7947 (mp0) cc_final: 0.7385 (mp0) REVERT: x 72 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8237 (ptpp) REVERT: Y 32 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8633 (tm-30) REVERT: b 66 THR cc_start: 0.9457 (p) cc_final: 0.9002 (t) REVERT: b 123 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8654 (mm110) REVERT: C 7 THR cc_start: 0.8601 (t) cc_final: 0.8152 (t) REVERT: C 22 GLN cc_start: 0.8383 (tp40) cc_final: 0.8081 (tp40) REVERT: c 70 LYS cc_start: 0.8968 (mttm) cc_final: 0.8734 (mmmt) REVERT: D 84 ARG cc_start: 0.8735 (tpp80) cc_final: 0.8426 (ttm-80) REVERT: d 44 LYS cc_start: 0.9281 (tttt) cc_final: 0.8861 (tptt) REVERT: E 68 LYS cc_start: 0.8311 (tttt) cc_final: 0.7490 (ptmm) REVERT: E 109 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6672 (mm-30) REVERT: E 194 ASN cc_start: 0.8694 (t0) cc_final: 0.8334 (t0) REVERT: e 12 GLN cc_start: 0.8952 (tp40) cc_final: 0.8484 (mp10) REVERT: F 319 ASN cc_start: 0.8521 (m110) cc_final: 0.8297 (m-40) REVERT: F 343 TYR cc_start: 0.8261 (p90) cc_final: 0.8033 (p90) REVERT: f 42 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8425 (tp) REVERT: f 50 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8273 (mtm-85) REVERT: G 14 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7692 (pp20) REVERT: G 55 LYS cc_start: 0.7792 (pttm) cc_final: 0.7341 (pttm) REVERT: G 99 MET cc_start: 0.7698 (ptp) cc_final: 0.7469 (ptm) REVERT: G 136 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8848 (mm) REVERT: G 237 GLN cc_start: 0.8766 (mt0) cc_final: 0.8539 (mt0) REVERT: G 320 ASN cc_start: 0.8542 (t0) cc_final: 0.8295 (t0) REVERT: g 111 ARG cc_start: 0.8872 (tpt170) cc_final: 0.8363 (tpp80) REVERT: H 92 LEU cc_start: 0.8674 (pp) cc_final: 0.8357 (mp) REVERT: H 168 ASP cc_start: 0.8291 (m-30) cc_final: 0.7961 (m-30) REVERT: h 6 ARG cc_start: 0.9023 (ttp80) cc_final: 0.8741 (ttp80) REVERT: h 43 PHE cc_start: 0.8963 (t80) cc_final: 0.8733 (t80) REVERT: h 97 SER cc_start: 0.8390 (m) cc_final: 0.8057 (m) REVERT: I 63 LEU cc_start: 0.9124 (mt) cc_final: 0.8918 (mt) REVERT: I 134 ARG cc_start: 0.9161 (ttm-80) cc_final: 0.8862 (ttm-80) REVERT: I 137 ASP cc_start: 0.9213 (m-30) cc_final: 0.8887 (m-30) REVERT: I 143 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8883 (pttm) REVERT: L 47 LYS cc_start: 0.1775 (pttm) cc_final: 0.1191 (pttm) REVERT: L 174 MET cc_start: 0.4631 (tpp) cc_final: 0.3394 (mmm) outliers start: 339 outliers final: 271 residues processed: 1634 average time/residue: 1.1755 time to fit residues: 3339.4085 Evaluate side-chains 1691 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1405 time to evaluate : 6.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain X residue 9 ASN Chi-restraints excluded: chain X residue 68 ARG Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 6 THR Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain j residue 11 THR Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 51 SER Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 78 MET Chi-restraints excluded: chain 7 residue 80 THR Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 153 ASP Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain n residue 34 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 99 TRP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 121 VAL Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 169 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 137 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain s residue 35 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain s residue 82 ASP Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 147 VAL Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 175 LEU Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 99 SER Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 67 ILE Chi-restraints excluded: chain Z residue 68 THR Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 105 SER Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 118 ILE Chi-restraints excluded: chain c residue 124 ILE Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 HIS Chi-restraints excluded: chain d residue 48 HIS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 67 VAL Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 350 LYS Chi-restraints excluded: chain g residue 9 ILE Chi-restraints excluded: chain g residue 27 ARG Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 109 LEU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 997 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 589 optimal weight: 3.9990 chunk 755 optimal weight: 20.0000 chunk 585 optimal weight: 4.9990 chunk 870 optimal weight: 7.9990 chunk 577 optimal weight: 0.9990 chunk 1030 optimal weight: 5.9990 chunk 644 optimal weight: 8.9990 chunk 628 optimal weight: 4.9990 chunk 475 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 GLN j 34 GLN j 104 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN ** s 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 162 GLN s 174 ASN s 208 ASN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN V 112 ASN W 87 ASN x 7 GLN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** d 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 ASN G 221 ASN ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 GLN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN I 28 GLN I 57 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 145584 Z= 0.281 Angle : 0.663 19.868 214514 Z= 0.343 Chirality : 0.040 0.352 26974 Planarity : 0.005 0.057 13552 Dihedral : 23.729 179.303 64942 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.54 % Favored : 92.25 % Rotamer: Outliers : 5.57 % Allowed : 20.30 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.10), residues: 7085 helix: 0.17 (0.11), residues: 2296 sheet: -1.15 (0.15), residues: 979 loop : -1.64 (0.10), residues: 3810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 99 HIS 0.007 0.001 HIS d 43 PHE 0.036 0.002 PHE d 39 TYR 0.046 0.002 TYR W 83 ARG 0.016 0.001 ARG s 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1799 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1471 time to evaluate : 7.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 19 TYR cc_start: 0.8510 (t80) cc_final: 0.7744 (t80) REVERT: R 240 MET cc_start: 0.8876 (mtt) cc_final: 0.8670 (mtm) REVERT: R 279 HIS cc_start: 0.8672 (p-80) cc_final: 0.7543 (p90) REVERT: R 317 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7621 (mm-30) REVERT: R 323 ASP cc_start: 0.8566 (m-30) cc_final: 0.8359 (m-30) REVERT: R 361 ASN cc_start: 0.7280 (m110) cc_final: 0.6856 (p0) REVERT: R 379 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9073 (m) REVERT: R 391 TYR cc_start: 0.8214 (m-80) cc_final: 0.7804 (m-80) REVERT: X 6 GLN cc_start: 0.7430 (mt0) cc_final: 0.7008 (mm-40) REVERT: X 42 LEU cc_start: 0.7829 (mt) cc_final: 0.7491 (tt) REVERT: i 36 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8016 (mmtt) REVERT: i 51 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8824 (pp) REVERT: i 65 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8791 (t) REVERT: J 40 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8651 (ttmt) REVERT: J 51 TYR cc_start: 0.9062 (m-10) cc_final: 0.8807 (m-80) REVERT: J 81 HIS cc_start: 0.8566 (m90) cc_final: 0.8359 (m170) REVERT: J 110 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6733 (mtm110) REVERT: J 158 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7348 (mmtm) REVERT: J 179 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8872 (pp) REVERT: J 183 ASP cc_start: 0.8607 (m-30) cc_final: 0.8120 (m-30) REVERT: j 60 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: j 94 LYS cc_start: 0.9367 (tppt) cc_final: 0.9144 (tppt) REVERT: j 102 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: j 105 ARG cc_start: 0.8387 (tmm-80) cc_final: 0.7779 (tmm160) REVERT: j 113 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8082 (tm-30) REVERT: K 138 HIS cc_start: 0.8339 (t-170) cc_final: 0.7922 (t-170) REVERT: K 231 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8653 (mppt) REVERT: k 34 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8732 (t) REVERT: k 40 VAL cc_start: 0.9464 (t) cc_final: 0.9154 (p) REVERT: k 44 VAL cc_start: 0.9297 (t) cc_final: 0.9064 (m) REVERT: 7 94 TYR cc_start: 0.8303 (p90) cc_final: 0.7850 (p90) REVERT: 7 107 ASP cc_start: 0.8184 (t0) cc_final: 0.7792 (t0) REVERT: 7 153 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7862 (t0) REVERT: l 75 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8642 (tttm) REVERT: l 79 GLN cc_start: 0.8095 (mt0) cc_final: 0.7600 (mm-40) REVERT: M 61 ARG cc_start: 0.8611 (ttt90) cc_final: 0.8285 (ttp-110) REVERT: M 62 ASN cc_start: 0.8463 (m-40) cc_final: 0.7721 (t0) REVERT: M 125 MET cc_start: 0.8344 (ttp) cc_final: 0.8138 (ttp) REVERT: m 17 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7513 (ttp-170) REVERT: m 39 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8699 (mmm-85) REVERT: m 65 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9121 (tt) REVERT: N 189 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8683 (mp0) REVERT: O 47 ASP cc_start: 0.6855 (t70) cc_final: 0.6621 (t70) REVERT: O 116 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7898 (mt-10) REVERT: O 125 LYS cc_start: 0.9265 (mtpp) cc_final: 0.9003 (mttt) REVERT: o 89 TYR cc_start: 0.8377 (m-10) cc_final: 0.8112 (m-80) REVERT: o 98 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8623 (mtpp) REVERT: o 109 ASN cc_start: 0.9187 (m110) cc_final: 0.8889 (m-40) REVERT: o 112 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8127 (mmmt) REVERT: p 198 SER cc_start: 0.9280 (t) cc_final: 0.9058 (p) REVERT: Q 42 ASN cc_start: 0.8800 (m110) cc_final: 0.8543 (m110) REVERT: Q 106 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: 5 154 GLU cc_start: 0.7153 (pp20) cc_final: 0.6748 (pp20) REVERT: S 6 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8151 (t) REVERT: S 90 ASP cc_start: 0.8533 (t70) cc_final: 0.8239 (t0) REVERT: S 100 THR cc_start: 0.9097 (m) cc_final: 0.8814 (p) REVERT: s 22 ASN cc_start: 0.8466 (t0) cc_final: 0.8115 (t0) REVERT: s 143 ASN cc_start: 0.8962 (t0) cc_final: 0.8674 (t0) REVERT: s 183 LYS cc_start: 0.9273 (mttt) cc_final: 0.9063 (mtmt) REVERT: s 185 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8570 (mm-30) REVERT: T 105 LEU cc_start: 0.8806 (tt) cc_final: 0.8472 (tp) REVERT: T 130 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8352 (t0) REVERT: T 140 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8083 (tp30) REVERT: T 148 ASP cc_start: 0.8214 (m-30) cc_final: 0.7954 (m-30) REVERT: U 136 LYS cc_start: 0.8724 (mttp) cc_final: 0.8047 (mttp) REVERT: V 13 TYR cc_start: 0.8740 (m-80) cc_final: 0.8419 (m-80) REVERT: W 107 PHE cc_start: 0.7868 (t80) cc_final: 0.7599 (t80) REVERT: x 66 LYS cc_start: 0.9063 (ptmt) cc_final: 0.8574 (ptmt) REVERT: x 68 GLU cc_start: 0.7945 (mp0) cc_final: 0.7222 (mp0) REVERT: x 70 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8352 (mtm180) REVERT: x 72 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8223 (ptpp) REVERT: Y 32 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8628 (tm-30) REVERT: Z 73 MET cc_start: 0.7990 (mpp) cc_final: 0.7708 (mpp) REVERT: a 53 ASP cc_start: 0.8092 (m-30) cc_final: 0.7871 (m-30) REVERT: b 66 THR cc_start: 0.9452 (p) cc_final: 0.8999 (t) REVERT: b 123 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8644 (mm110) REVERT: C 7 THR cc_start: 0.8538 (t) cc_final: 0.7986 (t) REVERT: C 55 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8712 (mmtm) REVERT: c 70 LYS cc_start: 0.8957 (mttm) cc_final: 0.8730 (mmmt) REVERT: D 84 ARG cc_start: 0.8714 (tpp80) cc_final: 0.8472 (ttm-80) REVERT: d 44 LYS cc_start: 0.9295 (tttt) cc_final: 0.8852 (tptt) REVERT: d 52 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8522 (mtmm) REVERT: E 68 LYS cc_start: 0.8270 (tttt) cc_final: 0.7469 (ptmm) REVERT: E 109 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6782 (mm-30) REVERT: E 128 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8484 (mtm180) REVERT: E 194 ASN cc_start: 0.8670 (t0) cc_final: 0.8353 (t0) REVERT: e 12 GLN cc_start: 0.8971 (tp40) cc_final: 0.8487 (mp10) REVERT: e 52 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8026 (ttm110) REVERT: F 319 ASN cc_start: 0.8562 (m110) cc_final: 0.8302 (m-40) REVERT: F 343 TYR cc_start: 0.8243 (p90) cc_final: 0.8023 (p90) REVERT: f 42 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8351 (tp) REVERT: f 50 ARG cc_start: 0.8498 (mtt180) cc_final: 0.8272 (mtm-85) REVERT: G 55 LYS cc_start: 0.7844 (pttm) cc_final: 0.7391 (pttm) REVERT: G 98 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7899 (ptt-90) REVERT: G 136 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8846 (mm) REVERT: G 160 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7846 (mm110) REVERT: G 296 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7743 (mp10) REVERT: G 320 ASN cc_start: 0.8516 (t0) cc_final: 0.8261 (t0) REVERT: g 111 ARG cc_start: 0.8854 (tpt170) cc_final: 0.8427 (tpp80) REVERT: H 57 ASN cc_start: 0.8120 (m-40) cc_final: 0.7430 (m110) REVERT: H 92 LEU cc_start: 0.8660 (pp) cc_final: 0.8331 (mp) REVERT: H 168 ASP cc_start: 0.8281 (m-30) cc_final: 0.7961 (m-30) REVERT: H 193 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8194 (pp20) REVERT: h 6 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8747 (ttp80) REVERT: h 43 PHE cc_start: 0.8903 (t80) cc_final: 0.8671 (t80) REVERT: h 97 SER cc_start: 0.8375 (m) cc_final: 0.8028 (m) REVERT: I 63 LEU cc_start: 0.9164 (mt) cc_final: 0.8875 (mt) REVERT: I 133 GLU cc_start: 0.8901 (pm20) cc_final: 0.8677 (pm20) REVERT: I 134 ARG cc_start: 0.9155 (ttm-80) cc_final: 0.8853 (ttm-80) REVERT: I 137 ASP cc_start: 0.9202 (m-30) cc_final: 0.8864 (m-30) REVERT: I 143 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8871 (pttm) REVERT: L 47 LYS cc_start: 0.1857 (pttm) cc_final: 0.1348 (pttp) REVERT: L 174 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.3296 (mmm) outliers start: 328 outliers final: 267 residues processed: 1642 average time/residue: 1.3178 time to fit residues: 3775.2335 Evaluate side-chains 1693 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1406 time to evaluate : 6.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain X residue 9 ASN Chi-restraints excluded: chain X residue 68 ARG Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 105 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain j residue 11 THR Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 60 GLU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 51 SER Chi-restraints excluded: chain k residue 60 LEU Chi-restraints excluded: chain k residue 70 ARG Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 78 MET Chi-restraints excluded: chain 7 residue 80 THR Chi-restraints excluded: chain 7 residue 90 MET Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 153 ASP Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 99 TRP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 121 VAL Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 169 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 54 ASN Chi-restraints excluded: chain s residue 82 ASP Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 141 ASP Chi-restraints excluded: chain s residue 147 VAL Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain s residue 208 ASN Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 109 TYR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 169 SER Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 99 SER Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Z residue 67 ILE Chi-restraints excluded: chain Z residue 68 THR Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 105 SER Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 124 ILE Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 HIS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 67 VAL Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain g residue 9 ILE Chi-restraints excluded: chain g residue 27 ARG Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 88 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain L residue 174 MET Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 637 optimal weight: 0.7980 chunk 411 optimal weight: 4.9990 chunk 615 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 655 optimal weight: 2.9990 chunk 701 optimal weight: 3.9990 chunk 509 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 809 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 GLN X 11 ASN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 GLN j 34 GLN j 104 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 19 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 194 GLN p 195 ASN s 54 ASN s 162 GLN ** s 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 208 ASN T 66 HIS ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN U 63 GLN V 112 ASN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN d 12 GLN E 8 GLN E 79 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS G 221 ASN G 291 ASN G 296 GLN g 98 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 GLN h 42 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 145584 Z= 0.184 Angle : 0.613 19.523 214514 Z= 0.318 Chirality : 0.037 0.355 26974 Planarity : 0.004 0.055 13552 Dihedral : 23.667 179.529 64941 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.13 % Favored : 92.66 % Rotamer: Outliers : 4.74 % Allowed : 21.64 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.10), residues: 7085 helix: 0.29 (0.11), residues: 2293 sheet: -1.08 (0.16), residues: 988 loop : -1.52 (0.10), residues: 3804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 99 HIS 0.009 0.001 HIS H 90 PHE 0.029 0.001 PHE s 172 TYR 0.038 0.001 TYR W 83 ARG 0.011 0.000 ARG m 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1499 time to evaluate : 6.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 19 TYR cc_start: 0.8447 (t80) cc_final: 0.7831 (t80) REVERT: R 233 MET cc_start: 0.8232 (pmm) cc_final: 0.7564 (pmm) REVERT: R 271 GLU cc_start: 0.8864 (pt0) cc_final: 0.8414 (pp20) REVERT: R 279 HIS cc_start: 0.8608 (p-80) cc_final: 0.7481 (p90) REVERT: R 317 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7686 (mm-30) REVERT: R 323 ASP cc_start: 0.8524 (m-30) cc_final: 0.8317 (m-30) REVERT: R 361 ASN cc_start: 0.7247 (m110) cc_final: 0.6893 (p0) REVERT: R 379 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.9001 (m) REVERT: X 6 GLN cc_start: 0.7368 (mt0) cc_final: 0.6932 (mm-40) REVERT: X 42 LEU cc_start: 0.7657 (mt) cc_final: 0.7333 (tt) REVERT: i 36 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7985 (mmtt) REVERT: i 51 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8711 (pp) REVERT: i 65 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8775 (t) REVERT: J 40 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8547 (ttmt) REVERT: J 51 TYR cc_start: 0.9024 (m-10) cc_final: 0.8808 (m-80) REVERT: J 110 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6931 (mtm110) REVERT: J 158 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7281 (mmtm) REVERT: J 179 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8811 (pp) REVERT: J 183 ASP cc_start: 0.8549 (m-30) cc_final: 0.8123 (m-30) REVERT: j 94 LYS cc_start: 0.9329 (tppt) cc_final: 0.9117 (tppt) REVERT: j 105 ARG cc_start: 0.8378 (tmm-80) cc_final: 0.7950 (tmm160) REVERT: j 113 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8110 (tm-30) REVERT: K 138 HIS cc_start: 0.8083 (t-170) cc_final: 0.7667 (t-170) REVERT: K 231 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8643 (mppt) REVERT: k 40 VAL cc_start: 0.9456 (t) cc_final: 0.9132 (p) REVERT: k 44 VAL cc_start: 0.9235 (t) cc_final: 0.9007 (m) REVERT: 7 94 TYR cc_start: 0.8243 (p90) cc_final: 0.7842 (p90) REVERT: 7 107 ASP cc_start: 0.8135 (t0) cc_final: 0.7747 (t0) REVERT: 7 153 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7811 (t0) REVERT: M 61 ARG cc_start: 0.8609 (ttt90) cc_final: 0.8363 (ttp-110) REVERT: M 125 MET cc_start: 0.8311 (ttp) cc_final: 0.8100 (ttp) REVERT: m 39 ARG cc_start: 0.8941 (mmm-85) cc_final: 0.8675 (mmm-85) REVERT: N 122 LYS cc_start: 0.8586 (mttp) cc_final: 0.8166 (mmmt) REVERT: N 189 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8688 (mp0) REVERT: O 116 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7811 (mt-10) REVERT: O 125 LYS cc_start: 0.9236 (mtpp) cc_final: 0.9018 (mttt) REVERT: o 98 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8618 (mtpp) REVERT: o 109 ASN cc_start: 0.9154 (m110) cc_final: 0.8877 (m-40) REVERT: o 112 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8017 (mmmt) REVERT: p 198 SER cc_start: 0.9230 (t) cc_final: 0.9004 (p) REVERT: Q 42 ASN cc_start: 0.8774 (m110) cc_final: 0.8524 (m110) REVERT: Q 87 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8015 (mtt) REVERT: Q 106 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: Q 159 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8567 (ttmm) REVERT: 5 154 GLU cc_start: 0.7126 (pp20) cc_final: 0.6709 (pp20) REVERT: S 6 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8108 (t) REVERT: S 90 ASP cc_start: 0.8476 (t70) cc_final: 0.8170 (t0) REVERT: S 100 THR cc_start: 0.9117 (m) cc_final: 0.8801 (p) REVERT: s 22 ASN cc_start: 0.8424 (t0) cc_final: 0.8099 (t0) REVERT: s 143 ASN cc_start: 0.8876 (t0) cc_final: 0.8025 (t0) REVERT: s 183 LYS cc_start: 0.9254 (mttt) cc_final: 0.8735 (mtmt) REVERT: s 185 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8395 (mm-30) REVERT: s 188 GLU cc_start: 0.8756 (mt-10) cc_final: 0.7961 (mp0) REVERT: T 105 LEU cc_start: 0.8741 (tt) cc_final: 0.8522 (tt) REVERT: T 130 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8177 (t0) REVERT: T 140 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8057 (tp30) REVERT: T 148 ASP cc_start: 0.8174 (m-30) cc_final: 0.7881 (m-30) REVERT: U 118 PHE cc_start: 0.8978 (t80) cc_final: 0.8748 (t80) REVERT: V 13 TYR cc_start: 0.8654 (m-80) cc_final: 0.8376 (m-80) REVERT: W 20 SER cc_start: 0.8860 (p) cc_final: 0.8615 (m) REVERT: W 107 PHE cc_start: 0.7824 (t80) cc_final: 0.7550 (t80) REVERT: x 66 LYS cc_start: 0.9008 (ptmt) cc_final: 0.8797 (ptmt) REVERT: x 70 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8345 (mtm180) REVERT: x 72 LYS cc_start: 0.8511 (ptmt) cc_final: 0.8196 (ptpp) REVERT: Y 32 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8587 (tm-30) REVERT: Y 41 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8347 (ttmm) REVERT: Y 60 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8280 (ptmm) REVERT: Z 73 MET cc_start: 0.8096 (mpp) cc_final: 0.7747 (mpp) REVERT: a 38 GLU cc_start: 0.8334 (pp20) cc_final: 0.8128 (pp20) REVERT: a 53 ASP cc_start: 0.8061 (m-30) cc_final: 0.7826 (m-30) REVERT: a 95 VAL cc_start: 0.9165 (t) cc_final: 0.8840 (m) REVERT: a 105 VAL cc_start: 0.9165 (t) cc_final: 0.8806 (p) REVERT: b 27 LYS cc_start: 0.7770 (tptt) cc_final: 0.7195 (tptt) REVERT: b 66 THR cc_start: 0.9442 (p) cc_final: 0.9012 (t) REVERT: b 123 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8702 (mm110) REVERT: C 55 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8716 (mmtm) REVERT: c 70 LYS cc_start: 0.8939 (mttm) cc_final: 0.8716 (mmmt) REVERT: D 84 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8313 (ttm-80) REVERT: d 44 LYS cc_start: 0.9245 (tttt) cc_final: 0.8823 (tptt) REVERT: E 68 LYS cc_start: 0.8183 (tttt) cc_final: 0.7701 (ttpp) REVERT: E 84 THR cc_start: 0.9115 (p) cc_final: 0.8894 (p) REVERT: E 109 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6844 (mm-30) REVERT: E 194 ASN cc_start: 0.8600 (t0) cc_final: 0.8270 (t0) REVERT: e 12 GLN cc_start: 0.9011 (tp40) cc_final: 0.8493 (mp10) REVERT: F 28 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8212 (mtp180) REVERT: F 261 MET cc_start: 0.8246 (mtm) cc_final: 0.8014 (mtm) REVERT: F 343 TYR cc_start: 0.8234 (p90) cc_final: 0.8021 (p90) REVERT: f 50 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8166 (mtm-85) REVERT: G 14 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7787 (pp20) REVERT: G 55 LYS cc_start: 0.7817 (pttm) cc_final: 0.7382 (pttm) REVERT: G 98 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7681 (ptt-90) REVERT: G 320 ASN cc_start: 0.8504 (t0) cc_final: 0.8253 (t0) REVERT: g 25 TYR cc_start: 0.7504 (m-80) cc_final: 0.6894 (m-10) REVERT: g 111 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8216 (tpp80) REVERT: H 92 LEU cc_start: 0.8621 (pp) cc_final: 0.8316 (mp) REVERT: H 168 ASP cc_start: 0.8254 (m-30) cc_final: 0.8047 (m-30) REVERT: H 193 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8156 (pp20) REVERT: H 232 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8122 (p0) REVERT: h 43 PHE cc_start: 0.8855 (t80) cc_final: 0.8509 (t80) REVERT: I 10 TYR cc_start: 0.8594 (m-80) cc_final: 0.8320 (m-10) REVERT: I 63 LEU cc_start: 0.9142 (mt) cc_final: 0.8934 (mt) REVERT: I 137 ASP cc_start: 0.9213 (m-30) cc_final: 0.8852 (m-30) REVERT: I 143 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8852 (pttm) REVERT: L 47 LYS cc_start: 0.1854 (pttm) cc_final: 0.1355 (pttp) REVERT: L 174 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.3322 (mmm) outliers start: 279 outliers final: 203 residues processed: 1639 average time/residue: 1.2114 time to fit residues: 3450.4628 Evaluate side-chains 1632 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1411 time to evaluate : 6.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain X residue 9 ASN Chi-restraints excluded: chain X residue 68 ARG Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 70 ARG Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 90 MET Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 153 ASP Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 99 TRP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 169 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 74 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 127 LEU Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 82 ASP Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 147 VAL Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain s residue 206 GLU Chi-restraints excluded: chain s residue 208 ASN Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 109 TYR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 SER Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain x residue 25 CYS Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 68 THR Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain b residue 105 SER Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 124 ILE Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain d residue 43 HIS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 67 VAL Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain g residue 27 ARG Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 109 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 274 GLN Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 88 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 174 MET Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 937 optimal weight: 30.0000 chunk 987 optimal weight: 20.0000 chunk 900 optimal weight: 10.0000 chunk 960 optimal weight: 10.0000 chunk 986 optimal weight: 10.0000 chunk 577 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 753 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 867 optimal weight: 10.0000 chunk 908 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 GLN ** J 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN j 16 GLN j 34 GLN ** j 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 125 ASN 7 157 ASN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 90 ASN p 123 GLN ** p 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 54 HIS 5 145 HIS S 45 ASN ** s 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 208 ASN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN U 63 GLN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 157 GLN V 112 ASN V 131 GLN x 7 GLN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 106 GLN c 44 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS F 3 HIS ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS H 32 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 ASN h 42 GLN h 87 ASN I 57 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.129 145584 Z= 0.629 Angle : 0.893 19.603 214514 Z= 0.452 Chirality : 0.051 0.453 26974 Planarity : 0.007 0.088 13552 Dihedral : 23.786 179.776 64940 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.73 % Rotamer: Outliers : 5.55 % Allowed : 21.07 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.10), residues: 7085 helix: -0.08 (0.11), residues: 2300 sheet: -1.27 (0.16), residues: 983 loop : -1.79 (0.10), residues: 3802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP O 99 HIS 0.010 0.002 HIS H 90 PHE 0.046 0.003 PHE s 172 TYR 0.041 0.003 TYR b 49 ARG 0.010 0.001 ARG 5 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1410 time to evaluate : 7.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 17 ASP cc_start: 0.9242 (t0) cc_final: 0.8883 (t0) REVERT: R 19 TYR cc_start: 0.8442 (t80) cc_final: 0.7466 (t80) REVERT: R 279 HIS cc_start: 0.8787 (p-80) cc_final: 0.7702 (p90) REVERT: R 313 ARG cc_start: 0.5070 (mtt180) cc_final: 0.4411 (mtt-85) REVERT: R 317 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7883 (mm-30) REVERT: R 344 ARG cc_start: 0.7168 (ttp80) cc_final: 0.5661 (ttp80) REVERT: R 361 ASN cc_start: 0.7352 (m110) cc_final: 0.6942 (p0) REVERT: R 379 VAL cc_start: 0.9384 (t) cc_final: 0.9067 (m) REVERT: X 6 GLN cc_start: 0.7301 (mt0) cc_final: 0.6872 (mm-40) REVERT: X 42 LEU cc_start: 0.7738 (mt) cc_final: 0.7384 (tt) REVERT: X 146 ILE cc_start: 0.7812 (pt) cc_final: 0.7559 (mp) REVERT: i 16 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6207 (mtm110) REVERT: i 36 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8089 (mmtt) REVERT: i 51 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8985 (pp) REVERT: i 65 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8801 (t) REVERT: J 40 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8765 (ttmt) REVERT: J 64 GLN cc_start: 0.8796 (tp40) cc_final: 0.8060 (tp40) REVERT: J 158 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7555 (mmtm) REVERT: J 175 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8522 (pmtt) REVERT: J 179 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9029 (pp) REVERT: J 183 ASP cc_start: 0.8628 (m-30) cc_final: 0.8126 (m-30) REVERT: j 94 LYS cc_start: 0.9434 (tppt) cc_final: 0.9226 (tppt) REVERT: j 105 ARG cc_start: 0.8406 (tmm-80) cc_final: 0.8042 (tmm-80) REVERT: j 113 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8219 (tm-30) REVERT: K 231 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8717 (mppt) REVERT: K 246 MET cc_start: 0.8553 (ppp) cc_final: 0.8225 (ppp) REVERT: k 40 VAL cc_start: 0.9493 (t) cc_final: 0.9244 (p) REVERT: 7 23 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.5888 (mpp80) REVERT: 7 153 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8070 (t0) REVERT: l 79 GLN cc_start: 0.8200 (mt0) cc_final: 0.7654 (mm-40) REVERT: M 61 ARG cc_start: 0.8685 (ttt90) cc_final: 0.8331 (ttm110) REVERT: M 62 ASN cc_start: 0.8401 (m-40) cc_final: 0.7645 (t0) REVERT: M 68 HIS cc_start: 0.8167 (p90) cc_final: 0.7827 (p90) REVERT: M 125 MET cc_start: 0.8459 (ttp) cc_final: 0.8173 (ttp) REVERT: m 17 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7864 (ttp-170) REVERT: N 99 HIS cc_start: 0.8808 (p90) cc_final: 0.8311 (p90) REVERT: N 189 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8680 (mt-10) REVERT: O 116 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7791 (mt-10) REVERT: O 125 LYS cc_start: 0.9295 (mtpp) cc_final: 0.9073 (mttt) REVERT: o 109 ASN cc_start: 0.9362 (m110) cc_final: 0.9049 (m-40) REVERT: p 170 LYS cc_start: 0.8509 (tptt) cc_final: 0.8297 (tptp) REVERT: p 198 SER cc_start: 0.9398 (t) cc_final: 0.9193 (p) REVERT: Q 4 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7416 (mt-10) REVERT: Q 42 ASN cc_start: 0.8880 (m110) cc_final: 0.8627 (m-40) REVERT: 5 154 GLU cc_start: 0.7119 (pp20) cc_final: 0.6679 (pp20) REVERT: S 100 THR cc_start: 0.9179 (m) cc_final: 0.8878 (p) REVERT: S 122 ILE cc_start: 0.8578 (mm) cc_final: 0.8282 (mt) REVERT: S 184 PHE cc_start: 0.9040 (p90) cc_final: 0.8805 (p90) REVERT: s 22 ASN cc_start: 0.8609 (t0) cc_final: 0.8287 (t0) REVERT: s 137 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8261 (p) REVERT: s 183 LYS cc_start: 0.9262 (mttt) cc_final: 0.9007 (mtmt) REVERT: s 185 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8456 (mm-30) REVERT: T 28 GLU cc_start: 0.7841 (tp30) cc_final: 0.7574 (tp30) REVERT: T 130 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8475 (t0) REVERT: T 140 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8104 (tp30) REVERT: U 136 LYS cc_start: 0.8713 (mttp) cc_final: 0.8028 (mttp) REVERT: V 13 TYR cc_start: 0.8914 (m-80) cc_final: 0.8574 (m-80) REVERT: V 58 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: W 107 PHE cc_start: 0.8007 (t80) cc_final: 0.7730 (t80) REVERT: x 66 LYS cc_start: 0.9115 (ptmt) cc_final: 0.8574 (ptmt) REVERT: x 68 GLU cc_start: 0.7932 (mp0) cc_final: 0.7224 (mp0) REVERT: x 72 LYS cc_start: 0.8644 (ptmt) cc_final: 0.8264 (ptpp) REVERT: x 135 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8435 (m) REVERT: Y 2 LYS cc_start: 0.7828 (tptt) cc_final: 0.7547 (tptt) REVERT: Z 55 ASN cc_start: 0.8909 (t0) cc_final: 0.8692 (t0) REVERT: a 53 ASP cc_start: 0.8226 (m-30) cc_final: 0.8001 (m-30) REVERT: a 95 VAL cc_start: 0.9217 (t) cc_final: 0.8926 (m) REVERT: a 105 VAL cc_start: 0.9255 (t) cc_final: 0.8944 (p) REVERT: b 66 THR cc_start: 0.9459 (p) cc_final: 0.8945 (t) REVERT: b 123 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8749 (mm-40) REVERT: C 55 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8788 (mmtm) REVERT: c 60 TYR cc_start: 0.8427 (t80) cc_final: 0.8174 (t80) REVERT: c 70 LYS cc_start: 0.8990 (mttm) cc_final: 0.8741 (mmmt) REVERT: c 135 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8489 (tm-30) REVERT: d 44 LYS cc_start: 0.9350 (tttt) cc_final: 0.8923 (tptt) REVERT: E 68 LYS cc_start: 0.8429 (tttt) cc_final: 0.7535 (ptmm) REVERT: E 109 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7051 (mm-30) REVERT: F 28 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8269 (mtp180) REVERT: F 261 MET cc_start: 0.8444 (mtm) cc_final: 0.8154 (mtm) REVERT: f 42 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8467 (tp) REVERT: f 50 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8360 (mtm-85) REVERT: G 55 LYS cc_start: 0.7821 (pttm) cc_final: 0.7317 (pttm) REVERT: G 320 ASN cc_start: 0.8563 (t0) cc_final: 0.8311 (t0) REVERT: g 111 ARG cc_start: 0.8937 (tpt170) cc_final: 0.8479 (tpp80) REVERT: H 32 GLN cc_start: 0.8481 (tt0) cc_final: 0.8193 (tt0) REVERT: H 57 ASN cc_start: 0.8150 (m-40) cc_final: 0.7444 (m110) REVERT: H 92 LEU cc_start: 0.8605 (pp) cc_final: 0.8318 (mt) REVERT: H 168 ASP cc_start: 0.8382 (m-30) cc_final: 0.8075 (m-30) REVERT: H 232 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8142 (p0) REVERT: h 43 PHE cc_start: 0.8891 (t80) cc_final: 0.8634 (t80) REVERT: h 97 SER cc_start: 0.8464 (m) cc_final: 0.8110 (m) REVERT: I 10 TYR cc_start: 0.8711 (m-80) cc_final: 0.8413 (m-10) REVERT: I 137 ASP cc_start: 0.9266 (m-30) cc_final: 0.8952 (m-30) REVERT: I 143 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8942 (pttm) REVERT: L 47 LYS cc_start: 0.2171 (pttm) cc_final: 0.1642 (pttp) REVERT: L 174 MET cc_start: 0.4540 (OUTLIER) cc_final: 0.3365 (mmm) outliers start: 327 outliers final: 261 residues processed: 1578 average time/residue: 1.3048 time to fit residues: 3611.8106 Evaluate side-chains 1672 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1393 time to evaluate : 6.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain X residue 9 ASN Chi-restraints excluded: chain X residue 68 ARG Chi-restraints excluded: chain X residue 121 ILE Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 16 ARG Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 52 GLN Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 105 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain j residue 118 ILE Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 51 SER Chi-restraints excluded: chain k residue 70 ARG Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 90 MET Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 153 ASP Chi-restraints excluded: chain 7 residue 162 GLN Chi-restraints excluded: chain 7 residue 187 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 89 TYR Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 91 CYS Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain Q residue 189 ASP Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 169 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 74 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 137 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 82 ASP Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 146 VAL Chi-restraints excluded: chain s residue 147 VAL Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain s residue 208 ASN Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 29 ILE Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 SER Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 58 GLN Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 99 SER Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 150 THR Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 67 ILE Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 134 ASP Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 24 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 105 SER Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 117 ARG Chi-restraints excluded: chain c residue 124 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain d residue 43 HIS Chi-restraints excluded: chain d residue 48 HIS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 67 VAL Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 304 GLN Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 88 ASN Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain L residue 174 MET Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 956 optimal weight: 20.0000 chunk 630 optimal weight: 6.9990 chunk 1015 optimal weight: 5.9990 chunk 619 optimal weight: 2.9990 chunk 481 optimal weight: 30.0000 chunk 705 optimal weight: 8.9990 chunk 1064 optimal weight: 10.0000 chunk 980 optimal weight: 20.0000 chunk 848 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 655 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 GLN J 166 ASN j 16 GLN j 34 GLN ** j 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 125 ASN 7 157 ASN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 90 ASN ** p 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 45 ASN s 11 GLN s 162 GLN s 208 ASN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 ASN V 131 GLN W 87 ASN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 106 GLN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS H 32 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 145584 Z= 0.266 Angle : 0.678 22.875 214514 Z= 0.350 Chirality : 0.040 0.345 26974 Planarity : 0.005 0.065 13552 Dihedral : 23.723 179.428 64936 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.47 % Favored : 92.29 % Rotamer: Outliers : 3.99 % Allowed : 23.14 % Favored : 72.87 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.10), residues: 7085 helix: 0.20 (0.11), residues: 2280 sheet: -1.22 (0.16), residues: 992 loop : -1.64 (0.10), residues: 3813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP O 99 HIS 0.012 0.001 HIS H 90 PHE 0.035 0.002 PHE W 28 TYR 0.037 0.002 TYR b 49 ARG 0.012 0.001 ARG N 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14170 Ramachandran restraints generated. 7085 Oldfield, 0 Emsley, 7085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1703 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1468 time to evaluate : 6.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 17 ASP cc_start: 0.9234 (t0) cc_final: 0.8838 (t0) REVERT: R 233 MET cc_start: 0.8391 (pmm) cc_final: 0.7716 (pmm) REVERT: R 271 GLU cc_start: 0.8777 (pt0) cc_final: 0.8330 (pp20) REVERT: R 278 GLU cc_start: 0.8722 (tp30) cc_final: 0.8478 (tp30) REVERT: R 279 HIS cc_start: 0.8677 (p-80) cc_final: 0.7552 (p90) REVERT: R 313 ARG cc_start: 0.5010 (mtt180) cc_final: 0.4391 (mtt-85) REVERT: R 317 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7810 (mm-30) REVERT: R 344 ARG cc_start: 0.6996 (ttp80) cc_final: 0.5598 (ttp80) REVERT: R 361 ASN cc_start: 0.7292 (m110) cc_final: 0.6944 (p0) REVERT: R 362 LYS cc_start: 0.6463 (mptt) cc_final: 0.5999 (mptt) REVERT: R 379 VAL cc_start: 0.9365 (t) cc_final: 0.9047 (m) REVERT: R 388 GLU cc_start: 0.8277 (tp30) cc_final: 0.8028 (tp30) REVERT: X 6 GLN cc_start: 0.7354 (mt0) cc_final: 0.6928 (mm-40) REVERT: X 42 LEU cc_start: 0.7613 (mt) cc_final: 0.7284 (tt) REVERT: X 99 GLU cc_start: 0.6412 (pp20) cc_final: 0.6206 (pp20) REVERT: X 146 ILE cc_start: 0.7841 (pt) cc_final: 0.7555 (mp) REVERT: i 16 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6136 (mtm110) REVERT: i 36 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8021 (mmtt) REVERT: i 51 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8751 (pp) REVERT: i 65 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8736 (t) REVERT: J 40 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8669 (ttmt) REVERT: J 64 GLN cc_start: 0.8718 (tp40) cc_final: 0.7986 (tp40) REVERT: J 158 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7297 (mmtm) REVERT: J 179 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8888 (pp) REVERT: J 183 ASP cc_start: 0.8456 (m-30) cc_final: 0.8182 (m-30) REVERT: J 187 GLU cc_start: 0.8515 (tp30) cc_final: 0.7797 (tp30) REVERT: j 94 LYS cc_start: 0.9356 (tppt) cc_final: 0.9151 (tppt) REVERT: j 102 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: j 105 ARG cc_start: 0.8394 (tmm-80) cc_final: 0.7682 (tmm160) REVERT: j 113 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8112 (tm-30) REVERT: K 138 HIS cc_start: 0.8350 (t-170) cc_final: 0.8093 (t-170) REVERT: K 246 MET cc_start: 0.8472 (ppp) cc_final: 0.8152 (ppp) REVERT: k 40 VAL cc_start: 0.9462 (t) cc_final: 0.9190 (p) REVERT: 7 23 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.5773 (mpp80) REVERT: 7 94 TYR cc_start: 0.8294 (p90) cc_final: 0.7855 (p90) REVERT: 7 97 PHE cc_start: 0.8983 (m-80) cc_final: 0.8558 (m-10) REVERT: 7 153 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7812 (t0) REVERT: l 79 GLN cc_start: 0.8101 (mt0) cc_final: 0.7630 (mm-40) REVERT: M 61 ARG cc_start: 0.8697 (ttt90) cc_final: 0.8344 (ttp-110) REVERT: M 62 ASN cc_start: 0.8414 (m-40) cc_final: 0.7604 (t0) REVERT: M 68 HIS cc_start: 0.8061 (p90) cc_final: 0.7690 (p90) REVERT: M 125 MET cc_start: 0.8347 (ttp) cc_final: 0.8097 (ttp) REVERT: m 16 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7874 (mtm-85) REVERT: N 122 LYS cc_start: 0.8606 (mttp) cc_final: 0.8139 (mmmt) REVERT: N 189 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8689 (mp0) REVERT: o 98 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8631 (mtpt) REVERT: o 109 ASN cc_start: 0.9276 (m110) cc_final: 0.9016 (m-40) REVERT: o 112 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8166 (mmmt) REVERT: Q 42 ASN cc_start: 0.8814 (m110) cc_final: 0.8574 (m110) REVERT: Q 106 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: 5 154 GLU cc_start: 0.7099 (pp20) cc_final: 0.6642 (pp20) REVERT: S 6 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8112 (t) REVERT: S 90 ASP cc_start: 0.8719 (t70) cc_final: 0.8260 (t0) REVERT: S 100 THR cc_start: 0.9146 (m) cc_final: 0.8830 (p) REVERT: S 122 ILE cc_start: 0.8506 (mm) cc_final: 0.8178 (mt) REVERT: s 22 ASN cc_start: 0.8542 (t0) cc_final: 0.8161 (t0) REVERT: s 183 LYS cc_start: 0.9226 (mttt) cc_final: 0.8964 (mtmt) REVERT: s 185 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8400 (mm-30) REVERT: T 28 GLU cc_start: 0.7645 (tp30) cc_final: 0.7168 (tp30) REVERT: T 130 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8216 (t0) REVERT: T 140 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8062 (tp30) REVERT: T 148 ASP cc_start: 0.8168 (m-30) cc_final: 0.7935 (m-30) REVERT: U 1 MET cc_start: 0.4461 (mpt) cc_final: 0.4045 (mpt) REVERT: V 13 TYR cc_start: 0.8688 (m-80) cc_final: 0.8439 (m-80) REVERT: V 14 MET cc_start: 0.8061 (tpp) cc_final: 0.7492 (tpp) REVERT: V 58 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: W 33 TYR cc_start: 0.8854 (t80) cc_final: 0.8623 (t80) REVERT: x 66 LYS cc_start: 0.9065 (ptmt) cc_final: 0.8834 (ptmt) REVERT: x 72 LYS cc_start: 0.8601 (ptmt) cc_final: 0.8258 (ptpp) REVERT: x 104 ASN cc_start: 0.8949 (p0) cc_final: 0.8639 (p0) REVERT: Y 41 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8375 (ttmm) REVERT: Z 101 GLU cc_start: 0.8279 (tt0) cc_final: 0.7793 (tt0) REVERT: a 53 ASP cc_start: 0.8183 (m-30) cc_final: 0.7949 (m-30) REVERT: a 95 VAL cc_start: 0.9218 (t) cc_final: 0.8920 (m) REVERT: b 66 THR cc_start: 0.9453 (p) cc_final: 0.9016 (t) REVERT: b 123 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8684 (mm-40) REVERT: b 126 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8667 (mtmm) REVERT: C 55 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8739 (mmtm) REVERT: c 34 MET cc_start: 0.7988 (mmt) cc_final: 0.7755 (mmm) REVERT: c 70 LYS cc_start: 0.8968 (mttm) cc_final: 0.8681 (mmmm) REVERT: D 84 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8354 (ttm-80) REVERT: d 44 LYS cc_start: 0.9278 (tttt) cc_final: 0.8839 (tptt) REVERT: E 68 LYS cc_start: 0.8289 (tttt) cc_final: 0.7535 (ptmm) REVERT: E 109 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6781 (mm-30) REVERT: E 143 GLU cc_start: 0.8933 (pm20) cc_final: 0.8704 (pm20) REVERT: F 28 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8198 (mtp180) REVERT: F 343 TYR cc_start: 0.8274 (p90) cc_final: 0.8061 (p90) REVERT: f 42 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8345 (tp) REVERT: G 14 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7885 (pp20) REVERT: G 55 LYS cc_start: 0.7887 (pttm) cc_final: 0.7427 (pttm) REVERT: G 144 LYS cc_start: 0.8949 (ptmm) cc_final: 0.8635 (ptmm) REVERT: G 320 ASN cc_start: 0.8486 (t0) cc_final: 0.8234 (t0) REVERT: g 25 TYR cc_start: 0.7696 (m-80) cc_final: 0.6936 (m-10) REVERT: g 111 ARG cc_start: 0.8861 (tpt170) cc_final: 0.8413 (tpp80) REVERT: H 57 ASN cc_start: 0.8046 (m-40) cc_final: 0.7386 (m110) REVERT: H 92 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8288 (mt) REVERT: H 168 ASP cc_start: 0.8298 (m-30) cc_final: 0.7980 (m-30) REVERT: H 232 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8037 (p0) REVERT: h 24 ASN cc_start: 0.9304 (t0) cc_final: 0.9091 (t0) REVERT: h 97 SER cc_start: 0.8416 (m) cc_final: 0.8096 (m) REVERT: I 10 TYR cc_start: 0.8638 (m-80) cc_final: 0.8340 (m-10) REVERT: I 137 ASP cc_start: 0.9251 (m-30) cc_final: 0.8961 (m-30) REVERT: I 143 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8867 (pttm) REVERT: L 47 LYS cc_start: 0.1865 (pttm) cc_final: 0.1637 (pttm) REVERT: L 156 LYS cc_start: 0.8036 (tptt) cc_final: 0.7786 (pptt) REVERT: L 174 MET cc_start: 0.4194 (OUTLIER) cc_final: 0.3012 (mmm) outliers start: 235 outliers final: 195 residues processed: 1598 average time/residue: 1.2035 time to fit residues: 3335.9626 Evaluate side-chains 1643 residues out of total 6051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1430 time to evaluate : 6.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain X residue 9 ASN Chi-restraints excluded: chain X residue 68 ARG Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 179 VAL Chi-restraints excluded: chain i residue 16 ARG Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 79 ASP Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 102 GLU Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 70 ARG Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 87 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 78 MET Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 126 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 150 SER Chi-restraints excluded: chain 7 residue 153 ASP Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 91 CYS Chi-restraints excluded: chain O residue 99 TRP Chi-restraints excluded: chain o residue 121 LEU Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 169 THR Chi-restraints excluded: chain S residue 6 THR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 137 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 82 ASP Chi-restraints excluded: chain s residue 147 VAL Chi-restraints excluded: chain s residue 164 ILE Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 176 ASP Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 205 LEU Chi-restraints excluded: chain s residue 206 GLU Chi-restraints excluded: chain s residue 208 ASN Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 34 GLU Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 SER Chi-restraints excluded: chain U residue 170 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 58 GLN Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 72 SER Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 71 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 36 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain a residue 102 SER Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain b residue 60 LYS Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 85 ASP Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 117 ARG Chi-restraints excluded: chain c residue 124 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 67 VAL Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 100 SER Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain g residue 31 ASN Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 42 GLN Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 88 ASN Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 174 MET Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 520 optimal weight: 1.9990 chunk 673 optimal weight: 5.9990 chunk 903 optimal weight: 8.9990 chunk 259 optimal weight: 0.9980 chunk 781 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 849 optimal weight: 7.9990 chunk 355 optimal weight: 0.9980 chunk 872 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 ASN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 96 GLN s 162 GLN s 208 ASN ** T 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN V 112 ASN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN G 221 ASN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 GLN h 42 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100623 restraints weight = 246771.232| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.55 r_work: 0.3120 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 145584 Z= 0.209 Angle : 0.635 24.395 214514 Z= 0.327 Chirality : 0.038 0.372 26974 Planarity : 0.005 0.066 13552 Dihedral : 23.625 179.931 64936 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.72 % Favored : 92.10 % Rotamer: Outliers : 4.01 % Allowed : 23.54 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.10), residues: 7085 helix: 0.27 (0.11), residues: 2302 sheet: -1.12 (0.16), residues: 985 loop : -1.54 (0.10), residues: 3798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP O 99 HIS 0.011 0.001 HIS H 90 PHE 0.046 0.002 PHE d 39 TYR 0.036 0.002 TYR b 49 ARG 0.018 0.001 ARG b 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49433.99 seconds wall clock time: 855 minutes 55.93 seconds (51355.93 seconds total)